[New: openFATE 309007] Add more scientific packages
Feature added by: Ricardo Gabriel Berlasso (RGBsuse) Feature #309007, revision 1 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "scy distro" but the few "heavy duty" scientific packages available is against this. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Luis Medinas (lmedinas) Feature #309007, revision 3 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "scy distro" but the few "heavy duty" scientific packages available is against this. + Discussion: + #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) + Octave is on Contrib that is my usecase but still i prefer to use + Matlab instead. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Jones de Andrade (johannesrs) Feature #309007, revision 4 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "scy distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. + #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) + That's absolutelly a MUST one! + + We heavilly use openSuse at my University for Scientific Applications. + On the other hand, unfortunatelly there is a lot of packages that are + not available, or "poorly available" (explain later) in the + repositories concerning that. + + At the moment, we use from 11.2 the following packages (everywhere in + the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, + g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit + and kalzium. + + Programs we use that are unavailable at the repositories (easy + installation/compilation thow): molden, gopenmol, maui, webmo (formely + webmol) and molekel. + + Programs we used to use but don't use anymore because they are too + hard to compile and unavailable in the repos: SciDavis and qtiplot. + + Programs poorly avialable: + openmpi, mpich: They are available, but they are not easily usable. I + say that because me and coleagues had a hard time in the past trying to + link programas with the version of those libraries that come with + opensuse, because it seemed to be too scatered around. We ended up + installing them from the producers in well known directories, and no + problems anymore. + fftw: same problem as above, solved in the very same way. + gromacs: the compilation provided is ok, but... no mpi, no double + + single precision executables? I would suggest two new packages: gromacs- + omp and gromacs-mpich. + torque: choosen the same approach since it's of critical use. Not sure + if it douldn't be simply installed, thow. + atiplot: already mentioned before, but in reality the package avialble + for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, + *except*... the executables! :p + + Programs that I do not know if they can be provided: gamess-us, + firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- + tools, (all available for free, but need subscription to download most + of them, and none is gpl). + + As you can see, I'm clearly chemistry (and cluster) biased. I'm certain + that other fields of research would easilly have other suggestions! And + I probably missed something! + + Seem that there is a LOT of room for improvement here! ;) Don't get me + wrong, openSuse is already MARVOLOUS, including for scientific + applications... But there is a lot of things here that can be improved. + ;) -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Ricardo Gabriel Berlasso (RGBsuse) Feature #309007, revision 6 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, - openSUSE could be the perfect "scy distro" but the few "heavy duty" + openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Hubert Stassen (drgullit) Feature #309007, revision 7 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) + #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) + johannesrs presented a very nice wishlist ... That would be an almost + complete software repositiry for the computational + chemistry/biology/physics communities. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Vojtech Zeisek (vojtaeus) Feature #309007, revision 8 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. + #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) + I'm biologist. Practicaly no program for biology (for science, not for + any playing or education; especially phylogeny, where I have the most + expereince) is available for openSUSE. When user is lucky, the needed + program is written in Java, but most of them must be compiled (but + there are EXE files for Windows and sometimes DEB packages), what is + not very comfortable, and for average user impossible. We do not have + neither so basic paskages as latest version of Rkward (the best + available GUI for R) for 11.2. So openSUSE is often refused, because + "it does not contain needed software"... :-( -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Jones de Andrade (johannesrs) Feature #309007, revision 9 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( + #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) + Hi vojtaeus! Thanks for the contribution! Would you please provide this + thread with a list of more important scientific softwares/packages for + use of biologists? I knew since the begining that my list would be + chemistry biased, and from your post I'm suposing that opensuse can + consider including a lot extra packages than only rkward (which I + looked into its homepage and, by the look of the screenshots, I have to + admit, for a non-biologist that seems powerfull!). So, a "wishlist", as + drgullit called mine suggestions, would be very nice. ;) -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Jens Staal (staalmannen) Feature #309007, revision 10 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) + #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) + Some molecular biology related packages that would be nice: + UGene (http://ugene.unipro.ru/) + GENtle (http://sourceforge.net/projects/gentle-m/) + R and graphical front-end to R + ImageJ + various NCBI software + (http://www.ncbi.nlm.nih.gov/guide/data-software/) + especially Cn3D and if possible automatically set up the installer so + that it works in the browser. + (I do not know the licencing of those though) + + And for scientific writing: Bibus (Endnote-replacement with PubMed + integration) + + Apart from all those things, there are tons of development projects + within bioinformatics (bioruby, biopython bioperl etc) I suppose those + would also be nice to have available even if I am not competent enough + to use them :( + + -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Jones de Andrade (johannesrs) Feature #309007, revision 12 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( + #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) + Good list, staalmannen! With that, I think we now here have a good + proposal of the basic needs from both Chemistry and Biology users. + + Thanks for recording the Bibus software! I don't know how I could + forget that one, and while the bibliografic reference options from + openoffice it self (that are being announced for some time now) does + not becomes a reality, that is the best option. It should already be + included in the main prodution for a while, and also deserved even an + openfate request for itself! -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Vojtech Zeisek (vojtaeus) Feature #309007, revision 13 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) + #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) + Here is short incomplete list of packages I would like to see in + openSUSE. If I find more, I'll add them. :-) Some of theim might be + somewhere in OBS, but it is not very likely. + ClustalX (basic tool to align DNA and protein sequences): + http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ + MEGA4 (it is packaged as RPM using Wine and some other strange + components, but it is very good tool ro make phylogenetic trees) + http://www.megasoftware.net/ + Artemis (viewer and annotation tool to manage sequences) + http://www.sanger.ac.uk/Software/Artemis/ + Biopython (library) http://biopython.org/ + Bioperl (library) http://bioperl.org/ + Molecular suite EMBOSS http://emboss.sourceforge.net/ + You can find some onformation on http://www.open-bio.org/ + KBibTeX (IMHO the best manager for BibTeX database) + http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ + PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ + MrBayes (construction of phylogenetic trees based on Bayesian + algorithm) http://mrbayes.csit.fsu.edu/ + BAPS (another Bayesian computing) + http://web.abo.fi/fak/mnf//mate/jc/software/baps.html + ARB (the best tool to work with rRNA) http://www.arb-home.de/ + MSA (analyzis of microsatellite data) + http://i122server.vu-wien.ac.at/MSA/MSA_download.html + Splitstree and another software for work with molecular genetic data + from http://www-ab.informatik.uni-tuebingen.de/software + Structure (Bayesian calculations of population data) and another + software from http://pritch.bsd.uchicago.edu/software.html + Software (mostly to work with data from Structure) from + http://rosenberglab.bioinformatics.med.umich.edu/software.html + AFLPdat (to analyze AFLP data) and another software from + http://www.etoology.net/index.php/software.html + R packages (there should be special OBS repo for it) + TCS (estimation of phylogenetic networks) + http://darwin.uvige.es/software/tcs.html + BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ + Mesquite (evolutionary analysis) http://mesquiteproject.org/ + Search for keywords like molecular, biology etc. within Debian packages + and You will find much more... ;-) + There are also programs running under Wine (I do not like this way, but + it more or less, with some effort, works), see for example Bioedit + (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... + I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Ricardo Gabriel Berlasso (RGBsuse) Feature #309007, revision 14 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! + #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) + Scilab is on Education now (not the last version, though), but there + are a lot of packages still missing. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Todd R (TheBlackCat) Feature #309007, revision 16 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! + #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) + There is already an idea specifically about Bibus: + https://features.opensuse.org/308261 #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. + #10: Todd R (theblackcat) (2010-03-09 20:48:31) + Sage, a general python-based computer algebra system, should also be + provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% + A0) This is especially true since the new KDE 4 advanced mathematics + software front-end Cantor, which ships as part of the KDE edu project, + supports it. + See https://features.opensuse.org/308459 (308459) for this + specifically. + + Another very useful one is Neuron, a very popular neuron-modelling + program. I personally know many people using this, it is probably the + single most common tool for modelling neurons: + http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) + + Another is AUTO, an very popular tool for ninlinear dynamics and + differential equations. I have seen this used in several classes of + mine, it is an important tool with a very long history: + http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) + -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Denny Beyer (lumnis) Feature #309007, revision 18 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 + #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) + Bibus is not bad - there are others around. Have you tried zotero www. + zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Bruno Friedmann (bruno_friedmann) Feature #309007, revision 20 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) + #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) + Perharps all of you should check this two repositories + http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ + It seems a lot's of what is asked is already there. We will need a + volunteer to build a Science page in wiki to help you to find what is + needed. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Jones de Andrade (johannesrs) Feature #309007, revision 21 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. + #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to + #13) + Well, given the repositories suggested above, I decided to make a compilation + of all asked software on this openfate, then verify which ones are + already available and which ones aren't. The list is below. We have a + total of 56 software packages/libraries/programs/suites requested. Of + those, including the suggested extra repositories (which should be + included in the opensuse official listings, together with "Education" + ones), I could find 21, but there are still 31 missing (and extra 4 + which have some "missing features or so" from my side). I guess this + means that, even having I made a few mistakes here and there, this is + still a long list of requests, which I suppose must be now moved as + requests for openSUSE 11.4. + ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok + bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok + gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely + webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs + torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO + autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO + Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO + MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO + R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ + OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron + NO auto NO -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Denny Beyer (lumnis) Feature #309007, revision 22 Title: Add more scientific packages Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO + #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) + ImageJ added + I created a new ImageJ package, where the program is build from source, + adds desktop entry etc. which was missing in the existing projects. + Please test the package and report back any findings, as I'm not a + ImageJ user. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Martin Seidler (pistazienfresser) Feature #309007, revision 23 Title: Add more scientific packages + Education Li-f-e: Unconfirmed + Priority + Requester: Desirable Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: zmi zmi (zmi007) Feature #309007, revision 25 Title: Add more scientific packages Education Li-f-e: Unconfirmed Priority Requester: Desirable Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. + #16: zmi zmi (zmi007) (2011-07-02 01:43:42) + Another side of physics packages I would like to see in openSUSE all + etsf software from + http://www.etsf.eu/resources/software/etsf_software_repository Here + are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim + Exciting ELK APE + gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO + http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl + http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based + Fortran interface to the GNU scientific library molden, gmolden + http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd + http://www.ks.uiuc.edu/Research/namd/ nlopt library + http://ab-initio.mit.edu/wiki/index.php/NLopt orca + http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ + rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz + http://home.gna.org/veusz/ MacMolPlt + http://www.scl.ameslab.gov/MacMolPlt xmakemol + http://www.nongnu.org/xmakemol/ vmd + http://www.ks.uiuc.edu/Research/vmd/ -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: zmi zmi (zmi007) Feature #309007, revision 26 Title: Add more scientific packages Education Li-f-e: Unconfirmed Priority Requester: Desirable Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ + #17: zmi zmi (zmi007) (2011-07-02 18:12:29) + visit https://wci.llnl.gov/codes/visit/home.html -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Andre Massing (susetroll) Feature #309007, revision 28 Title: Add more scientific packages Education Li-f-e: Unconfirmed Priority Requester: Desirable Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. + #18: Andre Massing (susetroll) (2011-07-18 20:23:44) (reply to #14) + I would like to add some packages which are interesting for people from + the FEM (FVM/FDM) communities dealing with numerically solving partial + differential equations. Of course an updated and fully functional + openmpi is a must :) High performance linear algebra solver: PETSc NO + SLEPc NO Armadillo NO Trilinos NO suitesparse (?) MTL4 (NO) UBLAS (NO) + Mesh/Graph partitioner ParMETIS (NO) METIS (in science repo) SCOTCH + (NO) Visualization (and more): mayavi (NO) or better whole enthought + tool suite. paraview (in science) Mesh generation: Netgen (in sciene) + Tetgen (NO) Triangle (NO) gmsh (in science) PDE solving environments + FEniCS with subpackages (NO) UFL, UFC, FFC, (SYFI) FIAT, INSTANT, + VIPER, DOLFIN, since I am close to the developer community I would like + to volunteer for packaging at least these one. FreeFem++ (NO) lifeV + (NO) DUNE (NO) dealii + Of course, this is a very (FEM) biased choice of packages, so please + add something which is missing here. #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ #17: zmi zmi (zmi007) (2011-07-02 18:12:29) visit https://wci.llnl.gov/codes/visit/home.html -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Andre Massing (susetroll) Feature #309007, revision 29 Title: Add more scientific packages Education Li-f-e: Unconfirmed Priority Requester: Desirable Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. #18: Andre Massing (susetroll) (2011-07-18 20:23:44) (reply to #14) I would like to add some packages which are interesting for people from the FEM (FVM/FDM) communities dealing with numerically solving partial differential equations. Of course an updated and fully functional openmpi is a must :) High performance linear algebra solver: PETSc NO SLEPc NO Armadillo NO Trilinos NO suitesparse (?) MTL4 (NO) UBLAS (NO) Mesh/Graph partitioner ParMETIS (NO) METIS (in science repo) SCOTCH (NO) Visualization (and more): mayavi (NO) or better whole enthought tool suite. paraview (in science) Mesh generation: Netgen (in sciene) Tetgen (NO) Triangle (NO) gmsh (in science) PDE solving environments FEniCS with subpackages (NO) UFL, UFC, FFC, (SYFI) FIAT, INSTANT, VIPER, DOLFIN, since I am close to the developer community I would like to volunteer for packaging at least these one. FreeFem++ (NO) lifeV (NO) DUNE (NO) dealii Of course, this is a very (FEM) biased choice of packages, so please add something which is missing here. + #19: Andre Massing (susetroll) (2011-07-18 20:34:19) (reply to #18) + Of course I forgot a few :) + Computational geometry related: CGAL gts bullet physics and collision + detection library (might be very interesting for game programmers) #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ #17: zmi zmi (zmi007) (2011-07-02 18:12:29) visit https://wci.llnl.gov/codes/visit/home.html -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Alberto Passalacqua (GreenGeeko) Feature #309007, revision 30 Title: Add more scientific packages Education Li-f-e: Unconfirmed Priority Requester: Desirable Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. #18: Andre Massing (susetroll) (2011-07-18 20:23:44) (reply to #14) I would like to add some packages which are interesting for people from the FEM (FVM/FDM) communities dealing with numerically solving partial differential equations. Of course an updated and fully functional openmpi is a must :) High performance linear algebra solver: PETSc NO SLEPc NO Armadillo NO Trilinos NO suitesparse (?) MTL4 (NO) UBLAS (NO) Mesh/Graph partitioner ParMETIS (NO) METIS (in science repo) SCOTCH (NO) Visualization (and more): mayavi (NO) or better whole enthought tool suite. paraview (in science) Mesh generation: Netgen (in sciene) Tetgen (NO) Triangle (NO) gmsh (in science) PDE solving environments FEniCS with subpackages (NO) UFL, UFC, FFC, (SYFI) FIAT, INSTANT, VIPER, DOLFIN, since I am close to the developer community I would like to volunteer for packaging at least these one. FreeFem++ (NO) lifeV (NO) DUNE (NO) dealii Of course, this is a very (FEM) biased choice of packages, so please add something which is missing here. #19: Andre Massing (susetroll) (2011-07-18 20:34:19) (reply to #18) Of course I forgot a few :) Computational geometry related: CGAL gts bullet physics and collision detection library (might be very interesting for game programmers) #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ #17: zmi zmi (zmi007) (2011-07-02 18:12:29) visit https://wci.llnl.gov/codes/visit/home.html + #20: Alberto Passalacqua (greengeeko) (2011-07-18 22:56:39) + The initiative is really very welcome! :-) openSUSE would benefit + significantly from this. However I would add a couple of + considerations: - Packages must be built by people who *uses* them. + Scientific packages are hard to create, and frequently pre-built + packages do not offer the same features of the upstream hand-built + package because the packager removed options to simplify the build + process. As a consequence, what is really needed here are packagers + with scientific experience, and given the intricacy of creating RPM's + and of using OBS, I don't know so many :-) - Often it is not worth + providing RPM's for some scientific project. This is, IMHO, the case + for very large projects with a lot of (often obsolete) dependencies, + which are provided in binary form from the developers. It is much + simpler for the user to download the full binary package and use it. At + the same time packaging those softwares (I think to Salome for + example), is extremely time consuming for the packager, and the + structure of OBS would lead to too many sub-packages, making it very + hard for a final user to have something easy to install/use. + Best, -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Cristea Bogdan (Bogdanc23) Feature #309007, revision 31 Title: Add more scientific packages Education Li-f-e: Unconfirmed Priority Requester: Desirable Package Wishlist: Unconfirmed Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. #18: Andre Massing (susetroll) (2011-07-18 20:23:44) (reply to #14) I would like to add some packages which are interesting for people from the FEM (FVM/FDM) communities dealing with numerically solving partial differential equations. Of course an updated and fully functional openmpi is a must :) High performance linear algebra solver: PETSc NO SLEPc NO Armadillo NO Trilinos NO suitesparse (?) MTL4 (NO) UBLAS (NO) Mesh/Graph partitioner ParMETIS (NO) METIS (in science repo) SCOTCH (NO) Visualization (and more): mayavi (NO) or better whole enthought tool suite. paraview (in science) Mesh generation: Netgen (in sciene) Tetgen (NO) Triangle (NO) gmsh (in science) PDE solving environments FEniCS with subpackages (NO) UFL, UFC, FFC, (SYFI) FIAT, INSTANT, VIPER, DOLFIN, since I am close to the developer community I would like to volunteer for packaging at least these one. FreeFem++ (NO) lifeV (NO) DUNE (NO) dealii Of course, this is a very (FEM) biased choice of packages, so please add something which is missing here. #19: Andre Massing (susetroll) (2011-07-18 20:34:19) (reply to #18) Of course I forgot a few :) Computational geometry related: CGAL gts bullet physics and collision detection library (might be very interesting for game programmers) #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ #17: zmi zmi (zmi007) (2011-07-02 18:12:29) visit https://wci.llnl.gov/codes/visit/home.html #20: Alberto Passalacqua (greengeeko) (2011-07-18 22:56:39) The initiative is really very welcome! :-) openSUSE would benefit significantly from this. However I would add a couple of considerations: - Packages must be built by people who *uses* them. Scientific packages are hard to create, and frequently pre-built packages do not offer the same features of the upstream hand-built package because the packager removed options to simplify the build process. As a consequence, what is really needed here are packagers with scientific experience, and given the intricacy of creating RPM's and of using OBS, I don't know so many :-) - Often it is not worth providing RPM's for some scientific project. This is, IMHO, the case for very large projects with a lot of (often obsolete) dependencies, which are provided in binary form from the developers. It is much simpler for the user to download the full binary package and use it. At the same time packaging those softwares (I think to Salome for example), is extremely time consuming for the packager, and the structure of OBS would lead to too many sub-packages, making it very hard for a final user to have something easy to install/use. Best, + #21: Cristea Bogdan (bogdanc23) (2011-07-18 23:28:02) + My scientific application proposals: IT++ (signal processing) and + aigaion2 (bibliography management). I would like also to emphasize the + fact that python, as replacement for MATLAB, does not receive too much + attention from the academic community and some advertisement would be + needed. + As for the proposition that packages build should be managed by + scientists I fully agree and I am willing to contribute. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Andreas Jaeger (a_jaeger) Feature #309007, revision 32 Title: Add more scientific packages Education Li-f-e: Unconfirmed Priority Requester: Desirable - Package Wishlist: Unconfirmed + Package Wishlist: Evaluation by engineering manager Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. #18: Andre Massing (susetroll) (2011-07-18 20:23:44) (reply to #14) I would like to add some packages which are interesting for people from the FEM (FVM/FDM) communities dealing with numerically solving partial differential equations. Of course an updated and fully functional openmpi is a must :) High performance linear algebra solver: PETSc NO SLEPc NO Armadillo NO Trilinos NO suitesparse (?) MTL4 (NO) UBLAS (NO) Mesh/Graph partitioner ParMETIS (NO) METIS (in science repo) SCOTCH (NO) Visualization (and more): mayavi (NO) or better whole enthought tool suite. paraview (in science) Mesh generation: Netgen (in sciene) Tetgen (NO) Triangle (NO) gmsh (in science) PDE solving environments FEniCS with subpackages (NO) UFL, UFC, FFC, (SYFI) FIAT, INSTANT, VIPER, DOLFIN, since I am close to the developer community I would like to volunteer for packaging at least these one. FreeFem++ (NO) lifeV (NO) DUNE (NO) dealii Of course, this is a very (FEM) biased choice of packages, so please add something which is missing here. #19: Andre Massing (susetroll) (2011-07-18 20:34:19) (reply to #18) Of course I forgot a few :) Computational geometry related: CGAL gts bullet physics and collision detection library (might be very interesting for game programmers) #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ #17: zmi zmi (zmi007) (2011-07-02 18:12:29) visit https://wci.llnl.gov/codes/visit/home.html #20: Alberto Passalacqua (greengeeko) (2011-07-18 22:56:39) The initiative is really very welcome! :-) openSUSE would benefit significantly from this. However I would add a couple of considerations: - Packages must be built by people who *uses* them. Scientific packages are hard to create, and frequently pre-built packages do not offer the same features of the upstream hand-built package because the packager removed options to simplify the build process. As a consequence, what is really needed here are packagers with scientific experience, and given the intricacy of creating RPM's and of using OBS, I don't know so many :-) - Often it is not worth providing RPM's for some scientific project. This is, IMHO, the case for very large projects with a lot of (often obsolete) dependencies, which are provided in binary form from the developers. It is much simpler for the user to download the full binary package and use it. At the same time packaging those softwares (I think to Salome for example), is extremely time consuming for the packager, and the structure of OBS would lead to too many sub-packages, making it very hard for a final user to have something easy to install/use. Best, #21: Cristea Bogdan (bogdanc23) (2011-07-18 23:28:02) My scientific application proposals: IT++ (signal processing) and aigaion2 (bibliography management). I would like also to emphasize the fact that python, as replacement for MATLAB, does not receive too much attention from the academic community and some advertisement would be needed. As for the proposition that packages build should be managed by scientists I fully agree and I am willing to contribute. + #22: Andreas Jaeger (a_jaeger) (2011-07-19 09:58:30) + Just ask to get the packages into openSUSE, it's easy to do - package + the software and declare that you will take care of bugs. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Vojtech Zeisek (vojtaeus) Feature #309007, revision 33 Title: Add more scientific packages Education Li-f-e: Unconfirmed Priority Requester: Desirable Package Wishlist: Evaluation by engineering manager Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) + #23: Vojtech Zeisek (vojtaeus) (2011-07-19 12:38:17) (reply to #8) + Some more biological software for work with DNA: CAP3 + http://pbil.univ-lyon1.fr/cap3.php http://seq.cs.iastate.edu/ cinema5 + http://aig.cs.man.ac.uk/research/utopia/cinema/cinema.php finchtv + http://www.geospiza.com/Products/finchtv.shtml Geneious + http://www.geneious.com/ GenePalette http://www.genepalette.org/ + Jalview http://www.jalview.org/ Sequence Manipulation Suite, for + example http://www.bioinformatics.org/sms2/ #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. #18: Andre Massing (susetroll) (2011-07-18 20:23:44) (reply to #14) I would like to add some packages which are interesting for people from the FEM (FVM/FDM) communities dealing with numerically solving partial differential equations. Of course an updated and fully functional openmpi is a must :) High performance linear algebra solver: PETSc NO SLEPc NO Armadillo NO Trilinos NO suitesparse (?) MTL4 (NO) UBLAS (NO) Mesh/Graph partitioner ParMETIS (NO) METIS (in science repo) SCOTCH (NO) Visualization (and more): mayavi (NO) or better whole enthought tool suite. paraview (in science) Mesh generation: Netgen (in sciene) Tetgen (NO) Triangle (NO) gmsh (in science) PDE solving environments FEniCS with subpackages (NO) UFL, UFC, FFC, (SYFI) FIAT, INSTANT, VIPER, DOLFIN, since I am close to the developer community I would like to volunteer for packaging at least these one. FreeFem++ (NO) lifeV (NO) DUNE (NO) dealii Of course, this is a very (FEM) biased choice of packages, so please add something which is missing here. #19: Andre Massing (susetroll) (2011-07-18 20:34:19) (reply to #18) Of course I forgot a few :) Computational geometry related: CGAL gts bullet physics and collision detection library (might be very interesting for game programmers) #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ #17: zmi zmi (zmi007) (2011-07-02 18:12:29) visit https://wci.llnl.gov/codes/visit/home.html #20: Alberto Passalacqua (greengeeko) (2011-07-18 22:56:39) The initiative is really very welcome! :-) openSUSE would benefit significantly from this. However I would add a couple of considerations: - Packages must be built by people who *uses* them. Scientific packages are hard to create, and frequently pre-built packages do not offer the same features of the upstream hand-built package because the packager removed options to simplify the build process. As a consequence, what is really needed here are packagers with scientific experience, and given the intricacy of creating RPM's and of using OBS, I don't know so many :-) - Often it is not worth providing RPM's for some scientific project. This is, IMHO, the case for very large projects with a lot of (often obsolete) dependencies, which are provided in binary form from the developers. It is much simpler for the user to download the full binary package and use it. At the same time packaging those softwares (I think to Salome for example), is extremely time consuming for the packager, and the structure of OBS would lead to too many sub-packages, making it very hard for a final user to have something easy to install/use. Best, #21: Cristea Bogdan (bogdanc23) (2011-07-18 23:28:02) My scientific application proposals: IT++ (signal processing) and aigaion2 (bibliography management). I would like also to emphasize the fact that python, as replacement for MATLAB, does not receive too much attention from the academic community and some advertisement would be needed. As for the proposition that packages build should be managed by scientists I fully agree and I am willing to contribute. #22: Andreas Jaeger (a_jaeger) (2011-07-19 09:58:30) Just ask to get the packages into openSUSE, it's easy to do - package the software and declare that you will take care of bugs. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Yasha Gindikin (SlonoInquisitor) Feature #309007, revision 34 Title: Add more scientific packages Education Li-f-e: Unconfirmed Priority Requester: Desirable Package Wishlist: Evaluation by engineering manager Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #23: Vojtech Zeisek (vojtaeus) (2011-07-19 12:38:17) (reply to #8) Some more biological software for work with DNA: CAP3 http://pbil.univ-lyon1.fr/cap3.php http://seq.cs.iastate.edu/ cinema5 http://aig.cs.man.ac.uk/research/utopia/cinema/cinema.php finchtv http://www.geospiza.com/Products/finchtv.shtml Geneious http://www.geneious.com/ GenePalette http://www.genepalette.org/ Jalview http://www.jalview.org/ Sequence Manipulation Suite, for example http://www.bioinformatics.org/sms2/ #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. #18: Andre Massing (susetroll) (2011-07-18 20:23:44) (reply to #14) I would like to add some packages which are interesting for people from the FEM (FVM/FDM) communities dealing with numerically solving partial differential equations. Of course an updated and fully functional openmpi is a must :) High performance linear algebra solver: PETSc NO SLEPc NO Armadillo NO Trilinos NO suitesparse (?) MTL4 (NO) UBLAS (NO) Mesh/Graph partitioner ParMETIS (NO) METIS (in science repo) SCOTCH (NO) Visualization (and more): mayavi (NO) or better whole enthought tool suite. paraview (in science) Mesh generation: Netgen (in sciene) Tetgen (NO) Triangle (NO) gmsh (in science) PDE solving environments FEniCS with subpackages (NO) UFL, UFC, FFC, (SYFI) FIAT, INSTANT, VIPER, DOLFIN, since I am close to the developer community I would like to volunteer for packaging at least these one. FreeFem++ (NO) lifeV (NO) DUNE (NO) dealii Of course, this is a very (FEM) biased choice of packages, so please add something which is missing here. #19: Andre Massing (susetroll) (2011-07-18 20:34:19) (reply to #18) Of course I forgot a few :) Computational geometry related: CGAL gts bullet physics and collision detection library (might be very interesting for game programmers) #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ #17: zmi zmi (zmi007) (2011-07-02 18:12:29) visit https://wci.llnl.gov/codes/visit/home.html #20: Alberto Passalacqua (greengeeko) (2011-07-18 22:56:39) The initiative is really very welcome! :-) openSUSE would benefit significantly from this. However I would add a couple of considerations: - Packages must be built by people who *uses* them. Scientific packages are hard to create, and frequently pre-built packages do not offer the same features of the upstream hand-built package because the packager removed options to simplify the build process. As a consequence, what is really needed here are packagers with scientific experience, and given the intricacy of creating RPM's and of using OBS, I don't know so many :-) - Often it is not worth providing RPM's for some scientific project. This is, IMHO, the case for very large projects with a lot of (often obsolete) dependencies, which are provided in binary form from the developers. It is much simpler for the user to download the full binary package and use it. At the same time packaging those softwares (I think to Salome for example), is extremely time consuming for the packager, and the structure of OBS would lead to too many sub-packages, making it very hard for a final user to have something easy to install/use. Best, #21: Cristea Bogdan (bogdanc23) (2011-07-18 23:28:02) My scientific application proposals: IT++ (signal processing) and aigaion2 (bibliography management). I would like also to emphasize the fact that python, as replacement for MATLAB, does not receive too much attention from the academic community and some advertisement would be needed. As for the proposition that packages build should be managed by scientists I fully agree and I am willing to contribute. #22: Andreas Jaeger (a_jaeger) (2011-07-19 09:58:30) Just ask to get the packages into openSUSE, it's easy to do - package the software and declare that you will take care of bugs. + #24: Yasha Gindikin (slonoinquisitor) (2011-07-30 22:45:48) + I would also add Gwyddion to the wishlist (see gwyddion.net). This is a + widely used program for probing microscopy. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Andre Massing (susetroll) Feature #309007, revision 35 Title: Add more scientific packages Education Li-f-e: Unconfirmed Priority Requester: Desirable + openSUSE Distribution: Unconfirmed + Priority + Requester: Desirable Package Wishlist: Evaluation by engineering manager Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #23: Vojtech Zeisek (vojtaeus) (2011-07-19 12:38:17) (reply to #8) Some more biological software for work with DNA: CAP3 http://pbil.univ-lyon1.fr/cap3.php http://seq.cs.iastate.edu/ cinema5 http://aig.cs.man.ac.uk/research/utopia/cinema/cinema.php finchtv http://www.geospiza.com/Products/finchtv.shtml Geneious http://www.geneious.com/ GenePalette http://www.genepalette.org/ Jalview http://www.jalview.org/ Sequence Manipulation Suite, for example http://www.bioinformatics.org/sms2/ #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. #18: Andre Massing (susetroll) (2011-07-18 20:23:44) (reply to #14) I would like to add some packages which are interesting for people from the FEM (FVM/FDM) communities dealing with numerically solving partial differential equations. Of course an updated and fully functional openmpi is a must :) High performance linear algebra solver: PETSc NO SLEPc NO Armadillo NO Trilinos NO suitesparse (?) MTL4 (NO) UBLAS (NO) Mesh/Graph partitioner ParMETIS (NO) METIS (in science repo) SCOTCH (NO) Visualization (and more): mayavi (NO) or better whole enthought tool suite. paraview (in science) Mesh generation: Netgen (in sciene) Tetgen (NO) Triangle (NO) gmsh (in science) PDE solving environments FEniCS with subpackages (NO) UFL, UFC, FFC, (SYFI) FIAT, INSTANT, VIPER, DOLFIN, since I am close to the developer community I would like to volunteer for packaging at least these one. FreeFem++ (NO) lifeV (NO) DUNE (NO) dealii Of course, this is a very (FEM) biased choice of packages, so please add something which is missing here. #19: Andre Massing (susetroll) (2011-07-18 20:34:19) (reply to #18) Of course I forgot a few :) Computational geometry related: CGAL gts bullet physics and collision detection library (might be very interesting for game programmers) #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ #17: zmi zmi (zmi007) (2011-07-02 18:12:29) visit https://wci.llnl.gov/codes/visit/home.html #20: Alberto Passalacqua (greengeeko) (2011-07-18 22:56:39) The initiative is really very welcome! :-) openSUSE would benefit significantly from this. However I would add a couple of considerations: - Packages must be built by people who *uses* them. Scientific packages are hard to create, and frequently pre-built packages do not offer the same features of the upstream hand-built package because the packager removed options to simplify the build process. As a consequence, what is really needed here are packagers with scientific experience, and given the intricacy of creating RPM's and of using OBS, I don't know so many :-) - Often it is not worth providing RPM's for some scientific project. This is, IMHO, the case for very large projects with a lot of (often obsolete) dependencies, which are provided in binary form from the developers. It is much simpler for the user to download the full binary package and use it. At the same time packaging those softwares (I think to Salome for example), is extremely time consuming for the packager, and the structure of OBS would lead to too many sub-packages, making it very hard for a final user to have something easy to install/use. Best, #21: Cristea Bogdan (bogdanc23) (2011-07-18 23:28:02) My scientific application proposals: IT++ (signal processing) and aigaion2 (bibliography management). I would like also to emphasize the fact that python, as replacement for MATLAB, does not receive too much attention from the academic community and some advertisement would be needed. As for the proposition that packages build should be managed by scientists I fully agree and I am willing to contribute. #22: Andreas Jaeger (a_jaeger) (2011-07-19 09:58:30) Just ask to get the packages into openSUSE, it's easy to do - package the software and declare that you will take care of bugs. #24: Yasha Gindikin (slonoinquisitor) (2011-07-30 22:45:48) I would also add Gwyddion to the wishlist (see gwyddion.net). This is a widely used program for probing microscopy. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Lars Vogdt (lrupp) Feature #309007, revision 37 Title: Add more scientific packages - Education Li-f-e: Unconfirmed + Education Li-f-e: New Priority Requester: Desirable openSUSE Distribution: Unconfirmed Priority Requester: Desirable Package Wishlist: Evaluation by engineering manager Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! - We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. - At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. - Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. - Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. - Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p - Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). - As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! - Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #23: Vojtech Zeisek (vojtaeus) (2011-07-19 12:38:17) (reply to #8) Some more biological software for work with DNA: CAP3 http://pbil.univ-lyon1.fr/cap3.php http://seq.cs.iastate.edu/ cinema5 http://aig.cs.man.ac.uk/research/utopia/cinema/cinema.php finchtv http://www.geospiza.com/Products/finchtv.shtml Geneious http://www.geneious.com/ GenePalette http://www.genepalette.org/ Jalview http://www.jalview.org/ Sequence Manipulation Suite, for example http://www.bioinformatics.org/sms2/ #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) - And for scientific writing: Bibus (Endnote-replacement with PubMed integration) - Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( - - #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. - Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. - Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) - Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) - #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. #18: Andre Massing (susetroll) (2011-07-18 20:23:44) (reply to #14) I would like to add some packages which are interesting for people from the FEM (FVM/FDM) communities dealing with numerically solving partial differential equations. Of course an updated and fully functional openmpi is a must :) High performance linear algebra solver: PETSc NO SLEPc NO Armadillo NO Trilinos NO suitesparse (?) MTL4 (NO) UBLAS (NO) Mesh/Graph partitioner ParMETIS (NO) METIS (in science repo) SCOTCH (NO) Visualization (and more): mayavi (NO) or better whole enthought tool suite. paraview (in science) Mesh generation: Netgen (in sciene) Tetgen (NO) Triangle (NO) gmsh (in science) PDE solving environments FEniCS with subpackages (NO) UFL, UFC, FFC, (SYFI) FIAT, INSTANT, VIPER, DOLFIN, since I am close to the developer community I would like to volunteer for packaging at least these one. FreeFem++ (NO) lifeV (NO) DUNE (NO) dealii Of course, this is a very (FEM) biased choice of packages, so please add something which is missing here. #19: Andre Massing (susetroll) (2011-07-18 20:34:19) (reply to #18) Of course I forgot a few :) Computational geometry related: CGAL gts bullet physics and collision detection library (might be very interesting for game programmers) #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ #17: zmi zmi (zmi007) (2011-07-02 18:12:29) visit https://wci.llnl.gov/codes/visit/home.html #20: Alberto Passalacqua (greengeeko) (2011-07-18 22:56:39) The initiative is really very welcome! :-) openSUSE would benefit significantly from this. However I would add a couple of considerations: - Packages must be built by people who *uses* them. Scientific packages are hard to create, and frequently pre-built packages do not offer the same features of the upstream hand-built package because the packager removed options to simplify the build process. As a consequence, what is really needed here are packagers with scientific experience, and given the intricacy of creating RPM's and of using OBS, I don't know so many :-) - Often it is not worth providing RPM's for some scientific project. This is, IMHO, the case for very large projects with a lot of (often obsolete) dependencies, which are provided in binary form from the developers. It is much simpler for the user to download the full binary package and use it. At the same time packaging those softwares (I think to Salome for example), is extremely time consuming for the packager, and the structure of OBS would lead to too many sub-packages, making it very hard for a final user to have something easy to install/use. Best, #21: Cristea Bogdan (bogdanc23) (2011-07-18 23:28:02) My scientific application proposals: IT++ (signal processing) and aigaion2 (bibliography management). I would like also to emphasize the fact that python, as replacement for MATLAB, does not receive too much attention from the academic community and some advertisement would be needed. As for the proposition that packages build should be managed by scientists I fully agree and I am willing to contribute. #22: Andreas Jaeger (a_jaeger) (2011-07-19 09:58:30) Just ask to get the packages into openSUSE, it's easy to do - package the software and declare that you will take care of bugs. #24: Yasha Gindikin (slonoinquisitor) (2011-07-30 22:45:48) I would also add Gwyddion to the wishlist (see gwyddion.net). This is a widely used program for probing microscopy. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Pierre Bonamy (flyos) Feature #309007, revision 38 Title: Add more scientific packages Education Li-f-e: New Priority Requester: Desirable openSUSE Distribution: Unconfirmed Priority Requester: Desirable Package Wishlist: Evaluation by engineering manager Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #23: Vojtech Zeisek (vojtaeus) (2011-07-19 12:38:17) (reply to #8) Some more biological software for work with DNA: CAP3 http://pbil.univ-lyon1.fr/cap3.php http://seq.cs.iastate.edu/ cinema5 http://aig.cs.man.ac.uk/research/utopia/cinema/cinema.php finchtv http://www.geospiza.com/Products/finchtv.shtml Geneious http://www.geneious.com/ GenePalette http://www.genepalette.org/ Jalview http://www.jalview.org/ Sequence Manipulation Suite, for example http://www.bioinformatics.org/sms2/ #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. #18: Andre Massing (susetroll) (2011-07-18 20:23:44) (reply to #14) I would like to add some packages which are interesting for people from the FEM (FVM/FDM) communities dealing with numerically solving partial differential equations. Of course an updated and fully functional openmpi is a must :) High performance linear algebra solver: PETSc NO SLEPc NO Armadillo NO Trilinos NO suitesparse (?) MTL4 (NO) UBLAS (NO) Mesh/Graph partitioner ParMETIS (NO) METIS (in science repo) SCOTCH (NO) Visualization (and more): mayavi (NO) or better whole enthought tool suite. paraview (in science) Mesh generation: Netgen (in sciene) Tetgen (NO) Triangle (NO) gmsh (in science) PDE solving environments FEniCS with subpackages (NO) UFL, UFC, FFC, (SYFI) FIAT, INSTANT, VIPER, DOLFIN, since I am close to the developer community I would like to volunteer for packaging at least these one. FreeFem++ (NO) lifeV (NO) DUNE (NO) dealii Of course, this is a very (FEM) biased choice of packages, so please add something which is missing here. #19: Andre Massing (susetroll) (2011-07-18 20:34:19) (reply to #18) Of course I forgot a few :) Computational geometry related: CGAL gts bullet physics and collision detection library (might be very interesting for game programmers) #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ #17: zmi zmi (zmi007) (2011-07-02 18:12:29) visit https://wci.llnl.gov/codes/visit/home.html #20: Alberto Passalacqua (greengeeko) (2011-07-18 22:56:39) The initiative is really very welcome! :-) openSUSE would benefit significantly from this. However I would add a couple of considerations: - Packages must be built by people who *uses* them. Scientific packages are hard to create, and frequently pre-built packages do not offer the same features of the upstream hand-built package because the packager removed options to simplify the build process. As a consequence, what is really needed here are packagers with scientific experience, and given the intricacy of creating RPM's and of using OBS, I don't know so many :-) - Often it is not worth providing RPM's for some scientific project. This is, IMHO, the case for very large projects with a lot of (often obsolete) dependencies, which are provided in binary form from the developers. It is much simpler for the user to download the full binary package and use it. At the same time packaging those softwares (I think to Salome for example), is extremely time consuming for the packager, and the structure of OBS would lead to too many sub-packages, making it very hard for a final user to have something easy to install/use. Best, #21: Cristea Bogdan (bogdanc23) (2011-07-18 23:28:02) My scientific application proposals: IT++ (signal processing) and aigaion2 (bibliography management). I would like also to emphasize the fact that python, as replacement for MATLAB, does not receive too much attention from the academic community and some advertisement would be needed. As for the proposition that packages build should be managed by scientists I fully agree and I am willing to contribute. #22: Andreas Jaeger (a_jaeger) (2011-07-19 09:58:30) Just ask to get the packages into openSUSE, it's easy to do - package the software and declare that you will take care of bugs. #24: Yasha Gindikin (slonoinquisitor) (2011-07-30 22:45:48) I would also add Gwyddion to the wishlist (see gwyddion.net). This is a widely used program for probing microscopy. + #25: Pierre Bonamy (flyos) (2016-04-12 14:26:50) + I know this is a quite old ticket, but I'd like to add the following + suggestion : the "Debian Med" team is doing a quite excellent work at + gathering and packaging scientific software for Debian and co. + Wouldn't it be possible to get source and build specs from them to + transfer to the "science" repo and provide package for OpenSuse (and + more, since OBS can be multi-distro)? -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Tristan Miller (psych0naut) Feature #309007, revision 39 Title: Add more scientific packages Education Li-f-e: New Priority Requester: Desirable openSUSE Distribution: Unconfirmed Priority Requester: Desirable Package Wishlist: Evaluation by engineering manager Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #23: Vojtech Zeisek (vojtaeus) (2011-07-19 12:38:17) (reply to #8) Some more biological software for work with DNA: CAP3 http://pbil.univ-lyon1.fr/cap3.php http://seq.cs.iastate.edu/ cinema5 http://aig.cs.man.ac.uk/research/utopia/cinema/cinema.php finchtv http://www.geospiza.com/Products/finchtv.shtml Geneious http://www.geneious.com/ GenePalette http://www.genepalette.org/ Jalview http://www.jalview.org/ Sequence Manipulation Suite, for example http://www.bioinformatics.org/sms2/ #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. #18: Andre Massing (susetroll) (2011-07-18 20:23:44) (reply to #14) I would like to add some packages which are interesting for people from the FEM (FVM/FDM) communities dealing with numerically solving partial differential equations. Of course an updated and fully functional openmpi is a must :) High performance linear algebra solver: PETSc NO SLEPc NO Armadillo NO Trilinos NO suitesparse (?) MTL4 (NO) UBLAS (NO) Mesh/Graph partitioner ParMETIS (NO) METIS (in science repo) SCOTCH (NO) Visualization (and more): mayavi (NO) or better whole enthought tool suite. paraview (in science) Mesh generation: Netgen (in sciene) Tetgen (NO) Triangle (NO) gmsh (in science) PDE solving environments FEniCS with subpackages (NO) UFL, UFC, FFC, (SYFI) FIAT, INSTANT, VIPER, DOLFIN, since I am close to the developer community I would like to volunteer for packaging at least these one. FreeFem++ (NO) lifeV (NO) DUNE (NO) dealii Of course, this is a very (FEM) biased choice of packages, so please add something which is missing here. #19: Andre Massing (susetroll) (2011-07-18 20:34:19) (reply to #18) Of course I forgot a few :) Computational geometry related: CGAL gts bullet physics and collision detection library (might be very interesting for game programmers) #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ #17: zmi zmi (zmi007) (2011-07-02 18:12:29) visit https://wci.llnl.gov/codes/visit/home.html #20: Alberto Passalacqua (greengeeko) (2011-07-18 22:56:39) The initiative is really very welcome! :-) openSUSE would benefit significantly from this. However I would add a couple of considerations: - Packages must be built by people who *uses* them. Scientific packages are hard to create, and frequently pre-built packages do not offer the same features of the upstream hand-built package because the packager removed options to simplify the build process. As a consequence, what is really needed here are packagers with scientific experience, and given the intricacy of creating RPM's and of using OBS, I don't know so many :-) - Often it is not worth providing RPM's for some scientific project. This is, IMHO, the case for very large projects with a lot of (often obsolete) dependencies, which are provided in binary form from the developers. It is much simpler for the user to download the full binary package and use it. At the same time packaging those softwares (I think to Salome for example), is extremely time consuming for the packager, and the structure of OBS would lead to too many sub-packages, making it very hard for a final user to have something easy to install/use. Best, #21: Cristea Bogdan (bogdanc23) (2011-07-18 23:28:02) My scientific application proposals: IT++ (signal processing) and aigaion2 (bibliography management). I would like also to emphasize the fact that python, as replacement for MATLAB, does not receive too much attention from the academic community and some advertisement would be needed. As for the proposition that packages build should be managed by scientists I fully agree and I am willing to contribute. #22: Andreas Jaeger (a_jaeger) (2011-07-19 09:58:30) Just ask to get the packages into openSUSE, it's easy to do - package the software and declare that you will take care of bugs. #24: Yasha Gindikin (slonoinquisitor) (2011-07-30 22:45:48) I would also add Gwyddion to the wishlist (see gwyddion.net). This is a widely used program for probing microscopy. #25: Pierre Bonamy (flyos) (2016-04-12 14:26:50) I know this is a quite old ticket, but I'd like to add the following suggestion : the "Debian Med" team is doing a quite excellent work at gathering and packaging scientific software for Debian and co. Wouldn't it be possible to get source and build specs from them to transfer to the "science" repo and provide package for OpenSuse (and more, since OBS can be multi-distro)? + #26: Tristan Miller (psych0naut) (2016-08-18 15:03:38) + To add to this, many of the existing packages in the Science repository + are for very old versions. Working research scientists generally depend + on cutting-edge tools (at minimum, the latest stable release), so + providing tools that are years out of date isn't helping very many + people. -- openSUSE Feature: https://features.opensuse.org/309007
Feature changed by: Karl Cheng (qantas94heavy) Feature #309007, revision 40 Title: Add more scientific packages - Education Li-f-e: New - Priority - Requester: Desirable - openSUSE Distribution: Unconfirmed - Priority - Requester: Desirable Package Wishlist: Evaluation by engineering manager Priority Requester: Important Requested by: Ricardo Gabriel Berlasso (rgbsuse) Partner organization: openSUSE.org Description: Right now, openSUSE have quite few "scientific packages". We have freemat on Education, xmgrace ... and a few more. But, for example, octave is only on Packman and SciDAVis is nowhere (for 11.2 at least). There are no packages for Scilab either, nor for PAW... Use Case: A physicist (or engineer) working on University that needs a good Linux distro for his/her work. Nowadays, even if openSUSE is more stable and reliable than fedora, the scientist will choose the later because its larger set of scientific packages. Business case (Partner benefit): openSUSE.org: To give openSUSE more presence on universities and research centers at "final user" level. Now openSUSE and its derivatives are found in clusters to run simulations (I've seen some of them) with ad-hoc programs, or in supercomputers, but not in the office computer for the single researcher. With its focus on stability, openSUSE could be the perfect "sci distro" but the few "heavy duty" scientific packages available is against this. Discussion: #1: Luis Medinas (lmedinas) (2010-02-14 21:52:25) Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. #2: Jones de Andrade (johannesrs) (2010-02-15 13:06:33) That's absolutelly a MUST one! We heavilly use openSuse at my University for Scientific Applications. On the other hand, unfortunatelly there is a lot of packages that are not available, or "poorly available" (explain later) in the repositories concerning that. At the moment, we use from 11.2 the following packages (everywhere in the repositories): ChemTool, Xdrawchem, Avogadro, Ghemical, Labplot, g3data, bkchem, wxmaxima, maxima, octave, qtoctave, gelemental, gabedit and kalzium. Programs we use that are unavailable at the repositories (easy installation/compilation thow): molden, gopenmol, maui, webmo (formely webmol) and molekel. Programs we used to use but don't use anymore because they are too hard to compile and unavailable in the repos: SciDavis and qtiplot. Programs poorly avialable: openmpi, mpich: They are available, but they are not easily usable. I say that because me and coleagues had a hard time in the past trying to link programas with the version of those libraries that come with opensuse, because it seemed to be too scatered around. We ended up installing them from the producers in well known directories, and no problems anymore. fftw: same problem as above, solved in the very same way. gromacs: the compilation provided is ok, but... no mpi, no double + single precision executables? I would suggest two new packages: gromacs- omp and gromacs-mpich. torque: choosen the same approach since it's of critical use. Not sure if it douldn't be simply installed, thow. atiplot: already mentioned before, but in reality the package avialble for opensuse 11.2 in a repo is a joke. It has the whole qtiplot, *except*... the executables! :p Programs that I do not know if they can be provided: gamess-us, firefly, nwchem, namd, vmd, lammps, autodock, autodock-tools, amber- tools, (all available for free, but need subscription to download most of them, and none is gpl). As you can see, I'm clearly chemistry (and cluster) biased. I'm certain that other fields of research would easilly have other suggestions! And I probably missed something! Seem that there is a LOT of room for improvement here! ;) Don't get me wrong, openSuse is already MARVOLOUS, including for scientific applications... But there is a lot of things here that can be improved. ;) #3: Hubert Stassen (drgullit) (2010-02-18 14:51:18) (reply to #2) johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities. #4: Vojtech Zeisek (vojtaeus) (2010-02-18 17:06:01) I'm biologist. Practicaly no program for biology (for science, not for any playing or education; especially phylogeny, where I have the most expereince) is available for openSUSE. When user is lucky, the needed program is written in Java, but most of them must be compiled (but there are EXE files for Windows and sometimes DEB packages), what is not very comfortable, and for average user impossible. We do not have neither so basic paskages as latest version of Rkward (the best available GUI for R) for 11.2. So openSUSE is often refused, because "it does not contain needed software"... :-( #5: Jones de Andrade (johannesrs) (2010-02-18 17:39:43) (reply to #4) Hi vojtaeus! Thanks for the contribution! Would you please provide this thread with a list of more important scientific softwares/packages for use of biologists? I knew since the begining that my list would be chemistry biased, and from your post I'm suposing that opensuse can consider including a lot extra packages than only rkward (which I looked into its homepage and, by the look of the screenshots, I have to admit, for a non-biologist that seems powerfull!). So, a "wishlist", as drgullit called mine suggestions, would be very nice. ;) #8: Vojtech Zeisek (vojtaeus) (2010-02-19 18:10:29) (reply to #5) Here is short incomplete list of packages I would like to see in openSUSE. If I find more, I'll add them. :-) Some of theim might be somewhere in OBS, but it is not very likely. ClustalX (basic tool to align DNA and protein sequences): http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ MEGA4 (it is packaged as RPM using Wine and some other strange components, but it is very good tool ro make phylogenetic trees) http://www.megasoftware.net/ Artemis (viewer and annotation tool to manage sequences) http://www.sanger.ac.uk/Software/Artemis/ Biopython (library) http://biopython.org/ Bioperl (library) http://bioperl.org/ Molecular suite EMBOSS http://emboss.sourceforge.net/ You can find some onformation on http://www.open-bio.org/ KBibTeX (IMHO the best manager for BibTeX database) http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ http://home.gna.org/kbibtex/ PerlPrimer (tool to dessign primers and PCR): http://perlprimer.sourceforge.net/ MrBayes (construction of phylogenetic trees based on Bayesian algorithm) http://mrbayes.csit.fsu.edu/ BAPS (another Bayesian computing) http://web.abo.fi/fak/mnf//mate/jc/software/baps.html ARB (the best tool to work with rRNA) http://www.arb-home.de/ MSA (analyzis of microsatellite data) http://i122server.vu-wien.ac.at/MSA/MSA_download.html Splitstree and another software for work with molecular genetic data from http://www-ab.informatik.uni-tuebingen.de/software Structure (Bayesian calculations of population data) and another software from http://pritch.bsd.uchicago.edu/software.html Software (mostly to work with data from Structure) from http://rosenberglab.bioinformatics.med.umich.edu/software.html AFLPdat (to analyze AFLP data) and another software from http://www.etoology.net/index.php/software.html R packages (there should be special OBS repo for it) TCS (estimation of phylogenetic networks) http://darwin.uvige.es/software/tcs.html BEAST (Bayesian MCMC analysis) http://beast.bio.ed.ac.uk/ Mesquite (evolutionary analysis) http://mesquiteproject.org/ Search for keywords like molecular, biology etc. within Debian packages and You will find much more... ;-) There are also programs running under Wine (I do not like this way, but it more or less, with some effort, works), see for example Bioedit (very good tool to edit sequence alignment) http://www.wine-reviews.net/applications/bioedit-biological-sequence-alignme... I think it is enough for now. :-) #23: Vojtech Zeisek (vojtaeus) (2011-07-19 12:38:17) (reply to #8) Some more biological software for work with DNA: CAP3 http://pbil.univ-lyon1.fr/cap3.php http://seq.cs.iastate.edu/ cinema5 http://aig.cs.man.ac.uk/research/utopia/cinema/cinema.php finchtv http://www.geospiza.com/Products/finchtv.shtml Geneious http://www.geneious.com/ GenePalette http://www.genepalette.org/ Jalview http://www.jalview.org/ Sequence Manipulation Suite, for example http://www.bioinformatics.org/sms2/ #6: Jens Staal (staalmannen) (2010-02-18 18:10:34) Some molecular biology related packages that would be nice: UGene (http://ugene.unipro.ru/) GENtle (http://sourceforge.net/projects/gentle-m/) R and graphical front-end to R ImageJ various NCBI software (http://www.ncbi.nlm.nih.gov/guide/data-software/) especially Cn3D and if possible automatically set up the installer so that it works in the browser. (I do not know the licencing of those though) And for scientific writing: Bibus (Endnote-replacement with PubMed integration) Apart from all those things, there are tons of development projects within bioinformatics (bioruby, biopython bioperl etc) I suppose those would also be nice to have available even if I am not competent enough to use them :( #7: Jones de Andrade (johannesrs) (2010-02-18 18:40:15) (reply to #6) Good list, staalmannen! With that, I think we now here have a good proposal of the basic needs from both Chemistry and Biology users. Thanks for recording the Bibus software! I don't know how I could forget that one, and while the bibliografic reference options from openoffice it self (that are being announced for some time now) does not becomes a reality, that is the best option. It should already be included in the main prodution for a while, and also deserved even an openfate request for itself! #11: Todd R (theblackcat) (2010-03-09 20:48:55) (reply to #6) There is already an idea specifically about Bibus: https://features.opensuse.org/308261 #12: Denny Beyer (lumnis) (2010-08-18 12:40:46) (reply to #6) Bibus is not bad - there are others around. Have you tried zotero www. zotero.org ? #9: Ricardo Gabriel Berlasso (rgbsuse) (2010-02-21 17:28:00) Scilab is on Education now (not the last version, though), but there are a lot of packages still missing. #10: Todd R (theblackcat) (2010-03-09 20:48:31) Sage, a general python-based computer algebra system, should also be provided ( http://www.sagemath.org/). (http://www.sagemath.org/%29.%C2% A0) This is especially true since the new KDE 4 advanced mathematics software front-end Cantor, which ships as part of the KDE edu project, supports it. See https://features.opensuse.org/308459 (308459) for this specifically. Another very useful one is Neuron, a very popular neuron-modelling program. I personally know many people using this, it is probably the single most common tool for modelling neurons: http://www.neuron.yale.edu/neuron/ (http://www.neuron.yale.edu/neuron/) Another is AUTO, an very popular tool for ninlinear dynamics and differential equations. I have seen this used in several classes of mine, it is an important tool with a very long history: http://sourceforge.net/projects/auto-07p/files/auto07p/ (http://sourceforge.net/projects/auto-07p/files/auto07p/) #13: Bruno Friedmann (bruno_friedmann) (2010-12-17 22:33:23) Perharps all of you should check this two repositories http://download.opensuse.org/repositories/science/ http://download.opensuse.org/repositories/science:/ It seems a lot's of what is asked is already there. We will need a volunteer to build a Science page in wiki to help you to find what is needed. #14: Jones de Andrade (johannesrs) (2011-01-10 22:19:27) (reply to #13) Well, given the repositories suggested above, I decided to make a compilation of all asked software on this openfate, then verify which ones are already available and which ones aren't. The list is below. We have a total of 56 software packages/libraries/programs/suites requested. Of those, including the suggested extra repositories (which should be included in the opensuse official listings, together with "Education" ones), I could find 21, but there are still 31 missing (and extra 4 which have some "missing features or so" from my side). I guess this means that, even having I made a few mistakes here and there, this is still a long list of requests, which I suppose must be now moved as requests for openSUSE 11.4. ChemTool ok Xdrawchem ok Avogadro ok Ghemical NO Labplot ok g3data ok bkchem ok wxmaxima ok maxima ok octave ok qtoctave ok gelemental ok gabedit NO kalzium ok molden NO gopenmol NO maui NO webmo (formely webmol) NO molekel NO SciDavis ok qtiplot NO openmpi mpich fftw gromacs torque NO gamess-us NO firefly NO nwchem NO namd NO vmd NO lammps NO autodock NO autodock-tools NO amber-tools NO ClustalX ok MEGA4 NO Artemis NO Biopython ok Bioperl NO EMBOSS ok KBibTeX ok PerlPrimer NO MrBayes NO BAPS NO ARB NO MSA NO Splitstree NO Structure NO AFLPdat NO R ok TCS NO BEAST NO Mesquite NO Bioedit NO UGene NO GENtle NO ImageJ OK????? Cn3D NO Bibus NO bioruby NO scilab ok sage NO Cantor ok neuron NO auto NO #15: Denny Beyer (lumnis) (2011-01-16 14:20:55) (reply to #14) ImageJ added I created a new ImageJ package, where the program is build from source, adds desktop entry etc. which was missing in the existing projects. Please test the package and report back any findings, as I'm not a ImageJ user. #18: Andre Massing (susetroll) (2011-07-18 20:23:44) (reply to #14) I would like to add some packages which are interesting for people from the FEM (FVM/FDM) communities dealing with numerically solving partial differential equations. Of course an updated and fully functional openmpi is a must :) High performance linear algebra solver: PETSc NO SLEPc NO Armadillo NO Trilinos NO suitesparse (?) MTL4 (NO) UBLAS (NO) Mesh/Graph partitioner ParMETIS (NO) METIS (in science repo) SCOTCH (NO) Visualization (and more): mayavi (NO) or better whole enthought tool suite. paraview (in science) Mesh generation: Netgen (in sciene) Tetgen (NO) Triangle (NO) gmsh (in science) PDE solving environments FEniCS with subpackages (NO) UFL, UFC, FFC, (SYFI) FIAT, INSTANT, VIPER, DOLFIN, since I am close to the developer community I would like to volunteer for packaging at least these one. FreeFem++ (NO) lifeV (NO) DUNE (NO) dealii Of course, this is a very (FEM) biased choice of packages, so please add something which is missing here. #19: Andre Massing (susetroll) (2011-07-18 20:34:19) (reply to #18) Of course I forgot a few :) Computational geometry related: CGAL gts bullet physics and collision detection library (might be very interesting for game programmers) #16: zmi zmi (zmi007) (2011-07-02 01:43:42) Another side of physics packages I would like to see in openSUSE all etsf software from http://www.etsf.eu/resources/software/etsf_software_repository Here are: ABINIT DP EXC Tosca Octopus fhi98PP PSPConvert Yambo V_Sim Exciting ELK APE gpaw https://wiki.fysik.dtu.dk/gpaw/ Quantum ESPRESSO http://www.quantum-espresso.org ROOT http://root.cern.ch fgsl http://www.lrz.de/services/software/mathematik/gsl/fortran/ object-based Fortran interface to the GNU scientific library molden, gmolden http://www.cmbi.ru.nl/molden/ molekel http://molekel.cscs.ch namd http://www.ks.uiuc.edu/Research/namd/ nlopt library http://ab-initio.mit.edu/wiki/index.php/NLopt orca http://www.thch.uni-bonn.de/tc/orca/ paraview http://www.paraview.org/ rasmol http://rasmol.org/ siesta http://www.icmab.es/siesta/ veusz http://home.gna.org/veusz/ MacMolPlt http://www.scl.ameslab.gov/MacMolPlt xmakemol http://www.nongnu.org/xmakemol/ vmd http://www.ks.uiuc.edu/Research/vmd/ #17: zmi zmi (zmi007) (2011-07-02 18:12:29) visit https://wci.llnl.gov/codes/visit/home.html #20: Alberto Passalacqua (greengeeko) (2011-07-18 22:56:39) The initiative is really very welcome! :-) openSUSE would benefit significantly from this. However I would add a couple of considerations: - Packages must be built by people who *uses* them. Scientific packages are hard to create, and frequently pre-built packages do not offer the same features of the upstream hand-built package because the packager removed options to simplify the build process. As a consequence, what is really needed here are packagers with scientific experience, and given the intricacy of creating RPM's and of using OBS, I don't know so many :-) - Often it is not worth providing RPM's for some scientific project. This is, IMHO, the case for very large projects with a lot of (often obsolete) dependencies, which are provided in binary form from the developers. It is much simpler for the user to download the full binary package and use it. At the same time packaging those softwares (I think to Salome for example), is extremely time consuming for the packager, and the structure of OBS would lead to too many sub-packages, making it very hard for a final user to have something easy to install/use. Best, #21: Cristea Bogdan (bogdanc23) (2011-07-18 23:28:02) My scientific application proposals: IT++ (signal processing) and aigaion2 (bibliography management). I would like also to emphasize the fact that python, as replacement for MATLAB, does not receive too much attention from the academic community and some advertisement would be needed. As for the proposition that packages build should be managed by scientists I fully agree and I am willing to contribute. #22: Andreas Jaeger (a_jaeger) (2011-07-19 09:58:30) Just ask to get the packages into openSUSE, it's easy to do - package the software and declare that you will take care of bugs. #24: Yasha Gindikin (slonoinquisitor) (2011-07-30 22:45:48) I would also add Gwyddion to the wishlist (see gwyddion.net). This is a widely used program for probing microscopy. #25: Pierre Bonamy (flyos) (2016-04-12 14:26:50) I know this is a quite old ticket, but I'd like to add the following suggestion : the "Debian Med" team is doing a quite excellent work at gathering and packaging scientific software for Debian and co. Wouldn't it be possible to get source and build specs from them to transfer to the "science" repo and provide package for OpenSuse (and more, since OBS can be multi-distro)? #26: Tristan Miller (psych0naut) (2016-08-18 15:03:38) To add to this, many of the existing packages in the Science repository are for very old versions. Working research scientists generally depend on cutting-edge tools (at minimum, the latest stable release), so providing tools that are years out of date isn't helping very many people. -- openSUSE Feature: https://features.opensuse.org/309007
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