This page contains links to common software and resources relevant to the use of Linux in science and engineering. Suggestions for other GPL or similarly-licenced scientific and engineering software for Linux are welcome, please email pete@seul.org

Astronomy
Chemistry
Databases and Database Utilities
Documents and Other Resources
Editors and Editing Tools
Electronics
Format Converters
Geographical Information Systems
Graphing
Libraries
Math
Meteorology
Parallel Computing
Projects
Reference Management
Sequence Analysis
Statistics
Troubleshooting
Visualization
X Servers

Contents

Astronomy

• IRAF, an astronomical image analysis program http://iraf.noao.edu/iraf-homepage.html
• Nightfall, a program producing animated views of eclipsing binary stars, and calculating synthetic lightcurves and radial velocity curves http://www.lsw.uni-heidelberg.de/~rwichman/Nightfall.html

Chemistry

• Chemsuite, a suite of programs for chemists http://chemsuite.seul.org/
• GDIS, a program to display and manipulate isolated molegules and periodic systems http://gdis.seul.org
• GPeriodic, an interactive periodic table application http://gperiodic.seul.org/
• Moldy, a mollecular dynamics simulator http://www.earth.ox.ac.uk/~keith/moldy.html

Databases and Database Utilities

• gASQL, a GUI-based database administration tool http://malerba.linuxave.net/
• GNOME Transcript, a GUI-based database tool supporting multiple simultaneous connections to different databases http://gtranscript.sourceforge.net/

Documents and Other Resources

• Numeric Python (NumPy) Project, a well-documented site providing a multidimensional array language extension to Python http://numpy.sourceforge.net/
• Python and Scientific Computing, an overview of existing numeric resources for Python http://www.python.org/topics/scicomp/

Editors and Editing Tools

• gBib, a BibTeX database manager http://gbib.seul.org/
• LyX is a WYSIWYG editor providing all of the features of LaTeX in an easily usable graphical interface http://www.lyx.org/
• Ted is a WYSIWYG editor for RTF files http://www.nllgg.nl/Ted/
• TeXmacs, a WYSIWYG scientific text editor http://www.math.u-psud.fr/~anh/TeXmacs/TeXmacs.html

Electronics

• GNU Electronic Design Automation (gEDA), a suite of tools for electronics design and simulation http://geda.seul.org/

Format Converters

• antiword converts DOC (MS Word) files to text or postscript. Although the documentation states that the software is not complete, it does a good job converting the files http://www.winfield.demon.nl/index.html

Geographical Information Systems

• FREEGIS is a GIS portal containing both GIS software (most of which runs on Linux) and geographical data http://freegis.org/
• The GRASS Geographical Information System http://www.baylor.edu/~grass/

Graphing

• Dia, a drawing tool similar to Visio supporting many different types of diagrams http://www.lysator.liu.se/~alla/dia/
• GNU Emacs Calc takes two data series of equal length from the stack and plots them through gnuplot which can then graph the data alpha.gnu.org:/gnu/calc/
• Grace, a WYSIWYG 2-d graphing tool http://plasma-gate.weizmann.ac.il/Grace/
• kpl is an application used to plot two-dimensional graphical representations of data sets and functions. http://frsl06.physik.uni-freiburg.de/privat/stille/kpl/
• SciGraphica is a WYSIWYG 2-d and 3-d graphing tool http://scigraphica.sourceforge.net/

Libraries

• FXT, a library for Fast Fourrier and numerous other transforms http://www.jjj.de/fxt/
• Geometry Utility Library, abstracts many 3d form manipulations http://gul.sourceforge.net/
• GNU Scientific Library (GSL), a collection of routines for numerical computing ftp://sourceware.cygnus.com/pub/gsl/
• GNU Triangulated Surface Library (GTS), a C-based library for topological, structural modelling and triangulation http://gts.sourceforge.net
• NetCDF, an interface and library for array-oriented data access http://www.unidata.ucar.edu/packages/netcdf/Newmat, a C++ library for extensive matrix manipulation http://webnz.com/robert/cpp_lib.htm
• Numeric Python (NumPy) Project, a well-documented http://numpy.sourceforge.net/
• Synchronous Interprocess Messaging Project for Linux (SIMPL), a library for implementing the Send/Receive/Reply messaging paradigm (similar to QNX) in Linux http://www.holoweb.net/~simpl

Math

• GNU Octave, an interactive / batch program for numerical simulation (very similar to Matlab) http://www.che.wisc.edu/octave/
• Matrix Math allows a user to quickly and easily perform mathematical operations on matrices http://www.angelfire.com/linux/linuxjeff/mtrxmath/
• Scilab, a scientific software package for numerical computation http://www-rocq.inria.fr/scilab/
• SNAC, an algebraic calculator for Gnome http://snac.seul.org/
• XPP, a system for the analysis and simulation of dynamic and probabilistic phenomena. http://www.cnbc.cmu.edu/~bard/files.html

Meteorology

• One Wire Weather is a RISC OS/Linux interface to the Dallas Semiconductor One Wire Weather Station. http://www.simon.melhuish.net/projects/oww/

Parallel Computing

• Cactus is a modular parallelisation framework which supports many architectures, allowing supercomputing simulation codes to be developed on a laptop running linux, and yet run with no modification on large T3Es, origins, or clusters http://www.cactuscode.org/

Projects

• The OpenScience Project http://www.openscience.org/
• Stone Soupercomputer is an excellent example of scientific ingenuity overcoming financial limitations by creating a Beowulf-class cluster from Linux and Alpha-based computers that have been discarded from normal usage. http://stonesoup.esd.ornl.gov/

Reference Management

• OpenReference is a Servlet/JSP based database application to manage your or your group's research references http://openreference.sourceforge.net/
• Pybibliographer is a bibliographic database management tool, which supports several current formats: BibTeX, Medline, Ovid, Refer. http://www.gnome.org/pybliographer/
• Scientific Image Database archives 2-D, 3-D images in a central directory (archive), and provides a perfect means to archive images within the setting of small to medium-sized research groups or wherever people collaborate on images http://sidb.sourceforge.net/
• Stone Soupercomputer is an excellent example of scientific ingenuity overcoming financial limitations by creating a Beowulf-class cluster from Linux and Alpha-based computers that have been discarded from normal usage. http://stonesoup.esd.ornl.gov/

Sequence Analysis

• EMBOSS is a suite of tools for sequence analysis - http://www.uk.embnet.org/Software/EMBOSS/

Statistics

• The R Statistical System http://www.r-project.org/

Troubleshooting

• Memtest86 allows an exhaustive analysis of memory integrity by running a substantial number of diagnostic tests http://reality.sgi.com/cbrady_denver/memtest86/

Visualization

• GGobi is a data visualization system for viewing high-dimensional data, and is described as "the next edition of XGobi" http://www.ggobi.org/
• XGobi is a visualization program for multivariate data, and XGvis is described as "a system for multidimensional scaling.and graph layout in any dimension." http://www.research.att.com/~andreas/xgobi/
• OpenVRML is a free cross-platform runtime for VRML, and includes libraries you can use to add VRML support to an application, and "Lookat", a simple stand-alone VRML browser. http://openvrml.sourceforge.net/

X Servers

• WeirdX allows Windows-based machines to run X applications http://www.jcraft.com/weirdx/

Software

Resources