Science on Linux
The aim of this page is to become a useful resource for scientist
and science students using Ubuntu (or any other) Linux. Please add
information or comments.
Linux is a great operating system for scientists, for many reasons:
It is stable, secure and runs on all sorts of hardware, from embedded systems to supercomputers.
It is possible to create a highly customised setup to do what you want.
Repetitive tasks can be automated.
There are lots of useful free scientific programs and tools.
Although some people say that linux is not user friendly enough for
the desktop yet, scientists are usually a bit more familier with
computers, and don't mind learning how to do things.
Some applications that scientists use in Linux. Please add some more.
See also: SAL (Scientific Applications on Linux) is a collection of
information and links to software that will be of interest to
scientists and engineers. The broad coverage of Linux applications will
also benefit the whole Linux/Unix community. There are currently 3,017
entries in SAL. http://sal.iatp.by/
Cernlib - A suite of data analysis tools and libraries created
for use in physics experiments, but also with applications to other
fields such as the chemical and biological sciences. Cernlib
JaxoDraw - A Java program for drawing Feynman diagrams JaxoDraw
ROOT - An Object Oriented Data Analysis Framework ROOT
Geant4 - A toolkit for the simulation of the passage of particles through matter Geant4
CLHEP - A Class Library for High Energy Physics CLHEP
Pluto++ - A Monte Carlo simulation tool for hadronic physics Pluto++
Data files from the Particle Data Group http://pdg.lbl.gov/2005/html/computer_read.html
GChemPaint - A 2D chemical structures editor GChemPaint
ghemical - A molecular modeling and computational chemistry package that provides molecular mechanics, semi-empirical (via MOPAC7), and ab initio (via MPQC) calculations ghemical
gdis - A molecular display program that supports OpenGL and POVRay rendering. gdis
OpenBabel - A chemical file format conversion program. OpenBabel
Chemtool and Xdrawchem - 2D molecule drawing programs similar to ChemDraw. Chemtool and xdrawchem
mpqc - The Massively Parallel Quantum Chemistry Program. Ab initio quantum chemical computational package. mpqc
Linux4Chemistry - list of linux applications which may be useful for chemists
Octave - GNU Octave is a high-level language, primarily intended for numerical computations. (Similar to MATLAB). Octave
SciCraft - Addon to Octave, clones
Simulink. Still in developement, blocks have to be written by the user.
It is supposed to specialize in bioinformatics functions SciCraft
Scilab - Another MATLAB-like software. Scilab
SciCos - A free Simulink-like addon to Scilab SciCos
Maxima - A computer algebra system (xmaxima is its X interface)
GNU MP - GNU Multiprecision arthmetic library. Useful if you need to use very big numbers in a C program. GMP
GSL - the Gnu Scientific Library GSL
R - for statistical computing and graphics. R
OOStatistics - A statistics macro for openoffice calc. OOStatistics
freefem - A PDE oriented language using Finite Element Method - 2D and 3D versions. freefem
SciPy - An open source library of scientific tools for Python. SciPy
F2PY - Fortran to Python interface generator provides a connection between Python and Fortran languages. F2PY
Eagle - A printed circuit board design tool. Eagle
oregano - Schematic capture, netlists, and spice for simulations. oregano
gEDA - GPL'd suite of Electronic Design Automation tools. gEDA
Qucs - An integrated circuit simulator Qucs
UbuntuGIS Geographical Information System
ncview - A very fast program for viewing netCDF files (a standard widely used in meteorology, climate and oceanography) ncview
Generic Mapping Tools (GMT) - a mapping program that can also be used to make pretty graphs. GMT
Xfig - A diagram and figure creation tool. Can import GIF,
JPEG, and EPS figures and can export to Postscipt, LaTeX, and bitmap
Dia - A "Visio" like diagram tool. Especially useful for simple circuits and flowcharts. Dia
BIKA - A laboratory information management system (LIMS) built on top of Zope and Plone, and coded in Python BIKA
GNUPlot - A command-line driven 2D/3D plotting tool. Can
perform data fitting and exports to PNG, PS, Xfig, and Latex formats.
Has python bindings (python-gnuplot) for including in other programs or
grace - A 2D WYSIWYG plotting tool that exports to JPEG, PNG, EPS, PDF, and SVG. Also does curve fitting. grace
PGPLOT - Fortran- or C-callable graphics subrutine package for making scientific graphs. PGPLOT
SciGraphica - A scientific application for data analysis and technical graphics. Attempts to be a "Microcal Origin" clone SciGraphica
Qtiplot - A 2D/3D, Qt based plotting tool that attempts to be another "Origin" clone Qtiplot
LabPlot - Another Qt based 2D/3D GUI plotting tool that also does curve fitting, supports many data formats, LaTeX labeling, GSL functions, and statistics. LabPlot
Veusz - A scientific plotting package written in Python. veusz.
Gri - A scientific graphics language. Gri
Word Processing Tools
LaTeX - WYGIWYW (What You Get Is What You Want) text mark up system. What real scientist write papers with. LaTeX
Lyx - A WYSIWYG LaTeX frontend. Lyx
Kile - A LaTeX-frontend for KDE, with support for syntax highlighting
and convenient palettes for all standard mathematical symbols and text
formatting. It also provides easy access to forward and inverse search
eqe - Allows you write equations in Latex and drag and drop them into other apps eqe
Conglomerate - An XML editor, to create DocBook or similar formats. Conglomerate
Jabref - A graphical bibtex bibliography manager which can be used in conjunction with lyx. It is java based. Jabref
Texmaker - Like Kile but loads faster Texmaker
TeXmacs - A wysiwyg scientific text editor TeXmacs
doubles as an interface for computer algebra systems like
[Maxima], maple, mupad, axiom, giac, GTybalt, Macaulay 2, pari, yacas
can also be used as a front end for [R], Octave, [GNUplot], [Xfig], [Dr. Geo], [Eukleides],[Qcl]
preview-latex - (almost) turns emacs into a WYSIWYG-LaTeX-frontend preview-latex
latex2html , tth and hevea for converting LaTeX to html.
gaim-latex - A small gaim (see GaimHowto) plugin which allow you to insert LaTeX formulae into im conversations. gaim-latex
Alternatives to Proprietry Scientific Software
hopefully this list will get long enough to deserve its own page.
Matrix based computing environment
Based on Octave (Available for Debian, I think)
Based on Scilab (Not found in Ubuntu Repos)
SciGraphica & Qtiplot
Data plotting and analysis
SciGraphica & Qtiplot
Computer controlled systems
Other Linux Distributions for Scientists
Quantian A Knoppix / Debian variant tailored to numerical and quantitative analysis.
Debian-Med Debian-Med is a "Custom Debian Distribution" for medical practice and research.
Scientific Linux Linux release put together by Fermilab and CERN based on RH
Madrake4Chemistry is about using Madrake Linux for chemistry
Unofficial Ubuntu/Debian repositories with science software
Mailing Lists about Linux and Science
Related Wiki Pages
UbuntuSciencePackages is a list of packages that are in the official Ubuntu Repositories that scientist use
UbuntuScienceMetaPackages discusses possible science metapackages