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Add more scientific packages

Feature state

Package Wishlist
Marketplace

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...

User benefit:

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.

Usecase

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.

Discussion


icons/user_comment.png L. M. wrote: (8 years ago)

Octave is on Contrib that is my usecase but still i prefer to use Matlab instead. 

icons/user_comment.png J. d. wrote: (8 years ago)

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. ;)

icons/user_comment.png H. S. wrote: (8 years ago)

johannesrs presented a very nice wishlist ... That would be an almost complete software repositiry for the computational chemistry/biology/physics communities.

icons/user_comment.png V. Z. wrote: (8 years ago)

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"... :-(

icons/user_comment.png J. d. wrote: (8 years ago)

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. ;)

icons/user_comment.png V. Z. wrote: (8 years ago)

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. :-)

icons/user_comment.png V. Z. wrote: (6 years ago)

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/

icons/user_comment.png J. S. wrote: (8 years ago)

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 :(

icons/user_comment.png J. d. wrote: (8 years ago)

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!

icons/user_comment.png T. R. wrote: (8 years ago)

There is already an idea specifically about Bibus: https://features.opensuse.org/308261

icons/user_comment.png D. B. wrote: (7 years ago)

Bibus is not bad - there are others around. Have you tried zotero www.zotero.org ?

icons/user_comment.png R. G. wrote: (8 years ago)

Scilab is on Education now (not the last version, though), but there are a lot of packages still missing.

icons/user_comment.png T. R. wrote: (8 years ago)

Sage, a general python-based computer algebra system, should also be provided (
http://www.sagemath.org/).  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 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/

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/

icons/user_comment.png B. F. wrote: (7 years ago)

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.

icons/user_comment.png J. d. wrote: (7 years ago)

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

icons/user_comment.png D. B. wrote: (7 years ago)

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.

icons/user_comment.png A. M. wrote: (6 years ago)

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.

icons/user_comment.png A. M. wrote: (6 years ago)

Of course I forgot a few :)

Computational geometry related:
CGAL
gts
bullet physics and collision detection library
(might be very interesting for game programmers)

icons/user_comment.png z. z. wrote: (6 years ago)

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/

icons/user_comment.png z. z. wrote: (6 years ago)
icons/user_comment.png A. P. wrote: (6 years ago)

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,

icons/user_comment.png C. B. wrote: (6 years ago)

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.

icons/user_comment.png A. J. wrote: (6 years ago)

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.

icons/user_comment.png Y. G. wrote: (6 years ago)

I would also add Gwyddion to the wishlist (see gwyddion.net). This is a widely used program for probing microscopy.

icons/user_comment.png P. B. wrote: (20 months ago)

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)?

icons/user_comment.png T. M. wrote: (15 months ago)

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.

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