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Free Scientific Software for Developing World? 212

Posted by Cliff
from the helping-a-good-cause dept.
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."

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Free Scientific Software for Developing World?

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  • by mirko (198274) on Thursday November 22, 2001 @11:21AM (#2600413) Journal
    ...is TeX [tug.org].

    This typesetting program was originally aimed at the scientist. I don't know of any other software that produces nicer documents.
    • gnuplot! with Latex/gnuplot combo everything you can imagine is possible, and even more... these tools have helped me sooo much, I never touch that excel or any other spreadsheet program when i have some serious plotting to do.
      • by kilgore_47 (262118)
        I think we should follow star trek's prime directive; when we encounter less advanced cultures, we should refuse to give them our technology and insist that they discover it on their own.
    • TeX doth indeed rock. I started using it for (of all things) doing a family cookbook. Which I found it did many times better than a normal word processor.

      Now I've started using it for reports and documents at work (anything to save me from MS word). I started using Lyx at first, but I found I actually liked doing LaTeX by hand better.
  • An old math favorite (Score:5, Informative)

    by imrdkl (302224) on Thursday November 22, 2001 @11:22AM (#2600418) Homepage Journal
    Was Are you ready for Calc III. This, and alot more math software can be had from the UofA Math Software Page [arizona.edu].
  • by Xpilot (117961) on Thursday November 22, 2001 @11:24AM (#2600421) Homepage
    Well there's always this [openchannelsoftware.com].

    I recall /. running a story about NASA donating some stuff to this site...
  • I know this isn't entirely the point of your question (and more than a little bit of this is motivated by my anger towards MS's recent settlement), but I just thought I'd put forward the idea that you shouldn't bother with Windows at all.

    If you're hurting for cash for software, the outlook is probably not all that great for hardware too, right? The cutting edge of Linux and the various BSDs all run well on hardware that the latest Windows versions cough and sputter on.

    Also, providing a Windows learning environment is only going to encourage use of Windows down the line, which will require further investments, software AND hardware upgrades etc.

    If you're working with a blank slate, and these people need training anyway, might as well put it towards something that won't come back and make serious demands on your checkbook. Save the money for additional learning resources, a CD burner to replicate software for yourself (this is legal with the Linux and BSD OSes), etc. Don't go down the proprietary road, or else soon enough you'll be dealing with the same MS-driven crap the entire Western world is trying to handle right now.
    • by Anonymous Coward
      I know this isn't entirely the point of your question (and more than a little bit of this is motivated by my anger towards VA's recent settlement), but I just thought I'd put forward the idea that you shouldn't bother with Linux at all.

      If you're hurting for cash for software, the outlook is probably not all that great for hardware too, right? The cutting edge of Windows and the various DOSs all run well on hardware that the latest Linux versions cough and sputter on.

      Also, providing a Linux learning environment is only going to encourage use of Linux down the line, which will require further investments, software AND hardware upgrades etc.

      If you're working with a blank slate, and these people need training anyway, might as well put it towards something that won't come back and make serious demands on your checkbook. Save the money for additional learning resources, a CD burner to replicate software for yourself (this is legal with the Windows and DOS OSes), etc. Don't go down the proprietary road, or else soon enough you'll be dealing with the same VA-driven crap the entire Western world is trying to handle right now.
  • by hearingaid (216439) <redvision@geocities.com> on Thursday November 22, 2001 @11:27AM (#2600431) Homepage

    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.

  • VI + EMACS (Score:1, Funny)

    by Anonymous Coward
    will be enough to put them off computers for life.
  • If you have no resources for purchasing scientific software, where did you get the money for purchasing MS Windows licenses?

    Moderators: THIS IS NOT A TROLL. The question is simple: if you're already w4r3zing Windows, what refrains you from w4r3zing your scientific software also, and in the process saving us from these terrible Ask Slashdots of late?
    • Microsoft products, Windows included, is licensed for signifigantly cheaper prices abroad.

      Microsoft also donates alot of Windows licenses and other software to scientific and other institutions overseas.
      • windows trap (Score:3, Interesting)

        by adapt (105738)


        yes, MS sells campus licenses at EXTREME discounts (like $20 for Office and less for the OSs), but the hardware requirements are heavier.


        most people in academia are not swimming in cash, so this means old hardware, and an array of diverse machines connected to a server. linux is the ideal software partner for a small research group, in my opinion.


        the other factor, as somebody else pointed above, is that GNU or public tools are used by almost everybody. most papers are swapped in .ps format and written in TeX on (insert favourite editor here :). in windows you can do the same, but integrated tools like Scientific Workplace cost money, and they are not really needed after you learn some shell and vi tricks.


        still, the crucial factor that made me wipe out windows for linux was stability. when you do not have a double Xeon crunching numbers, you appreciate the fact that linux will not crash during the 3 days it must be ON. ;-)

    • [offtopic]What's a non-terrible ask slashdot, or are you just upset that half of them don't involve games anymore? Given current events, I find it hard to believe that trying to get some of the more poor places in the world up 'n running in so far as marketable skills and data goes constitutes a poor Ask Slashdot.[/offtopic]
  • by gylle (531234) on Thursday November 22, 2001 @11:30AM (#2600442)
    SAL [kachinatech.com] is a good resource for finding science apps that run on Linux. Worldwide mirrors, many apps are free.
  • by Anonymous Coward on Thursday November 22, 2001 @11:33AM (#2600457)
    This is most likely the most complete site out there when it comes to science on linux. http://sal.kachinatech.com/
  • linux.box.sk [linux.box.sk]

    They may not all be the best but as a physics student some can be kinda cool to play around with.
  • Netlib and more (Score:5, Informative)

    by apsmith (17989) on Thursday November 22, 2001 @11:34AM (#2600459) Homepage
    The standard resource for free scientific software (unfortunately mostly written in Fortran) is Jack Dongarra's netlib: http://www.netlib.org/ [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 [ncsa.edu] at least seems to have tried to make money off their things lately...
    • Re:Netlib and more (Score:5, Informative)

      by Wile E. Heresiarch (12248) on Thursday November 22, 2001 @12:00PM (#2600566)
      I do quite a bit of number crunching. Here are
      some of the resources I use:

      Netlib (www.netlib.org [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 [cmu.edu]) -- Collection of statistical software, in various languages, including C, Fortran, and S.

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

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

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

      R (www.r-project.org [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 (Score:2, Informative)

        by altstadt (125250)

        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 [ku-eichstaett.de]. This is about as close as it gets to being a MatLab clone.

  • by fiiz (263633) on Thursday November 22, 2001 @11:34AM (#2600462) Homepage
    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
    • After finding the differences between octave and matlab too much as pointed out I tried finding the unix/linux version. The student version is only sold in the US and the full version was going to cost more than a car. So I got desperate and with minimal tweaking found matlab Student Edition 5.3 ran quite happily, though slowly, under linux with WINE. Just another option for those on a budget :)
  • by matthayes (459103) <matthew.hayes@gmai3.14l.com minus pi> on Thursday November 22, 2001 @11:36AM (#2600471) Homepage
    Developed at CERN [wwwinfo.cern.ch]
    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.
    • Also try the ROOT [root.cern.ch] 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...
      • Also try the ROOT [root.cern.ch] 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.

        I wasn't aware of this but I'm going to check it out.
        Also, it's possible to call CERN libraries from C/C++ but amusingly, you need to #include <cfortran.h>. Who says the scientific community is underfunded?
        Joking aside, I've used far too much Fortran doing scientific stuff.

        Matt.
    • I've used PAW quite a bit for my work. It's quite effective at stuff, but the documentation is abyssmal. I found it really really painful to learn, and as a result I didn't get very far into it.

      Something almost as hard to learn but somewhat easier to actually use is Physica [triumf.ca], developed at TRIUMF [triumf.ca]. It's the main program I used to do my M.Sc. analysis work. :)

      For data aquisition (and generally running an experiment), I strongly suggest looking into MIDAS [midas.psi.ch]. It's really powerful, and has a web interface (with optional password protection), electronic log book, etc, which is really helpful for experimenters to keep tabs on things from home. Especially when "home" is in another city (or even country).

  • by 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
  • I am a student of Physics at the University of Tokyo and my superiors have instituted a plan that accomplishes many of these aims.

    We have correspondence programs with several universities in Africa in which we will provide to them our outmoded hardware. It is unfortunate that often, we are not able to replace our hardware as often as we would prefer, but when we do, we attempt to find a physics department without adequate hardware.

    Also in the course of completing their theses, graduate students must write various software tools to assist them. The copyright to these tools belongs to the University if I am not mistaken. Although my University does not distribute these freely as some would prefer, they are sometimes provided to the other universities which have the hardware necessary to run them (with the consent of the programmer student of course).

    Yes, there is more that may be done, but I believe that we are working to genuinely assist other physics programs which are less fortunate that we are in some respects. Does anyone else know of similar programs?

    R. Suzuka
  • 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 [ox.ac.uk] amongst other pages.

  • Stuff that I use (Score:2, Informative)

    by Mochatsubo (201289)
    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/
  • Now here's something where the average joe without coding skills can help promote free software. How about offering to burn distros & RPMs/DEBs and mail them to africa or other places where the infrastructure isn't so great? The costs shouldn't be too horrible ... maybe we can set up a network of volunteers for something like that? I myself don't have a CD-burner at the moment (relocated from US->EU recently), but I can punch out a simple database-driven website quickly ... if anyone's interested, mail arminh(AT)usa.net ... maybe we can get something going?
  • If you're in need of a package to draw electronic circuits and do general schematic capture stuff, check out Pulsonix [pulsonix.com]. These guys have made a fully-featured electronics schematic capture program freely available to anyone who wants to download it. The only downsides are (a) it's 19MB, and (b) it's Windows-only. Highly recommended.

    The package also contains a PCB design package and other good stuff; however, you have to pay to unlock these (not excessive amounts by the standards of most design packages, but £1-2K is a lot for someone in a developing country or your typical hobbyist). If you're on a real budget, just use the schematic capture part to produce netlists, and then use an old DOS/Win3.11 PCB layout program such as BoardMaker for the PCB design.

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

    For graphing:

    For Numerical Analysis:

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

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

  • by stevelinton (4044) <sal@dcs.st-and.ac.uk> on Thursday November 22, 2001 @11:46AM (#2600509) Homepage
    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
  • by eno2001 (527078) on Thursday November 22, 2001 @11:48AM (#2600517) Homepage Journal
    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
  • by s20451 (410424)

    Octave [octave.org] is a matrix manipulation package, released under GPL - basically a clone of MATLAB. It has scripting capabilities, which allow development of simulation software.

  • TISEAN (Score:2, Informative)

    by Skorpion (88485)
    A very good package for chaos-theory-oriented numerical data analysis is TISEAN [mpipks-dresden.mpg.de].

    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 [gnu.org] extremely useful at numerical data analysis. You also would want to include Python [python.org] and NumPy [pfdubois.com] - python extension for numerical computations.

    HTH

    Alex

  • I managed to get my Physics PhD using almost entirely free tools.
    The thesis was written in LaTeX, using emacs, and made printer friendly with dvips.
    The data plots were done in gnuplot.
    The simulations were written in c with gcc or Fortran with g77. For the matrix analysis algorithms I used LAPACK. For minimization routines I used some of the Numerical Recipes routines, which aren't free software exactly, but Numerical Recipes is an easy book to buy used off Amazon.
    I know that all of this stuff is really old-skool, but, it all works fine.
  • by doop (57132) on Thursday November 22, 2001 @12:00PM (#2600563)
    I'm doing a PhD on simulations of soft condensed matter [qmw.ac.uk], and mainly use either free software, or stuff we wrote in-house. Off the top of my head:
    • VTK [kitware.com]is a very good package for scientific visualization.
    • Maxima [sourceforge.net] 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 [www.ucc.ie] 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 [latex-project.org] -- 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 [arxiv.org], which contains preprints of a lot of scientific papers.
  • Sacrilege! (Score:1, Offtopic)

    You've really done it now... you posted a question to /. in which you referred to "the Debian version of Linux". Sorry, no relevant answers for you, all you get now is flames and trolls pointing out the difference between Linux distributions and versions of the Linux kernel.
  • "We are looking at the Debian version of Linux..."

    Debian is readily available for a modest price on CD from vendors such as Cheap Bytes. Since all the software in Debian is Free you can purchase a few sets of CD's and then duplicate them as needed. You can even resell the duplicates to help defray your costs.
  • The Perl Data Language [perl.org]

    PDL turns perl in to a free, array-oriented, numerical language similar to such commerical packages as IDL and MatLab.

  • These people have heard of and know all about free software. I'm a physics PhD myself so I'm sure that any physics dept. in the world uses GNUplot, F77 (free fortran compiler), LaTeX etc etc

    The problem they have is downloading the software over crap pipes you say?
    Why not simply get the people they are colaberating with in the richer countries to post the software!? Its not hard, and if you are posting results and reserch papers to each other all the time, it is not as nieve as it sounds! (These guys do colaberate with other physics depts, right?)

  • a very good site ... (Score:1, Informative)

    by fymidos (512362)
    is Scientific Applications for Linux (SAL), the one i use is in greece http://sal.duth.gr [sal.duth.gr], but there are mirrors around the world.
    I think the official site is at http://sal.kachinatech.com/ [kachinatech.com].

    many applications there , not all free though ..
  • by adapt (105738) on Thursday November 22, 2001 @12:17PM (#2600622) Homepage
    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...

  • by rainTown (536725) on Thursday November 22, 2001 @12:19PM (#2600626)
    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/
  • Why not get the African countries to prosecute Microsoft for anticompetitive practices and force MS to just give them the software to pay penalties?
  • by ceoyoyo (59147)
    I'm a student at a magnetic resonance research centre and we're looking for a new development platform. We've been using IDL but they've announced they won't be supporting Mac OS X. The leading candidate right now is Python with Numerical Python, Scientific Python and VTK.
  • Ecology (Score:1, Informative)

    by 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.
  • Its at http://www.members.home.net/europax

    Rob.
  • I'm surprised no one has mentioned LyX,
    http://www.lyx.org
    an excellent free GUI for LaTeX. Writing my dissertation would have been even more painfull without it.
  • I use an open-source data analysis package called Weka [waikato.ac.nz].

    It was developed in Java, and it's quite easy to modify and extend as you see fit. Solid documentation available on the website. Excellent CLI, decent GUI, decent graphics. Really useful for doing basic statistical analysis and using some of the more interesting machine learning techniques.

  • I wonder if a company like wolfram [wolfram.com] would donate mathematica for an endevour like this. It's unrealistic to try and make money of third world developement.. and if the ultimate goal here is to move these countries out of the third world, getting them hooked on the product would be great for the future.
  • linux is the answer (Score:2, Interesting)

    by dummkopf (538393)
    being a physicist myself (theory/computational physics) i have noticed that the main trend is to get rid of the expensive sun workstations and geat cheap pcs with linux on them. while we can have endless fights of what distro is the best, it seems that (at least in america) redhat (7.2 is highly recommendable and available via cd) is the choice for most scientific groups.

    not only is it a free os, it also provides ALL the core tools you need to do research! for example you have TeX (+ several excellent text editors), the whole gnu compiler suite (and debuggers), excellent plotting tools for data and image manipulation (gnuplot, gimp, xgrace, ...) and many more. Institutions like CERN, or space telescope provide full packages with tools to analyze all kinds of data.

    there are a lot of other scientific applications you can get for free for linux if you are in an academic environment and which are awesome tools to use for researchers. i have seen many responses already with good pointers to different places (SAL, freshmeat, CERN, IBM Open DX).

    finally, once can also make computational clusters with linux -- really inexpensive ones!
  • mupad (Score:4, Informative)

    by platypus (18156) on Thursday November 22, 2001 @01:02PM (#2600746) Homepage
    Take al ook at mupad [mupad.de]

    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.
    • by dido (9125)

      Have tried this. My ripes include the fact that is that it is somewhat slow (compared to proprietary computer algebra systems like Maple or Mathematica anyhow), and (gasp) it uses XView. Yes, the old GUI toolkit Sun once created for Open Look and their OpenWindows desktop.

      The worst part about it is that it's NOT open source/free software, which means that you're basically betting that the folks at the University of Paderborn who developed it aren't going to stop maintaining it or will suddenly stop making versions of it that are freely usable. Keep this in mind if you decide to use it.

  • Grass [baylor.edu] is a very powerful, free GIS system which is quite useful to scientists. A good GIS application can be used for any number of things such as terrain and weather modeling, migration pattern tracking, etc.
  • FlashBoltzmann also wanted to know if any of these programs we free and available on a microscoft windows platform. Ya, ya I know winblows sux monkey sphinkter and yadda yadda yadda...
  • There is an organization called MERLOT [merlot.org]. It's more of an online system where professors from Canada and the US submit links to sites with learning tools and programs.
    Anybody can submit links but each link is graded by professors from Universities and Colleges that pay a fee (a really big fee). This system ensures that only the good tools get online. It takes a minimum of 3 stars out of 5 to be linked. This encourages improvements (rejections get feedback) in tools to become easier to use and more educational.
    It's FREE (no registration at all) to and layed out into easy to navigate catagories (Arts, Biology, Math, Physics, etc...)
  • by andrew cooke (6522) <andrew@acooke.org> on Thursday November 22, 2001 @01:23PM (#2600805) Homepage
    http://iraf.noao.edu/iraf-homepage.html [noao.edu] 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).
  • This isn't going to help them as far as the bandwidth problem goes, but Intel now offers their Fortran compiler free for unsupported noncommercial use. This includes F90, which opens up a lot more opportunities. It does need a (free, still) license, so it's a little tricky to obtain, but still very worthwhile. As far as I've seen it's the only free F90 compiler for Linux and the only free F77 compiler besides g77, and it's likely to be far faster than g77 as well.
  • by adapt (105738)
    Ptolemy [berkeley.edu] is a good tool for modelling and simulation.


    From their website:

    "The Ptolemy project studies modeling, simulation, and design of concurrent, real-time, embedded systems. The focus is on assembly of concurrent components. The key underlying principle in the project is the use of well-defined models of computation that govern the interaction between components. A major problem area being addressed is the use of heterogeneous mixtures of models of computation."

  • For my thesis in astrophysics, I have almost exclusively used the R [r-project.org]-system. I find it brilliant. It was developed for statistic, but IMHO, it can be used for any numerical computational task, though in some areas, it may need more development (for example, it lacks 2D FFT, but that should be easy to fix [fftw.org].

    R comes with Woody (Next Debian release).

  • A note to FlashBoltzmann (admittedly a bit of a digression)--I notice that you point out that a lot of these folks have slow connections. I suspect that's true in a direct sense, but isn't it true that continental bandwidth to/from Africa is still pretty limited as well? It seems to me that there's a chance that an archive of related software, located on the African contient, might help the downloading time issues and give you a place to put a bunch of related software to make it easier for folks to find....
  • by Anonymous Coward
    For doing math. It understands matricies of
    arbitrary dimension so you can multiply
    a 6 x 4 x 8 matrix by a 4 x 8 x 2 matrix and
    end up with a 6x2 matrix (I think). Advantages
    are c-like syntax (scilab/matlab are UGLY),
    Graphing, and MPI interface. Downside is
    that it doesn't have that big a user following.

    You can find out more here:

    ftp://ftp-icf.llnl.gov/pub/Yorick/doc/index.html.

    Or hit up google.

    -- cary
  • just a test...
  • Numerical Python (Score:3, Informative)

    by Devil's Avocado (73913) on Thursday November 22, 2001 @03:38PM (#2601145)
    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
  • CERNlib is a package for high energy physics created by CERN, the people that brought us the web.

    It is geared for high energy physics data analysis, but it has many useful tools for doing things such as histogramming data and plotting data, as well as many other numerical routines. MINUIT, the minimization package that comes with CERNlib is the best around.

    The package is FORTRAN based, and works with g77/Linux as well as other systems.

  • A lot of people are providing excellent links to free scientific software resources, but one of the key points mentioned was the lack of a high speed Internet connection. FlashBoltzman also specifically said they were looking at Debian because of the applications bundled with it.

    Based on this, I think what would help the most would be hard copies of the scientific software people have mentioned. I would also recommend looking at SuSE's [suse.com] boxed distribution, because it contains 7 CDs or 1 DVD worth of software. Spending a few hundred U.S. dollars to get a box into every organization is probably much cheaper than the amount they would have to spend on their slow Internet connections to download several GB of data to each organization.

    However, those scientific and research packages mentioned aren't going to be part of any distribution. FlashBoltzman can post the resources listed here to a web page, but maybe he should routinely grab software and then each month or quarter burn a few CDs or DVDs to send to Africa.
  • In the past few years I converted our lab over to Linux and here are some of the tools we use for analysis:

    • GCC [gnu.org] for C/C++/FORTRAN coding. It's free, it's not the fastest in the world but it's competent.
    • Octave [octave.org] 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 [www.ucc.ie] 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 [sourceforge.net] 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 [tug.org] 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 [openoffice.org] 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 [liv.ac.uk] 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 [kachinatech.com] is a pretty comprehensive database of unix tools. HTH.

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