Free Scientific Software for Developing World?

FlashBoltzmann asks: "I'm a physics student in the US working with a group of physicists, mostly from Africa, who are interested in helping their colleagues on the continent obtain free software for scientific and educational use. Often, many science departments in Africa have little or almost nonexistent funding to purchase new software packages, especially for scientific research or education. Some know of the free software available but say it takes up large amounts of time over often slow internet connections to find and obtain it. I am asking for any recommendations on freeware or open source software, for any operating system, that anyone knows about. We are looking at the Debian version of Linux for a lot of the great software that comes with it but resources for MS Windows would be helpful as well."

"Free educational software of any level is appreciated though we prefer college and graduate level software. Also, field specific software is great, e.g. software for condensed matter physics. Eventually we'll probably combine the software on CDs to be distributed to these scientists. Any help is appreciated especially with programs that perform simulations, mathematical and statistical analysis and plotting, compilers, lab software, etc. The users of the software will most likely be physicists or mathematicians."

Comments

The one to begin with...

[mirko]

...is TeX.

This typesetting program was originally aimed at the scientist. I don't know of any other software that produces nicer documents.

An old math favorite

[imrdkl]

Was Are you ready for Calc III. This, and alot more math software can be had from the UofA Math Software Page.

Open Channel Software

[Xpilot]

Well there's always this.

I recall /. running a story about NASA donating some stuff to this site...

Try NA/European physicists & mathematicians

[hearingaid]

I worked for a little while in a government research library, and about half the people in the building were both scientists and programmers. They developed a lot of their own tools, and most of them were coding for some *nix, many on Linux.

They didn't care about other people getting their code. I would expect universities to be the same way.

As for bandwidth, that's much less of a problem now with CD burners. I'm assuming your Third World people have CD-ROMs, but given that, if you can talk to some First World scientists & get them to burn and ship, it might well be cheaper.

SAL: Scientific Applications on Linux

[gylle]

SAL is a good resource for finding science apps that run on Linux. Worldwide mirrors, many apps are free.

Netlib and more

[apsmith]

The standard resource for free scientific software (unfortunately mostly written in Fortran) is Jack Dongarra's netlib: http://www.netlib.org/

It's best in linear algebra (matrix problems etc) but there's other good stuff in there - FFT routines, statistical stuff, some deep mathematics, and more... Also, not free, but good, is the standby Numerical Recipes book, which includes source code for a large variety of uses, particularly solution of nonlinear optimization problems.

Other stuff is available free from the supercomputer centers - at least they used to give stuff away free, though NCSA at least seems to have tried to make money off their things lately...

Re:Netlib and more

[Wile E. Heresiarch]

I do quite a bit of number crunching. Here are
some of the resources I use:

Netlib (www.netlib.org) -- Yes, it's mostly Fortran, but that's a good thing! Just use f2c (easy to find) and translate to C if that's what you want. Don't underestimate the power of decades-old programs -- old == widely used and well-tested.

StatLib (lib.stat.cmu.edu) -- Collection of statistical software, in various languages, including C, Fortran, and S.

SAL, Scientific Applications on Linux (sal.kachinatech.com) -- a very large collection of links.

Freshmeat (www.freshmeat.net) -- Not scientifically oriented, but there is much scientific stuff there, along with all kinds of miscellany.

Octave (www.octave.org) -- A package for matrix manipulations, similar to Matlab, but free. Useful for all kinds of problems.

R (www.r-project.org) -- An implementation of the S language for statistics, but also useful for general problems, similar to Octave. S+ is a commercial implementation of S.

Well, that ought to be enough to get started. To echo something other posters have mentioned -- don't even bother with Windows software. If your budget is tight, save your money for hardware, don't waste it on the MS tax.

Re:Netlib and more

[altstadt]

Why is it that whenever this topic comes up, everybody always talks about Octave and gnuplot as if these are the only things available?

If you want a self contained program that runs on multiple platforms, take a look at Euler. This is about as close as it gets to being a MatLab clone.

astro software & some stats too.

[fiiz]

It is actually not that easy to find free physics software.

For professional astronomy software, I recommend http://star-www.rl.ac.uk/

Some nice but steep stats software in the R project http://www.r-project.org/

And you can use Octave & gnuplot for basic maths. (admittedly not as good as mathematica,matlab or some other maths package.)

This URL http://www.seul.org/sci/seul-sci10.html has a review of linux & GPL packages that are useful to scientists.

It is also probably worth asking some of the software vendors if they would like to donate something, as really, you never know! (if the cause is good...)

Good luck!

fz

Physics Analysis Workstation.

[matthayes]

Developed at CERN
Great for graphical representation, and statistics. Released under GPL.

I remember using it about three years ago under Red Hat for reconstruting cosmic ray showers. Can't see any possible problems with Debian...
It was great for what I was doing.

Matt.

scientific apps for linux

[Anonymous Coward]

grüt5! here are the linx you need:

scientific applications for linux:
http://sal.kachinatech.com/sal1.shtml
for ee:
http://www.drzyzgula.org/bob/electronics/linux.s ht ml
scilab (math&calc. like matlab):
http://www-rocq.inria.fr/scilab/
texmacs (kickass easy wysiwig scientific document editor):
http://www.texmacs.org
(and also has a lot of links to other scientific software)
scigraphica:
http://scigraphica.sourceforge.net/
linux apps /science:
http://www.linuxapps.com/?page=category&category =s citech

Theorem proving software

[reachinmark]

For the more logic inclined mathematicians, as well as anyone interested in structured proofs, theorem proving, etc, the HOL theorem prover is a very powerful engine. On the down side - it can be tricky to learn, but there is a large quantit of documentation and a big user base to help get people started.

See: http://archive.comlab.ox.ac.uk/formal-methods/hol. html amongst other pages.

Stuff that I use

[Mochatsubo]

Python with Numeric Python and Scipy make for a fine numerical computing environment (www.python.org, www.pfdubois.com/numpy/, www.scipy.org).

The GNU scientific library (GSL) can be found here: http://sources.redhat.com/gsl/

Intel Image Processing Library (C): http://developer.intel.com/software/products/perfl ib/ipl/

Intel Signal Processing Library (C): http://developer.intel.com/software/products/perfl ib/spl/

VTK is an *extensive* visualization toolkit (C++): http://public.kitware.com/VTK/

useful research programs ( and libraries )

[hagbard5235]

Here are the things that I am aware of that have been found quite useful:

For graphing:

• Grace ( formerly xmgr )

For Numerical Analysis:

• GSL ( Gnu Scientific Library ):

language bindings for perl,python, and C++ for GSL are also available.

Check out the Scientific Computing FAQ: which I've been having trouble reaching so you might want to try the Google cache of it.

GAP -- Computational Group Theory and more

[stevelinton]

GAP is a powerful software system for computational abstract algebra and discrete mathematics, especially group theory. See http://www.gap-system.org for details (including mirrors) and download. It's distributed under a "copyleft" not too different from the GPL.

If you want to use GAP for research or teaching and can't download it (we've had people whose bandwidth is too low, and people whose countries do not allow arbitrary internet downloads for political/religious reasons) let us know (mail one of the addresses on the Web site) and we can usually manage to send a CD.

Steve Linton

Seriously... check out Freshmeat.net

[eno2001]

They have a scientific/engineering Visualization section that has a lot of cool stuff. Here are some examples:

K-3D modeling, rendering and animation software (Win32 as well):
http://midas.psi.ch/

Isotopic Pattern Calculator (Link may be wrapped):
http://www.uni-duesseldorf.de/MathNat/pc1-AK_Wei nk auf/ipc/ipc_d.html

MayaVi (Visualization Software):
http://mayavi.sourceforge.net/

MIDAS (Data acq software for particle physics):
http://midas.psi.ch/

GraphThing (Graph Theory tool):
http://members.optushome.com.au/davidsymonds/gt/

GNU TeXmacs (Technical writing tool, great for technical docs with formuli):
http://www.texmacs.org/

There are 130 projects on Freshmeat, which is probably just the "tip of the iceberg".

I am not a troll. ;P

Re:Physics Analysis Workstation - ROOT

[Dave Bailey]

Also try the ROOT package. It's also developed at CERN (by the PAW people) but is in C++ (with a built in C++ interpreter) and has much more to it than PAW.

It's aimed at the Particle Physics community but is currently in use in a wide range of fields from Astronomy to banking!

Oh yes, runs on Linux and Windows...

TISEAN

[Skorpion]

A very good package for chaos-theory-oriented numerical data analysis is TISEAN.

It does excellent job on its part. There is also some documentation on the site, including one of the creators' Ph. D. thesis that explains some of the theory behind the software. On Linux it requires gcc and GNU Fortran complier to compile (compilation is pretty straightforward).

I also found GNU awk extremely useful at numerical data analysis. You also would want to include Python and NumPy - python extension for numerical computations.

HTH

Alex

Things I use at work...

[doop]

I'm doing a PhD on simulations of soft condensed matter, and mainly use either free software, or stuff we wrote in-house. Off the top of my head:

• VTKis a very good package for scientific visualization.
• Maxima is a Free computer algebra system, a bit like Mathematica. It can solve equations, do calculus, plot things, produce TeX output of what you've done, and lots more. Incredibly useful for long tedious bits of algebra.
• gnuplot is a versatile graphing package (2D and 3D, but maxima or VTK are IMO better for 3d stuff). As well as graphing, it can try to fit arbitrary functions to your experimental data.
• LaTeX -- it's very hard indeed to typeset equations better than LaTeX can.

If you're interested in condensed matter physics (or a few other areas), then you should have a look at the Los Alamos E-print server, which contains preprints of a lot of scientific papers.

Geomview for visualization

[spork_testicle]

1. Geomview is a very nice freeware surface renderer. I have been using it for years, it supports an external command language that can be driven via a named pipe and thus do animations from within other code. File format is basically ASCII (with some binary extensions) and can get big, but this works very nice if you have opengl extensions and a decent graphics card.

2. For volume rendering i recommend VTK the visualization toolkit. A bit high on overhead required to use it, but quite powerful when you learn. In addition to volume rendering, supports isosurfaces (via marching cubes), segmentation algorithms, and many other image classifications. Delauney triangulation, and many of the elements needed for production visualization pipelines.

3. BLAS and LAPACK are absolutely essential. Basic Linear Algebra and Linear Algebra subroutines for everything from optimized matrix-matrix operations to Singular Value Decomposition and cholesky factorization of band diagonal symmetric yadayada. I use this stuff daily and the LAPACK subroutines would be one of the first things I would compile in a new environment. The LAPACK subs call BLAS subs. Note that I have these in fortran but called from C/C++. I dont know if they have been ported to C yet.

4. Stay away from those fancy "data explorer" deals. Complete waste of time. Chances are with a little more work you can do a better job, in a smaller package, with a *ton* less overhead by writing a bit of code. Learn a command line parser (you could prolly use getopt) and write your own library. I recommend brewing up 1D 2D and 3D storage classes that are reusable via C++ classes. For 2D/3D we use files with an ascii header and binary data, and have written utilities to do math on or between them. We also spent the time to write our own plotting software direct to postscript, so I have not had to struggle with the crap that is the freely available plotting software. GNU plot is simply pathetic. And if you pay for something like NCAR it is at least as bad but costs a hell of a lot more.

5. As far as those fancy environments go, I have used AVS, KHOROS, IBM explorer, and the SGI IRIS explorer. One of these that was free and probably the easiest to use is now not free (khoros). The IBM data explorer is also free now, but it is a total piece of crapola in my not so humble opinion.

6. Finally. Get the numerical algorithms book for your fav language. You wont regret it.

a very good site ...

[fymidos]

is Scientific Applications for Linux (SAL), the one i use is in greece http://sal.duth.gr, but there are mirrors around the world.
I think the official site is at http://sal.kachinatech.com/ .

many applications there , not all free though ..

octave and matlab (student version)

[adapt]

while you can get Octave for free with most Linux dists. and you can contact the Octave people for tips about installation. the US student version of Matlab is cheap and does not have matrix size limitations AND there is a Linux version in the package. also, if you check Matlab website [mathworks.com , mathtools.net] , they have a huge ftp site of free goodies, i.e. Matlab toolboxes, that probably can be used with Octave too.

since i installed my student version of Matlab at home, i have used less my Octave. Matlab also can be bought at academic prices, which are still too expensive for cash-strapped academia.

as for linux vs. windows, if you have to leave you computer on for 10 days for a simulation, then linux stability is a nice bonus...

lotsa *nix sci freeware in french

[rainTown]

I found these links for linux scientific freeware on this page http://www.freepatents.org/liberty/logiciels.html

Its in French... but then again the majority of my African friends speak it.... there is a lot in there .....sorry for the lack of form....and i didn't check all the links.... hope its useful...

Sciences et ingénierie
Scientific Applications on Linux http://SAL.KachinaTech.COM/
Index très complet d'applications scientifiques et professionnelles (gratuites, shareware ou commerciales) qui tournent sous Linux.

Statistiques
fiasco http://www.fsf.org/software/fiasco/index.html
xldlas http://a42.com/~thor/xldlas/
MacAnova http://www.stat.umn.edu/~gary/macanova/macanova.ho me.html
R http://www.ci.tuwien.ac.at/R/contents.html
Calcul formel
MuPAD http://www.mupad.de
Maple http://www.maplesoft.com/
Mathematica http://www.wolfram.com/
Macsyma http://www.macsyma.com/
Magma http://www.maths.usyd.edu.au :8000/u/magma/
Macaulay2 http://www.math.uiuc.edu/Macaulay2/
Singular http://www.mathematik.uni-kl.de/~zca/Singular/
Analyse numérique
Scilab http://www-rocq.inria.fr/scilab/
Matlab http://www.mathworks.com/products/matlab/mlover.sh tml
Octave http://www.che.wisc.edu/octave/

Ecology

[Anonymous Coward]

there is a free software package for teaching ecology available from
http://www.cbs.umn.edu/populus/

it teaches some of the basic differential equations, some cellular automata, an "interaction engine" wherein you can enter your own diff eq's and view their outputs (only 2 or 3 can be viewed simultaneously), and a bunch of other things...

it is currently being developed in Java, and is available for all operating systems (that have Java)

check it out! it's "fun for the whole family!" you will see models that you have done in your school years (simple population growth) and a lot you probably haven't.

mupad

[platypus]

Take al ook at mupad

It's some sort of mathematica lookalike, superior in some cases and they have free versions.

It's been a while since I used it, but it was great.

IRAF for Astronomy/Image Processing

[andrew cooke]

http://iraf.noao.edu/iraf-homepage.html is the standard data processing package in American/British astronomy (and possibly Europe too these days). I just noticed it is packaged inside Debian...

Although aimed at astronomy, it would be useful general image processing (particularly good at automating procedures over many images).

Numerical Python

[Devil's Avocado]

One of the issues I've often run up against when doing scientific programming is the desire for a *real* programming language to support the number crunching. This often caused huge frustration for me when I used Matlab and IDL. One of the nicest solutions I've found for numerical programming is the Numerical Python package. (http://www.pfdubois.com/numpy/ ) You get the numerical expressiveness of Matlab or IDL with the power of Python as a programming language for the half of your program that *doesn't* deal with crunching numbers. (In my experience it's actually usually more than half, even in heavily numeric code!)

Here are a few more links:
The Python website: http://www.python.org
The Scientific Python Project: http://www.scipy.org

Cheers,
-DA

A few favourites we use

[Professor J Frink]

In the past few years I converted our lab over to Linux and here are some of the tools we use for analysis:

• GCC for C/C++/FORTRAN coding. It's free, it's not the fastest in the world but it's competent.
• Octave is a great, free replacement for Matlab. For general data manipulation it seems fine, where it really lacks relative to Matlab is in the GUI.
• Gnuplot is a great all-round, all-purpose, scriptable plotting tool that can also do fitting. For general everyday tasks gnuplot gets used a lot in our lab.
• SciGraphica is a great 2d/3d/vector/polar/ plotting and analysis package. It is a little like an Origin clone so is pretty easy to pick up, and can be extended with Python plugins. I am one of the developers ;0) (although far too busy atm to contribute, anyone want to help?). More suitable for publication-quality plots and still heavily in development. A new release is imminent. Plug ;0).
• teTeX is the main (La)TeX distribution for Linux and you'll most probably have it in Debian anyway but for writing reports, articles, books, theses, even letters you shouldn't need to use anything else. Really.
• OpenOffice if you have to deal with mad, crazy, annoying .doc using people.

There's plenty more where they came from. Most distrbutions come with a lot of these things anyway. These are mainly analysis or document tools, there's plenty of other things for both these areas and any other which plenty of other posters have shown. I've written a little guide for my local group. Some of it's out of date (and some of it's wrong but I have better things to fix) but it does have a list of common tools we use. And, of course, SAL is a pretty comprehensive database of unix tools. HTH.