Ubuntu Scientists
From:http://www.blogjava.net/ivanwan/archive/2005/09/26/14113.html Pending=true#Post
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.
Introduction
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.
Applications
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.
Physics
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.
JaxoDraw - A program for drawing Feynman diagrams
ROOT - An Object Oriented Data Analysis Framework
Geant4 - A toolkit for the simulation of the passage of particles through matter
CLHEP - A Class Library for High Energy Physics
Pluto++ - A Monte Carlo simulation tool for hadronic physics
Data files from the Particle Data Group
Chemistry
GChemPaint - A 2D chemical structures editor
ghemical - A molecular modeling and computational chemistry package that provides molecular mechanics, semi-empirical (via MOPAC7), and ab initio (via MPQC) calculations
gdis - A molecular display program that supports OpenGL and POVRay rendering.
OpenBabel - A chemical file format conversion program.
Chemtool and Xdrawchem - 2D molecule drawing programs similar to ChemDraw. and
mpqc - The Massively Parallel Quantum Chemistry Program. Ab initio quantum chemical computational package.
- list of linux applications which may be useful for chemists
Biology
Bioconductor - bioinformatics tools
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
- an open-source software toolkit for performing registration and segmentation. Created to support the .
Mathematics
- GNU Octave is a high-level language, primarily intended for numerical computations. (Similar to MATLAB).
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
Scilab - Another MATLAB-like software.
SciCos - A free Simulink-like addon to Scilab
Maxima - A computer algebra system (xmaxima is its X interface)
is a nice front end for
Here is a about using as a Maxima frontend
GNU MP - GNU Multiprecision arthmetic library. Useful if you need to use very big numbers in a C program.
GSL - the Gnu Scientific Library
R - for statistical computing and graphics.
OOStatistics - A statistics macro for openoffice calc.
freefem - A PDE oriented language using Finite Element Method - 2D and 3D versions.
SciPy - An open source library of scientific tools for Python.
F2PY - Fortran to Python interface generator provides a connection between Python and Fortran languages.
Astronomy
KStars - A virtual planetarium.
xephem - A very comprehensive ephemeris/planetarium. Old interface.
Nightfall - An astronomy application for fun, education, and science.
Electronics
Eagle - A printed circuit board design tool.
oregano - Schematic capture, netlists, and spice for simulations.
gEDA - GPL'd suite of Electronic Design Automation tools.
Qucs - An integrated circuit simulator
Computer Science
Geography
Geographical Information System
ncview - A very fast program for viewing netCDF files (a standard widely used in meteorology, climate and oceanography)
Generic Mapping Tools (GMT) - a mapping program that can also be used to make pretty graphs.
Distributed Computing
openmosix - Turns a network of ordinary computers into a supercomputer.
boinc - A software platform for distributed computing using volunteered computer resources
projects include Climateprediction.net,Einstein@home,LHC@home,Predictor@home,SETI@home
Tools
Xfig - A diagram and figure creation tool. Can import GIF, JPEG, and EPS figures and can export to Postscipt, LaTeX, and bitmap files.
Dia - A "Visio" like diagram tool. Especially useful for simple circuits and flowcharts.
BIKA - A laboratory information management system (LIMS) built on top of Zope and Plone, and coded in Python
Plotting Tools
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 scripts.
grace - A 2D WYSIWYG plotting tool that exports to JPEG, PNG, EPS, PDF, and SVG. Also does curve fitting.
PGPLOT - Fortran- or C-callable graphics subrutine package for making scientific graphs.
SciGraphica - A scientific application for data analysis and technical graphics. Attempts to be a clone
Qtiplot - A 2D/3D, Qt based plotting tool that attempts to be another "Origin" clone
LabPlot - Another Qt based 2D/3D GUI plotting tool that also does curve fitting, supports many data formats, LaTeX labeling, functions, and statistics.
Veusz - A scientific plotting package written in Python. .
Gri - A scientific graphics language.
Word Processing Tools
- WYGIWYW (What You Get Is What You Want) text mark up system. What real scientist write papers with.
- A WYSIWYG LaTeX frontend.
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 facilities.
eqe - Allows you write equations in Latex and drag and drop them into other apps
Conglomerate - An XML editor, to create or similar formats.
Jabref - A graphical bibtex bibliography manager which can be used in conjunction with lyx. It is java based.
Texmaker - Like but loads faster
- A wysiwyg scientific text editor
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], , [GNUplot], [Xfig], [Dr. Geo], [Eukleides],[Qcl]
preview-latex - (almost) turns emacs into a WYSIWYG-LaTeX-frontend
, and for converting to html.
gaim-latex - A small gaim (see ) plugin which allow you to insert formulae into im conversations.
Ubuntu Packages
Science Section
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Mathematics Section
, , .
TeX Section
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Alternatives to Proprietry Scientific Software
hopefully this list will get long enough to deserve its own page.
Proprietary | Free alternative | Info | Link |
Matlab | Matrix based computing environment | ||
Matlab | Scilab | see above | |
Simulink | SciCraft | Based on Octave (Available for Debian, I think) | |
Simulink | SciCos | Based on Scilab (Not found in Ubuntu Repos) | |
Origin | SciGraphica & Qtiplot | Data plotting and analysis | & |
Hardware
Labview for linux (non-free)
Data acquisition
National Instruments GPIB drivers for linux.
Comedi - Open source drivers, tools and libraries.
Computer controlled systems
RTAI - Real-Time Application Interface is a hard real-time extension to the Linux kernel
Other information
Other Linux Distributions for Scientists
A Knoppix / Debian variant tailored to numerical and quantitative analysis.Debian-Med Debian-Med is a "Custom Debian Distribution" for medical practice and research.
debian-med metapackages are in Ubuntu(Universe): to list them type: apt-cache search debian-med
Linux release put together by Fermilab and CERN based on RH
is about using Madrake Linux for chemistry
Unofficial Ubuntu/Debian repositories with science software
of packages
of Packages
Daniel Leidert ( )
Mailing Lists about Linux and Science
Related Wiki Pages
is a list of packages that are in the official Ubuntu Repositories that scientist use
discusses possible science metapackages
Forum Threads
Links
- scientific software on sourceforge
- links to science software
- scientific software on freshmeat
- scientific linux software
- scientific apps for gnome