Open Source Scientific Apps?

Paranoid Diatribe asks: "I'm a Unix admin for a scientific computing environment at a large public university. In the past few weeks, I've had the (dis)pleasure of dealing with several vendors to get their applications re-licensed to run on various machines. These are vendors of scientific applications like MOLGEN, apps from MSI, and S-PLUS. There are many others. The majority use the most evil of license managers, Flex-LM. I spend more time messing with Flex, license key files, and calling the damned vendors than I do actually administering the boxes they run on. As such, I am becoming very disenchanted with these commercial vendors. Is there a compilation of alternative scientific computing apps (GPL, BSD, or other open license would be preferable) and how they match up to their commercial counterparts? I'm aware of Freshmeat.net and a small list at the OpenGL site (though many of these are commercial as well), but I was wondering if there was a better list of such apps."

Some hints

[mvw]

First you should talk with your customers, the scientists that use your software.

Usually there are folks around who know the open software in that area pretty good. Sometimes there are even people around who might be able to write it themselves, if they had the time/funding to do it.

Aside from that, I found some gems in the FreeBSD ports collection:

Look here [freebsd.org]

Browse the math, biology [freebsd.org] etc categories.

Of course you won't find applications for all problems, some stuff (I used to work for LabControl and their partner Chemical Concepts) is not only complicated and needs experience, but often is pretty boring, which nobody would do for free.

Linux needs a replacement for MathCAD

[ecloud]

I'd like to see someone try to create a clone of it. It was my favorite math program in college (but I haven't tried Mathematica... I hear it's pretty good). It has a really friendly way of editing equations, and the results really look good too - like TeX.

I think a project like this could be started using some code from LyX's equation editor, but I would like to see it use the same keymappings as those of MathCAD because they are much quicker. Of course it should be able to produce TeX output, for easy integration into technical papers. (One of MathCAD's drawbacks is that you usually need to do your whole paper in MathCAD itself... this was especially true in the pre-Windows versions when I first got started using it.)

It should then be integrated with one or more freeware backends... and some promising ones exist already, such as Maple, and some others listed on SAL.

Someday, if it doesn't get done in the meantime, I might be interested in heading up the UI effort, but I'm not enough of a mathematician to create the algorithms from scratch. I'm also too busy with other projects to start this now.

Scientific computing link

[AMK]

Another useful link: the Scientific Computing topic guide [python.org] at python.org.

I work on a semiconductor-related project, and it's amazing how poorly written the fabulously expensive layout tools are. Take L-Edit as an example; the interfaces are ugly and poorly designed, the software quality is doubtful (it dumps core when you try to run it on a 16-bit X display). A free version, written to modern standards, would have a serious chance at winning out over the commercial stuff, or at least provide them with some competition.

Linux Metapage

[andkaha]

At the Linux Metapage (http://stommel.tamu.edu/~baum/linux-meta.html [tamu.edu]) there's pointers to a lot of different types of software for Linux.

In particular, there's a pointers to to SAL (http://SAL.KachinaTech.COM/index.shtml [kachinatech.com]) and LinuxApps (http://www.linuxapps.com/ [linuxapps.com]) and other software lists that might interest scientific Linux users.

bits 'n' pieces

[kojak]

One comment is that (we) in the scientific community have been very slow to collaborate on bits of software. For example simple things often get re-implemented (badly) by students and postdocs all the time, whereas if people in each subject area actually made of concerted architechting effort, then everybody could hang their latest scheme off of the OO core that did (for example) the i/o and all that stuff. Also academics often get hung up over distributing source and so on, because they compete. As a community, we need to learn from the work we've done on OS in the last two decades.

Also can I make a plea: Bob von Dreele: release GSAS source please! Somebody release NASTRAN source! John Goldak et al, please release your codes so somebody might actualy use them one day!

Open-source scientfic software

[Alien Perspective]

Well, I get most of mine from CERN. It's free, it's open source.

But, of course, it's not for the types that have to have their hands held. No glitz to it at all.

But if you need complete elliptic integrals of the 2nd kind, and demand 10-place precision, they're hard to beat.

Oh yeah, about 10 years ago they bundled in a little program with their libraries..something to make it easier to get at the documentation. Called it "WWW.EXE" as I recall.

I still have it on a backup tape.

SAL (Scientific Applications on Linux)

[Bingo Foo]

http://sal.kachinatech.com/index.shtml [kachinatech.com]

Works for me.

R and other stuff

[KjetilK]

I'm using the R statistics system for my thesis, it's truly astonishing what the R team has come up with in such a short time. Go to CRAN [r-project.org]. R has a GNU license, and is similar to S and S-plus in syntax. In fact, one of the original designers of the S system just joined the R core team. R is object-oriented, has many very nice array manipulation features and graphics capabilities, and is still evolving rapidly.

It can be used on Unices (the use of emacs as frontend is strongly recommended, it's an excellent collection of modes for it in the ESS package) and on Win32, there's a GUI for it on that platform.

Then, there's the PDL, offering "Number crunching capabilities for perl" [aao.gov.au], I haven't used that either, but I hear it is good. Probably meant as an alternitive to IDL, that I have used, I didn't like it's syntax, so I did some hacking to replace the features I needed from IDL in R.

As an alternative to MATLAB, I hear SCILAB [inria.fr] can be used. It doesn't seem to evolve very fast, and I haven't used it.

Now, I miss an alternative to Mathematica. Mathematica is the only proprietary software (and that I would think about using...) I can think of that still is better than Open Source alternatives. I have heard that some emacs package does have symbolic mathematical capabilities, but I don't what it is.