Mailinglist Archive: opensuse-features (367 mails)

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[openFATE 309007] Add more scientific packages
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-alignment-editor-on-linux-with-wine.html
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




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openSUSE Feature:
https://features.opensuse.org/309007

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