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{{From|https://help.ubuntu.com/community/UbuntuScience}}
{{From|https://help.ubuntu.com/community/UbuntuScience}}
{{Languages|UbuntuHelp:UbuntuScience}}
{{Languages|UbuntuHelp:UbuntuScience}}
The aim of this page is to become a useful resource for scientists, engineers and students using Ubuntu (or any other) Linux. Please add information or comments.
Legend:
== Introduction ==
GNU/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.
A guide for installing various applications on Ubuntu with assorted tips and tricks is at [[UbuntuHelp:UbuntuScience/Howto|UbuntuScience/Howto]] (still a work in progress....)
== Applications ==
Some applications that scientists use in Linux. Please add some more.
=== Legend ===
https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircle.png - installed by default in Ubuntu <<BR>>
https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircle.png - installed by default in Ubuntu <<BR>>
https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=IconKubuntuCircle.png - installed by default in Kubuntu <<BR>>
https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=IconKubuntuCircle.png - installed by default in Kubuntu <<BR>>
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* [http://www.gromacs.org GROMACS] [http://packages.ubuntu.com/gromacs {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
* [http://www.gromacs.org GROMACS] [http://packages.ubuntu.com/gromacs {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
* [http://www.chemdoodle.com ChemDoodle] - A chemical structure environment. More than just another program for drawing molecules (although it does that easily), it's a brand new application for interacting with chemical data and creating chemical art.
* [http://www.chemdoodle.com ChemDoodle] - A chemical structure environment. More than just another program for drawing molecules (although it does that easily), it's a brand new application for interacting with chemical data and creating chemical art.
=== Computer Science ===
=== Earth Sciences (Geology/Geography) ===
=== Earth Sciences (Geology/Geography) ===
* Ubuntu:UbuntuGIS This is the page where suggestions and software lists for a professional "out of the box" Ubuntu based GIS workstation should be collected.
* [http://grass.itc.it GRASS] [http://packages.ubuntu.com/grass {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Geographic Resources Analysis Support System Commonly referred to as GRASS, is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/map production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many government agencies and environmental consulting companies.
* [http://grass.itc.it GRASS] [http://packages.ubuntu.com/grass {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Geographic Resources Analysis Support System Commonly referred to as GRASS, is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/map production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many government agencies and environmental consulting companies.
* [http://qgis.org/ QGIS] [http://packages.ubuntu.com/qgis {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Quantum GIS (QGIS) supports shapefile viewing and editing, spatial data storage with [[UbuntuHelp:PostgreSQL|PostgreSQL]]/PostGIS, projection on-the-fly, map composition, and a number of other features via a plugin interface.
* [http://qgis.org/ QGIS] [http://packages.ubuntu.com/qgis {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Quantum GIS (QGIS) supports shapefile viewing and editing, spatial data storage with [[UbuntuHelp:PostgreSQL|PostgreSQL]]/PostGIS, projection on-the-fly, map composition, and a number of other features via a plugin interface.
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* [http://ccl.northwestern.edu/netlogo/ NetLogo] - A Java-based programmable modeling environment for simulating natural and social phenomena.
* [http://ccl.northwestern.edu/netlogo/ NetLogo] - A Java-based programmable modeling environment for simulating natural and social phenomena.
* [http://www.simulistics.com/ Simile] - A proprietary ($$$) System Dynamics and object-based modeling and simulation software package similar to Stella, Model Maker, Vensim, etc. It is advertised as "Visual modeling software for the earth, environmental and life sciences". A free evaluation version, which limits the size of saved models, is available.
* [http://www.simulistics.com/ Simile] - A proprietary ($$$) System Dynamics and object-based modeling and simulation software package similar to Stella, Model Maker, Vensim, etc. It is advertised as "Visual modeling software for the earth, environmental and life sciences". A free evaluation version, which limits the size of saved models, is available.
=== Econometrics ===
* [http://gretl.sourceforge.net/ Gretl] [http://packages.ubuntu.com/gretl {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - The GNU Regression, Econometric and Time-Series Library (gretl) is a package for econometric analysis.
=== Electronics ===
* [http://www.cadsoft.de/ Eagle] [http://packages.ubuntu.com/eagle {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png}}] - A printed circuit board design tool.
* [http://arrakis.gforge.lug.fi.uba.ar/index.php oregano] [http://packages.ubuntu.com/oregano {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Schematic capture, netlists, and spice for simulations.
* [http://www.geda.seul.org/ gEDA] [http://packages.ubuntu.com/geda {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - GPL suite of Electronic Design Automation tools.
* [http://qucs.sourceforge.net/index.html Qucs] [http://packages.ubuntu.com/qucs {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - An integrated circuit simulator.
* [http://icarus.com/eda/verilog/ Icarus Verilog] [http://packages.ubuntu.com/verilog {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Icarus Verilog is a Verilog simulation and synthesis tool. It operates as a compiler, compiling source code written in Verilog (IEEE-1364) into some target format.
=== Engineering Sciences ===
* [http://www.ribbonsoft.com/qcad.html QCad] [http://packages.ubuntu.com/qcad {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A 2D-Computer Aided Design application similar AutoCAD. It is available in the universe repositories.
* [http://www.cycas.de/ CyCAS ] - A commercial Computer Aided Design application for architects. There is a public version available.
* [http://www.arcad.de/index.php ARCAD ] - A commercial Computer Aided Design application for architects.
* [http://www.brlcad.org BRL-CAD] - A Open Source 3D-CAD program. It is a Constructive Solid Geometry (CSG) solid modeling system with over 20 years development and production use by the U.S. military.
* [http://www.tech.oru.se/cad/varkon/ Varkon] [http://packages.ubuntu.com/varkon {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Open Source 3D- (parametric) and 2D-Developmentplatform for a CAD program. It is available in the universe repositories.
* [http://caelinux.com/CMS/index.php?option=com_content&task=view&id=44&Itemid=40 Salome] - A Open Source software suite including Pre-/Post processing Tools: 3D-CAD, Mesher, FEM-Software
* [http://juergen-riegel.net/FreeCAD/Docu/index.php/Main_Page Free-CAD] - Modern Open Source 3D-Solid CAD. FreeCAD will aim directly to mechanical engineering, product design and related features (like Catia, and Solid-Works). Early state of Development.
* [http://www.gcad3d.org gCAD3D] - A 3D-surface-CAD/CAM. Program is freeware.
* [http://www.graphiteone-cad.com/en/index.htm Graphiteone] - 3D and 2D commercial mechanical engineering CAD. Version 1.3: Free for personal use only. Version 2.0: With Parasolid-Kernel from UGS, Evaluationlicence for one month available.
* [http://www.geuz.org/gmsh/ Gmsh] an automatic 3D finite element grid generator with a built-in CAD engine and post-processor.
* [http://www.oofem.org/en/oofem.html OOFem] a free finite element code with object oriented architecture for solving mechanical, transport and fluid mechanics problems.
* [http://www.collabcad.com CollabCAD] - 3D and 2D commercial mechanical engineering CAD/CAM based on open source software . Freeware-Version available.
* [http://www.varicad.com Varicad] - Modern 3D and 2D commercial mechanical engineering CAD. Cheap CATIA, Pro/E - LIGHT. Trialversion for one month available.
* [http://www.webersys.com Webersys] - 3D and 2D commercial mechanical engineering CAD/CAM. Trialversion for one month available.
* [http://www.cad-schroer.com/index.php?screen=1&ziel=Products-MEDUSA&land=com MEDUSA] - 2D/3D commercial mechanical engineering CAD. Free for personal use only.
* [http://www.ptc.com/appserver/mkt/products/home.jsp?k=403 Pro/ENGINEER] - A 3D-commercial mechanical engineering and design CAD tool.
* [http://www.tech-edv.co.at/lunix/CADlinks.html A list of CAD software for Linux]
* XFoil is a program to design and/or calculate airfoils. See [http://ubuntuforums.org/showthread.php?t=288920 this forum thread] on how to install it.
=== Mathematics ===
* [http://gnudatalanguage.sourceforge.net/ GDL] [http://packages.ubuntu.com/gnudatalanguage {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}]- GNU Data Language is a high level language for numerical computations and data visualization similar to IDL (Interactive Data Language from Research Systems Inc.).
* [[UbuntuHelp:Octave|Octave]] [http://packages.ubuntu.com/octave {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - GNU Octave is a high-level language, primarily intended for numerical computations. (Similar to [[UbuntuHelp:MATLAB|MATLAB]]). [http://www.octave.org/ Octave]
* [http://www.scicraft.org/ SciCraft] - Add-on to Octave, clones Simulink. Still in development, blocks have to be written by the user. It is supposed to specialize in bioinformatics functions.
* [http://scilabsoft.inria.fr/ Scilab] [http://packages.ubuntu.com/scilab {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png}}] - Another MATLAB-like application.
* [http://www.scicos.org/ SciCos] - A free Simulink-like add-on to Scilab.
* [http://maxima.sourceforge.net/ Maxima] [http://packages.ubuntu.com/maxima {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A computer algebra system (xmaxima is its X interface).
* [http://wxmaxima.sourceforge.net/ wxMaxima] [http://packages.ubuntu.com/wxmaxima {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A nice front end for Maxima.
* The wxmaxima package doesn't work in Ubuntu 6.06. Please go to the [[UbuntuHelp:wxMaxima|wxMaxima]] page in this wiki for a work around.
* Here is a [http://arxiv.org/html/cs.SC/0504039 tutorial] about using Te''''''Xmacs as a Maxima frontend
* [http://members3.jcom.home.ne.jp/imaxima/ imaxima] embeds a Maxima session in Emacs and uses [[UbuntuHelp:LaTeX|LaTeX]] to render output
* [http://www.swox.com/gmp/ GNU MP] [http://packages.ubuntu.com/libgmp3c2 {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=UbuntuGrey.png}}] - GNU Multi-Precision arithmetic library. Useful if you need to use very big numbers in a C program.
* <<Anchor(GSL)>>[http://www.gnu.org/software/gsl/ GSL] [http://packages.ubuntu.com/gsl-bin {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - The Gnu Scientific Library.
* [http://www.ooomacros.org/user.php#106652 OOStatistics] - A statistics macro for OpenOffice Calc.
* [http://www.freefem.org/ freefem] [http://packages.ubuntu.com/freefem {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A partial differential equation oriented language using Finite Element Method - 2D and 3D versions.
* [http://www.openfoam.org/ OpenFOAM] - A former commercial computational fluid dynamics code that is now under GPL, see end of this page and
* [[UbuntuHelp:OpenFOAM|OpenFOAM]] has instructions on how to install [[UbuntuHelp:OpenFOAM|OpenFOAM]] on Ubuntu.
* [http://www.scipy.org/ SciPy] [http://packages.ubuntu.com/python-scipy {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - An open source library of scientific tools for Python.
* [http://www.scipy.org/Cookbook SciPy CookBook]
* A [http://www.scipy.org/Topical_Software wiki page] similar to this one.
* [http://cens.ioc.ee/projects/f2py2e/ F2PY] [http://packages.ubuntu.com/python-f2py {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Fortran to Python interface generator provides a connection between Python and Fortran languages.
* [http://www.ginac.de/ GiNaC] [http://packages.ubuntu.com/ginac-tools {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - C++ library for symbolic computations.
* [http://www.sagemath.org/ SAGE] - An open source computer algebra system. Their goal is to create a viable free and open source alternative to the commercial programs Magma, Maple, Mathematica, and MATLAB.
* [[UbuntuHelp:Mathematica|Mathematica]] - A proprietary computer algebra system. [http://www.mathematica.com Mathematica]
* [[UbuntuHelp:Maple|Maple]] - A proprietary computer algebra system. [http://www.maplesoft.com Maple]
* [http://www.ittvis.com/idl/ IDL] - A proprietary data visualization & data analysis platform.
* [[UbuntuHelp:MATLAB|MATLAB]] - A proprietary numerical computing environment and programming language .[http://www.mathworks.com/ MATLAB]
* [[UbuntuHelp:GeoGebra|GeoGebra]] - A free and multi-platform dynamic mathematics software for schools that joins geometry, algebra and calculus. It received several international awards including the European and German educational software awards. [http://www.geogebra.org/ Geogebra]
* [http://pdl.perl.org/ PDL] [http://packages.ubuntu.com/pdl {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Perl Data Language is a powerful data mathematics and data manipulation package for Perl.
* [http://www.mupad.de/ Mupad] - A proprietary computer algebra system.
* [http://www.clucalc.info/ Clucalc] - A tool for 3D visualisations, Clifford algebras and scientific calculations.
* [http://sourceforge.net/projects/auto2000 AUTO 2000] - Software for continuation and bifurcation problems in ordinary differential equations.
* [http://www.gap-system.org/ GAP - Groups, Algorithms, Programming] [http://packages.ubuntu.com/gap {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - a System for Computational Discrete Algebra.
* [http://pari.math.u-bordeaux.fr/ Pari/GP] [http://packages.ubuntu.com/pari-gp {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - designed for fast computations in number theory.
* [http://www.mathematik.uni-muenchen.de/~forster/sw/aribas.html Aribas][http://packages.ubuntu.com/aribas {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - an interactive interpreter for big integer arithmetic and multi-precision floating point arithmetic
* [http://yacas.sourceforge.net/ Yacas] [http://packages.ubuntu.com/yacas {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - an easy to use, general purpose Computer Algebra System, a program for symbolic manipulation of mathematical expressions.
==== Statistics ====
* [http://www.spss.com/ SPSS] The propietary statistical reference package. Written in Java, since version 16 (currently 17) runs on Linux, although it has some problems with Compiz Fusion ('''Solution''':  ''sudo gedit /etc/environment''. Add at the end: ''AWT_TOOLKIT="MToolkit"''. Save and restart).
* [http://www.gnu.org/software/pspp/ PSPP/PSPPIRE]  It is intended as a free replacement of the proprietary program SPSS. PSPPIRE is the PSPP GUI. 
* [http://www.r-project.org/ R] [http://packages.ubuntu.com/r-base {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - for statistical computing and graphics.
* [http://stats.math.uni-augsburg.de/JGR/ JGR] - Java GUI for R.
* [http://rkward.sourceforge.net/ RKWard] [http://packages.ubuntu.com/rkward {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - An easy to use, transparent front end to the R language.
* [http://www.stat.auckland.ac.nz/~ihaka/120/ Some R tutorials and examples].
* [http://addictedtor.free.fr/graphiques/ R Graph Gallery] - Collection of graphics that can be created using R. Includes the R commands used to create the graphics.
=== Medicine ===
* [http://www.debian.org/devel/debian-med/ Debian-med] - A set of metapackages that Ubuntu inherits from Debian for medical practice and research.
* [http://www.nongnu.org/aeskulap/ Aeskulap] - A medical image viewer.
* [http://www.gnumed.org/ GNUmed] [http://packages.ubuntu.com/gnumed-common {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Medical practice software.
* [http://www.orcero.org/irbis/kradview/ kradview] - DICOM viewer.
* [http://www.openclinica.org/ OpenClinica] - A web-based Clinical Data Management Software (CDMS) platform for managing multi-site clinical research studies.
* [http://opendicom.sourceforge.net/ openDICOM.NET] - DICOM imaging software.
=== Physics ===
=== Physics ===
* [http://wwwasd.web.cern.ch/wwwasd/cernlib/ Cernlib] [http://packages.ubuntu.com/cernlib {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - 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.
* [http://wwwasd.web.cern.ch/wwwasd/cernlib/ Cernlib] [http://packages.ubuntu.com/cernlib {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - 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.
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* [http://www.mcstas.org/ McStas] - A neutron scattering instrument Monte Carlo simulation package, which simulates neutron spectrometers and beam lines.
* [http://www.mcstas.org/ McStas] - A neutron scattering instrument Monte Carlo simulation package, which simulates neutron spectrometers and beam lines.
''More Physics applications'' - [[UbuntuHelp:UbuntuScience/Physics|UbuntuScience/Physics]]
''More Physics applications'' - [[UbuntuHelp:UbuntuScience/Physics|UbuntuScience/Physics]]
=== Tools ===
== Ubuntu Packages: Science Section ==
* [http://sourceforge.net/projects/bika BIKA] - A laboratory information management system (LIMS) built on top of Zope and Plone, and coded in Python.
* [http://www.unipress.waw.pl/fityk Fityk][http://packages.ubuntu.com/fityk {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A curve fitting and data analysis program, specialized in peak fitting.
* [http://bumblebeeman.sourceforge.net/ Bumblebee] - A system for managing instruments and other resources (e.g. analytical equipment) that must be shared between a number of users.
* [http://www.frantz.fi/software/g3data.php g3data] [http://packages.ubuntu.com/g3data {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - "g3data is used for extracting data from graphs. In publications graphs often are included, but the actual data is missing. g3data makes the extracting process much easier."
==== Fortran Compilers ====
* [http://www.intel.com/cd/software/products/asmo-na/eng/compilers/282048.htm Intel Fortran Compiler 9.0] for noncommercial, nonacademic use. Please respect the license agreements. A step by step installation guide can be found here: http://www.ubuntuforums.org/showthread.php?t=89571 (Post by Chickenmonger)
* [http://gcc.gnu.org/wiki/GFortran gfortran][http://packages.ubuntu.com/gfortran {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - The GNU Fortran 95 compiler.
* [http://g95.sourceforge.net/ g95] - The goal of the g95 project is to create a free, open source Fortran 95 compiler and runtime libraries.
==== Plotting Tools ====
* [http://plplot.sourceforge.net PLplot] [http://packages.ubuntu.com/libplplot9 {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A powerful 2D and 3D scientific plotting library with C, C++, Fortran, Java, Python, Perl, Octave, and Tcl interfaces. Device plugins include X, wxWidgets, Gnome Canvas Widget, and Tk GUIs as well as Post''''''Script, PNG, JPEG, and GIF file devices.
* [http://www.gnuplot.info/ GNUplot] [http://packages.ubuntu.com/gnuplot {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A command-line driven 2D/3D plotting tool. Can perform data fitting and exports to PNG, PS, Xfig, and [[UbuntuHelp:LaTeX|LaTeX]] formats. Has python bindings (python-gnuplot) for including in other programs or scripts.
* [http://icculus.org/~jcspray/plotdrop/ plotdrop] [http://packages.ubuntu.com/plotdrop {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A minimal GNOME front end to GNUPlot.
* [http://t16web.lanl.gov/Kawano/gnuplot/index-e.html gnuplot tips (not so Frequently Asked Questions).]
* [http://plasma-gate.weizmann.ac.il/Grace/ grace][http://packages.ubuntu.com/grace {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A 2D WYSIWYG plotting tool that exports to JPEG, PNG, EPS, PDF, and SVG. Also does curve fitting.
* [http://www.astro.caltech.edu/~tjp/pgplot/ PGPLOT] [http://packages.ubuntu.com/pgplot5 {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png}}] - Fortran- or C-callable graphics subroutine package for making scientific graphs.
* [http://rlplot.sourceforge.net/ RLPlot] [http://packages.ubuntu.com/rlplot {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - RLPlot is a GUI based program for displaying scientific data in standard formats. It has full support for all error-bar types and it has greater flexibility with displaying colour and texture in charts than gnuplot (filled bar chart boxes are possible without any additional programs). Output is generated on the X display here further changes can be made to the graph using point and click methods. Images can be exported as scalable vector graphics (SVG) as well as EPS, WMF and TIFF formats.
* [http://glx.sourceforge.net/ Graphics Layout Engine] - '''GLE''' is a full featured scripting language that includes variables, subroutines, logic control, looping, a graphing tool, and more to produce high quality output. It has a full range of facilities for producing publication-quality graphs, diagrams, posters and slides. GLE provides [[UbuntuHelp:LaTeX|LaTeX]] quality fonts together with a flexible graphics module, which allows the user to specify any feature of a graph (down to the line width of the subticks, for example). Complex pictures can be drawn with user-defined subroutines and simple looping structures. Essentially, GLE is a scripting language and if you are used to writing software, using [[UbuntuHelp:LaTeX|LaTeX]], or any other non-WYSIWYG tools, then you will enjoy using GLE. An autopackage is also available.
* [http://scigraphica.sourceforge.net/ SciGraphica] [http://packages.ubuntu.com/scigraphica {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A scientific application for data analysis and technical graphics. Attempts to be a [http://www.originlab.com/ "Microcal Origin"] clone.
* [http://soft.proindependent.com/qtiplot.html Qtiplot ] [http://packages.ubuntu.com/qtiplot {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A 2D/3D, Qt based plotting tool that attempts to be another "Origin" clone.
* [http://labplot.sourceforge.net/ LabPlot] [http://packages.ubuntu.com/labplot {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Another Qt based 2D/3D GUI plotting tool that also does curve fitting, supports many data formats, [[UbuntuHelp:LaTeX]] labeling, [[UbuntuHelp:[GSL|GSL|[GSL|GSL]]] functions, and statistics.
* [http://home.gna.org/veusz/ Veusz] - A scientific plotting package written in Python.
* [http://gri.sourceforge.net/ Gri] [http://packages.ubuntu.com/gri {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A scientific graphics language.
* [http://matplotlib.sourceforge.net Matplotlib] [http://packages.ubuntu.com/python-matplotlib {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - a cross platform 2d plotting library for Python.
* [http://pyx.sourceforge.net/index.html PyX] [http://packages.ubuntu.com/python-pyx {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Python graphics package for the creation of Postscript and PDF files - useful for graphing.
* [http://mayavi.sourceforge.net/ MayaVi] [http://packages.ubuntu.com/mayavi {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - An easy to use scientific data visualizer.
* [http://www.paraview.org Paraview] - An application designed with the need to visualize large data sets in mind.
* [http://kst.kde.org/ kst] [http://packages.ubuntu.com/kst {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A plotting and data viewing program.
* [http://lybniz2.sourceforge.net/ Lybniz] [http://packages.ubuntu.com/lybniz {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A simple function graph plotter (graphic calculator), in Python and GTK. Ubuntu .deb available.
* [http://kde-apps.org/content/show.php?content=43071 Zhu3D] - Interactive 3D plotting program using OpenGL.
==== Plot Digitizers ====
* [http://plotdigitizer.sourceforge.net/ Plot Digitizer] - A Java program used to digitize scanned plots of functional data.
* [http://www.frantz.fi/software/g3data.php g3data] [http://packages.ubuntu.com/g3data {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A program for extracting data from graphs.
* [http://digitizer.sourceforge.net/ Engauge Digitizer] [http://packages.ubuntu.com/engauge-digitizer {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - a Qt-based system including zoom and curve-tracing functionality, apparently (it seemed a little unintuitive on my first play with it).
==== Image Processing Tools ====
* [http://rsb.info.nih.gov/ij/ ImageJ] - Java-based image processing.
* [http://www.vips.ecs.soton.ac.uk/index.php VIPS] [http://packages.ubuntu.com/libvips-tools {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A free image processing system.
==== Vector Drawing Tools ====
* [http://www.xfig.org Xfig] [http://packages.ubuntu.com/xfig {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A diagram and figure creation tool. Can import GIF, JPEG, and EPS figures and can export to Postscript, [[UbuntuHelp:LaTeX|LaTeX]], and bitmap files.
* [http://www.skencil.org Skencil] [http://packages.ubuntu.com/skencil {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - An excellent vector drawing package. Especially useful for creating and annotating existing Postscript figures. Numerous plugins are available, most notably a [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]] plugin. Can import many different formats.
* [http://bourbon.usc.edu/tgif/ Tgif] [http://packages.ubuntu.com/tgif {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Another excellent Postscript drawing program. Most suitable for black and white Postscript figures.
* [http://www.inkscape.org/ Inkscape] [http://packages.ubuntu.com/inkscape {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircle.png}}] - Excellent vector drawing program. Uses SVG format by default, but can write to EPS, PDF and [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]] with PSTricks macros, among other formats.
* [http://www.elisanet.fi/ptvirtan/software/textext/index.html Textext] Inkscape extension to add editable [[UbuntuHelp:LaTeX|LaTeX]] text objects to a document
* [http://www.gnome.org/projects/dia/ Dia] [http://packages.ubuntu.com/dia {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A "Visio" like diagram tool. Especially useful for simple circuits and flowcharts.
* [http://ipe.compgeom.org/ Ipe] [http://packages.ubuntu.com/ipe {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A drawing editor for creating figures in PDF or (encapsulated) Postscript format. Incorporates [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]] code quite well.
* [http://jpicedt.sourceforge.net/ jPicEdt] - Java based drawing program which can generate [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]], eepic and pstricks code from a user-friendly graphical interface.
* [http://latexdraw.sourceforge.net/ LaTeXDraw] - Java based drawing program which can generate and edit pstricks code for [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]].
==== Word Processing Tools ====
* [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]] https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=UbuntuGrey.png - WYGIWYW (What You Get Is What You Want) text mark up system. What scientists in several fields (e.g., physics, mathematics) write papers with. [http://www.latex-project.org/ LaTeX]
* [[UbuntuHelp:Lyx|Lyx]] [http://packages.ubuntu.com/lyx {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A WYSIWYM (What You See Is What You Mean) [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]] frontend. [http://www.lyx.org/ LyX]
* <<Anchor(Kile)>> [http://kile.sourceforge.net/ Kile] [http://packages.ubuntu.com/kile {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|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.
* [http://rlehy.free.fr/ ekee] - Allows you to write equations in [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]] and drag and drop them into other applications.
* [http://ooolatex.sourceforge.net/ OOoLatex] - A set of Open''''''Office macros designed to integrate [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]] equations.
* [http://www.conglomerate.org/ Conglomerate] [http://packages.ubuntu.com/conglomerate {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - An XML editor, to create [[UbuntuHelp:DocBook|DocBook]] or similar formats.
* [http://www.gnomefiles.org/app.php/Pytexipng/ Pytexipng] - A [[UbuntuHelp:LaTeX|LaTeX]] formula converter to png images using a nice GTK GUI. Pytexipng can convert a [[UbuntuHelp:LaTeX|LaTeX]] formula into a png image file that can be used on any WYSIWYG word processor application as Open``Office.org Writer, Abiword or KWord.
* [http://www.xm1math.net/texmaker/ Texmaker] [http://packages.ubuntu.com/texmaker {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Like [[UbuntuHelp:[Kile|Kile]]] but loads faster.
* [http://www.texmacs.org/ TeXmacs] [http://packages.ubuntu.com/texmacs {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A WYSIWYG scientific text editor.
* doubles as an interface for computer algebra systems like [Maxima], [[UbuntuHelp:Maple|Maple]], mupad, axiom, giac, GTybalt, Macaulay 2, pari, yacas.
* can also be used as a front end for [R], [[UbuntuHelp:Octave|Octave]], [GNUplot], [Xfig], [Dr. Geo], [Eukleides], [Qcl].
* [http://www.gnu.org/software/auctex/preview-latex.html preview-latex] https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - (almost) turns Emacs into a WYSIWYG-[[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]]-frontend.
* [http://wiki.lyx.org/LyX/InstantPreview Can also be used in lyx].
* [http://www.latex2html.org/ latex2html] [http://packages.ubuntu.com/latex2html {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png}}], [http://hutchinson.belmont.ma.us/tth/ tth] [http://packages.ubuntu.com/tth {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png}}] and [http://pauillac.inria.fr/~maranget/hevea/ hevea] [http://packages.ubuntu.com/hevea {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=UbuntuGrey.png}}] for converting [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]] to html.
* [http://sourceforge.net/projects/pidgin-latex/] - A small Pidgin (see [[UbuntuHelp:Pidgin|Pidgin]]) plugin that allows you to insert [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]] formulas into IM conversations.
* [[UbuntuHelp:MiktexPackageManager|MiktexPackageManager]] - is used to install TeX packages from a MiKTeX package repository. Can be used with other TeX systems. It is similar to apt-get for [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]]. [http://miktex.org/unx/ MiKTeX Tools]
==== Bibliographic Tools ====
* Bibtex https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=UbuntuGrey.png - A program and file format for bibliographies in [[UbuntuHelp:[[UbuntuHelp:LaTeX|LaTeX]]|[[UbuntuHelp:LaTeX|LaTeX]]]] documents.
* [http://www.tug.org/tex-archive/info/bibtex/tamethebeast/ttb_en.pdf A comprehensive Bibtex manual]
* [http://pybliographer.org/ Pybliographer ] [http://packages.ubuntu.com/pybliographer {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A tool for managing bibliographic databases. Pybliographer is the graphical interface.
* [http://jabref.sourceforge.net/ Jabref] [http://packages.ubuntu.com/jabref {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png}}] - A Java-based BibTeX bibliography manager that can be used in conjunction with LyX.
* [http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ KBibTeX] [http://packages.ubuntu.com/kbibtex {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A BibTeX editor for KDE.
* Ubuntu:Bibus - Bibus is a bibliographic database. Bibus works with Open''''''Office.org 2.0. [http://bibus-biblio.sourceforge.net/ Bibus]
* [http://www.scripps.edu/~cdputnam/software/bibutils/ Bibutils] - Collection of command line tools for bibliography format convertion. Format examples: BiBTeX, RIS, End''''''Note, COPAC, ISI, Pub''''''Med...
* [http://icculus.org/~jcspray/referencer/ Referencer] [http://packages.ubuntu.com/referencer {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Referencer is a Gnome application to organize documents or references, and ultimately generate a BibTeX bibliography file. Features include: Automatic metadata retrieval; smart web links; import from BibTeX, Reference Manager and EndNote; tagging.
* [http://www.periapsis.org/tellico/ Tellico] [http://packages.ubuntu.com/tellico {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A KDE application for organizing your collections. It allows to add special tags to entries, and sort entries along any field (author, year, keywords, etc.).
* [http://alexandria.rubyforge.org/ Alexandria] [http://packages.ubuntu.com/alexandria {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A Gnome application for organizing your book collections. It allows to  sort entries along any field (author, year, etc.), and to retrieve book information from Internet.
* [http://www.molspaces.com/cb2bib/ cb2Bib] - The cb2Bib is a tool for rapidly extracting unformatted, or unstandardized, bibliographic references from email alerts, journal Web pages, and PDF files.
* The cb2Bib reads the clipboard text contents and process it against a set of predefined patterns. If this automatic detection is successful, cb2Bib formats the clipboard data according to the structured BibTeX reference standard.
* Otherwise, if no predefined format pattern is found or if detection proves to be difficult, manual data extraction is greatly simplified by cb2Bib. In most cases, such manual data extraction will provide with a new, personalized pattern to be included within the predefined pattern set for future automatic extractions.
* Once the bibliographic reference is correctly extracted, it is added to a specified BibTeX database file. Optionally, article PDF files, if available, are renamed to its citeID and moved to a desired directory as a personal article library.
==== Distributed Computing ====
* [http://openmosix.sourceforge.net/ openmosix] - Turns a network of ordinary computers into a supercomputer.
* [http://boinc.berkeley.edu/ BOINC] [http://packages.ubuntu.com/boinc-client {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A software platform for distributed computing using volunteered computer resources.
* Projects include: Climateprediction.net, Einstein@Home, LHC@home, Predictor@home, SETI@home.
* [http://gridcafe.web.cern.ch/gridcafe/whatisgrid/whatis.html the Grid@CERN] - From the people who brought you the world wide web, a service for sharing computer power and data storage which aims ultimately to turn the global network of computers into one vast computational resource.
* [[UbuntuHelp:FoldingAtHome|FoldingAtHome]] - A protein folding simulation run by the Stanford University.
== Ubuntu Packages ==
===== Science Section =====
[http://packages.ubuntu.com/feisty/science/ 7.04],
[http://packages.ubuntu.com/feisty/science/ 7.04],
[http://packages.ubuntu.com/gutsy/science/ 7.10],
[http://packages.ubuntu.com/gutsy/science/ 7.10],
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[http://packages.ubuntu.com/intrepid/science/ 8.10],
[http://packages.ubuntu.com/intrepid/science/ 8.10],
[http://packages.ubuntu.com/jaunty/science/  9.04 ].
[http://packages.ubuntu.com/jaunty/science/  9.04 ].
===== Mathematics Section =====
[http://packages.ubuntu.com/feisty/math/ 7.04],
[http://packages.ubuntu.com/gutsy/math/ 7.10],
[http://packages.ubuntu.com/heron/math/ 8.04],
[http://packages.ubuntu.com/intrepid/math/ 8.10],
[http://packages.ubuntu.com/jaunty/math/  9.04 ].
===== TeX Section =====
[http://packages.ubuntu.com/feisty/tex/ 7.04],
[http://packages.ubuntu.com/gutsy/tex/ 7.10],
[http://packages.ubuntu.com/heron/tex/ 8.04],
[http://packages.ubuntu.com/intrepid/tex/ 8.10],
[http://packages.ubuntu.com/jaunty/tex/  9.04 ].
== Alternatives to Proprietary Scientific Software ==
== Alternatives to Proprietary Scientific Software ==
See [[UbuntuHelp:UbuntuScience/AlternativesToProprietarySoftware|UbuntuScience/AlternativesToProprietarySoftware]]
See [[UbuntuHelp:UbuntuScience/AlternativesToProprietarySoftware|UbuntuScience/AlternativesToProprietarySoftware]]
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* EPICS - A set of Open Source software tools, libraries and applications to create distributed soft real-time control systems for scientific instruments such as a particle accelerators, telescopes and other large scientific experiments. [http://www.aps.anl.gov/epics/index.php]
* EPICS - A set of Open Source software tools, libraries and applications to create distributed soft real-time control systems for scientific instruments such as a particle accelerators, telescopes and other large scientific experiments. [http://www.aps.anl.gov/epics/index.php]
== Other information ==
== Other information ==
* [[UbuntuHelp:UbuntuScience/Howto|UbuntuScience/Howto]] (still a work in progress....)
=== Other Linux Distributions for Scientists ===
=== Other Linux Distributions for Scientists ===
* [http://scubuntu.meraka.org.za/wiki  Scubuntu] - The aim of the Scubuntu project is to develop a flavour of Ubuntu Linux for use by scientists.
* [http://scubuntu.meraka.org.za/wiki  Scubuntu] - The aim of the Scubuntu project is to develop a flavour of Ubuntu Linux for use by scientists.
* [http://dirk.eddelbuettel.com/quantian.html Quantian] - A Knoppix / Debian variant tailored to numerical and quantitative analysis.
* [http://dirk.eddelbuettel.com/quantian.html Quantian] - A Knoppix / Debian variant tailored to numerical and quantitative analysis.
* [http://www.debian.org/devel/debian-med/ 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: <code><nowiki> apt-cache search debian-med </nowiki></code>
* [https://www.scientificlinux.org/ Scientific Linux] - Linux release put together by Fermilab and CERN based on RH
* [https://www.scientificlinux.org/ Scientific Linux] - Linux release put together by Fermilab and CERN based on RH
* [http://groundstate.ca/mdk4chem Madrake4Chemistry] - Mandrake Linux for chemistry
* [http://groundstate.ca/mdk4chem Madrake4Chemistry] - Mandrake Linux for chemistry
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* [http://sal.iatp.by/ SAL] (Scientific Applications on Linux) is a collection of information and links to software that will be of interest to scientists and engineers. Not updated since 2001.
* [http://sal.iatp.by/ SAL] (Scientific Applications on Linux) is a collection of information and links to software that will be of interest to scientists and engineers. Not updated since 2001.
* [http://scibuntu.sourceforge.net/ Scibuntu] - A script to install scientific tools.
* [http://scibuntu.sourceforge.net/ Scibuntu] - A script to install scientific tools.
=== Books ===
----
----
[[category:CategoryScience]]
[[category:CategoryScience]]


[[category:UbuntuHelp]]
[[category:UbuntuHelp]]

2010年5月20日 (四) 00:34的最新版本

{{#ifexist: :UbuntuScience/zh | | {{#ifexist: UbuntuScience/zh | | {{#ifeq: {{#titleparts:UbuntuScience|1|-1|}} | zh | | }} }} }} {{#ifeq: {{#titleparts:UbuntuScience|1|-1|}} | zh | | }}

Legend: IconsPage?action=AttachFile&do=get&target=iconCircle.png - installed by default in Ubuntu <
> IconsPage?action=AttachFile&do=get&target=IconKubuntuCircle.png - installed by default in Kubuntu <
> IconsPage?action=AttachFile&do=get&target=edubuntu.png - installed by default in Edubuntu <
> IconsPage?action=AttachFile&do=get&target=UbuntuGrey.png - Main (officially supported) Ubuntu repository, not installed by default <
> IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Universe (community maintained) repository <
> IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - Multiverse (non-free) repository <
> Those installed by default are in Main (officially supported) Ubuntu repository. For information about the Ubuntu repositories see Repositories. Clicking on the icon next a program should take you to information about the Ubuntu package.

Astronomy

More Astronomy applications - UbuntuScience/Astronomy

Biology

More Biology applications - UbuntuScience/Biology

Biophysics

Chemistry

Earth Sciences (Geology/Geography)

Ecology and Environmental Sciences

  • Swarm - A conceptual framework for designing, describing, and conducting experiments on ABMs.
  • Repast - The Recursive Porous Agent Simulation Toolkit.
  • NetLogo - A Java-based programmable modeling environment for simulating natural and social phenomena.
  • Simile - A proprietary ($$$) System Dynamics and object-based modeling and simulation software package similar to Stella, Model Maker, Vensim, etc. It is advertised as "Visual modeling software for the earth, environmental and life sciences". A free evaluation version, which limits the size of saved models, is available.

Physics

More Physics applications - UbuntuScience/Physics

Ubuntu Packages: Science Section

7.04, 7.10, 8.04, 8.10, 9.04 .

Alternatives to Proprietary Scientific Software

See UbuntuScience/AlternativesToProprietarySoftware

Hardware

  • Labview for linux (non-free) [1]

Data acquisition

  • National Instruments GPIB drivers for linux. [2]
  • 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. [3]
  • EPICS - A set of Open Source software tools, libraries and applications to create distributed soft real-time control systems for scientific instruments such as a particle accelerators, telescopes and other large scientific experiments. [4]

Other information

Other Linux Distributions for Scientists

Unofficial Ubuntu/Debian repositories with science software

Mailing Lists about Linux and Science

Related Wiki Pages

Online Forums

Ubuntu Education & Science Forum Some forum threads

Links