ivaneeo's blog

Ubuntu Scientists

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. http://sal.iatp.by/

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. 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

Chemistry

• 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

Biology

• Bioconductor - bioinformatics tools Bioconductor

• Howto install Bioinformatics Tools for Linux

• 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

• Insight Toolkit (ITK) - an open-source software toolkit for performing registration and segmentation. Created to support the Visible Human Project .

  • unofficial debian packages

Mathematics

• 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)

  • wxMaxima is a nice front end for Maxima

  • Here is a tutorial about using TeXmacs as a Maxima frontend

• 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

  • SciPy Tutorial

• F2PY - Fortran to Python interface generator provides a connection between Python and Fortran languages. F2PY

Astronomy

• KStars - A virtual planetarium. KStars

• xephem - A very comprehensive ephemeris/planetarium. Old interface. xephem

• Nightfall - An astronomy application for fun, education, and science. http://www.lsw.uni-heidelberg.de/users/rwichman/Nightfall.html

Electronics

• 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

Computer Science

Geography

• 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

Distributed Computing

• openmosix - Turns a network of ordinary computers into a supercomputer. openmosix

• boinc - A software platform for distributed computing using volunteered computer resources boinc

  • 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. Xfig

• 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

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. gnuplot

• 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 facilities. Kile

• 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

Ubuntu Packages

Science Section

• warty (4.10), hoary (5.04), breezy (5.10).

Mathematics Section

• warty (4.10), hoary (5.04), breezy (5.10).

TeX Section

• warty (4.10), hoary (5.04), breezy (5.10).

Alternatives to Proprietry Scientific Software

hopefully this list will get long enough to deserve its own page.

Hardware

• Labview for linux (non-free) http://sine.ni.com/nips/cds/view/p/lang/en/nid/2541

Data acquisition

• National Instruments GPIB drivers for linux. http://www.ni.com/linux/gpib.htm

• Comedi - Open source drivers, tools and libraries. comedi

Computer controlled systems

• RTAI - Real-Time Application Interface is a hard real-time extension to the Linux kernel http://www.rtai.org/

Other information

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.

  • debian-med metapackages are in Ubuntu(Universe): to list them type:  apt-cache search debian-med 

• 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

• repository of ROOT packages

• Yaroslav Halchenko repository

• repository of ITK Packages

• Teemu Ikonen repository

• Daniel Leidert repository ( read)

• Carlo Segre repository

Mailing Lists about Linux and Science

• debian-science mailing list

Related Wiki Pages

UbuntuSciencePackages is a list of packages that are in the official Ubuntu Repositories that scientist use

UbuntuScienceMetaPackages discusses possible science metapackages

Forum Threads

• Are there any scientists-biologists out there using Ubuntu?

• Ubuntu Science Metapackage

Links

• DebianScience

• sourceforge - scientific software on sourceforge

• DebianLinux.Net-Scientific Software - links to science software

• freshmeat - scientific software on freshmeat

• http://www.linuxlinks.com/Software/Scientific/ - scientific linux software

• gnome-files - scientific software - scientific apps for gnome

• kde-apps.org- scientific software - scientific apps for kde

• Educypedia - collection of links about scientific and educational material.

• Linux Equivalents of Windows scientific apps

• Openscience project is dedicated to writing and releasing free and Open Source scientific software.

Books

(2005-09-26 06:17:30由KevinGoldstein編輯)