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There is a wealth of scientific software available for Linux that comes preinstalled with popular distributions. The electronic circuit simulation package Spice is included in Red Hat Linux, as well as gnuplot for data graphs and xfig for diagrams and technical drawings.
The ever-expanding list of scientific software for Linux is maintained at http://SAL.KachinaTech.com/; we highly recommend it. For data acquisition, there is the Linux Lab Project (http://obelix.chemie.fu-berlin.de/), created by Claus Schroeter of Berlin's Freie Universitat. Besides drivers for specific hardware, you can find the Linux Driver Development Kit there. It is an excellent resource for writers of new Linux device drivers. LLP also runs a mailing list for the lab computing, data acquisition and interfacing communities.
As to specific software we find especially useful, Xmgr, available from http://plasma-gate.weizmann.ac.il/Xmgr/, is a very nice publication-quality plotting tool. Matlab is described at http://www.mathworks.com/ and Octave can be found at http://www.che.wisc.edu/octave/. The Kermit program is available from http://www.columbia.edu/kermit/.
Mesa (http://www.ssec.wisc.edu/~brianp/Mesa.html) contains the OpenGL-look-alike 3-D library, and also provides a collection of links to various visualization resources; in particular, the University of Minnesota's Geometry Center (http://www.geom.umn.edu/) and the VTK visualization toolkit (http://www.cs.rpi.edu/~martink/).
Finally, we have collected several packages that might be of interest to the general laboratory-going public. If you are interested, please contact us at przemek@nist.gov or nickm@nist.gov.
Working at a government institution, we are required to avoid any appearance of partiality. Even though certain trade names and company products are mentioned in the present paper, in no case does such mention imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the products are necessarily the best available for the purpose.