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