查看“特殊:Badtitle/NS100:UbuntuScience”的源代码

{{From|https://help.ubuntu.com/community/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.

== 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]] (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=IconKubuntuCircle.png - installed by default in Kubuntu <br>
https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=edubuntu.png - installed by default in Edubuntu <br>
https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=UbuntuGrey.png - Main (officially supported) Ubuntu repository, not installed by default <br>
https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Universe (community maintained) repository <br>
https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - Multiverse (non-free) repository <br>

For information about the Ubuntu repositories see [[UbuntuHelp:Repositories]]. Clicking on the icon next a program should take you to information about the Ubuntu package.

=== Astronomy ===

* [http://edu.kde.org/kstars/ KStars] [http://packages.ubuntu.com/kstars  https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=edubuntu.png]- A virtual planetarium.

* [http://www.clearskyinstitute.com/xephem/index.html XEphem] - A very comprehensive ephemeris/planetarium. Old interface.

* [http://www.hs.uni-hamburg.de/DE/Ins/Per/Wichmann/Nightfall.html Nightfall] -  An astronomy application for fun, education, and science.

* [http://www.stellarium.org/ Stellarium] [http://packages.ubuntu.com/stellarium  https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png]- Stellarium is a free open source planetarium that shows a realistic sky in 3D, just like what you see with the naked eye, binoculars or a telescope.

* [http://earth.google.com/ Google Earth] - 3D earth viewing application includes a sky view.

''More Astronomy applications'' - [[UbuntuHelp:UbuntuScience/Astronomy]]

=== Biology ===

* [http://www.bioperl.org BioPerl] [http://packages.ubuntu.com/bioperl https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - a collection of Perl modules that are useful for programmers in bioinformatics/biology
* also see [http://www.biojava.org BioJava] and [http://www.biopython.org BioPython]

* [http://darwin.zoology.gla.ac.uk/%7Erpage/treeviewx/index.html Tree View X] [http://packages.ubuntu.com/treeviewx https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - Tree View X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs).

* [http://www.tree-puzzle.de/ Tree-puzzle] [http://packages.ubuntu.com/tree-puzzle https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.

* [[Anchor(ITK)]][http://www.itk.org/ Insight Toolkit (ITK)] - an open-source software toolkit for performing registration and segmentation.   Created to support the [http://www.nlm.nih.gov/research/visible/visible_human.html Visible Human Project ].
*** [http://www.cs.mu.oz.au/~gavinb/projects/itk.php unofficial debian packages ]

''More Biology applications'' - [[UbuntuHelp:UbuntuScience/Biology]]

=== Biophysics ===

* [http://pymol.sourceforge.net/ Pymol] [http://packages.ubuntu.com/pymol https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - An open source visualization program. Reads many formats, including crystallographic map files

* [http://www.ysbl.york.ac.uk/~emsley/coot/ Coot] - Superb tool for crystallographers

* [http://www.ks.uiuc.edu/Research/vmd/ VMD] - Another visualization program, this one better suited for reading trajectories from simulations, or generating custom graphics. Takes Tcl and Python scripts, making it very flexible. Also includes good built in analysis tools, such as Vol''''''Map


=== Chemistry ===

* [http://www.nongnu.org/gchempaint/ GChemPaint] [http://packages.ubuntu.com/gchempaint https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - A 2D chemical structures editor.

* [http://www.uku.fi/%7Ethassine/ghemical/ ghemical] [http://packages.ubuntu.com/ghemical https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - A molecular modeling and computational chemistry package that provides molecular mechanics, semi-empirical (''via'' MOPAC7), and ''ab initio'' (''via'' MPQC) calculations.

* [http://gdis.seul.org/ gdis] [http://packages.ubuntu.com/gdis https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - A molecular display program that supports OpenGL and POVRay rendering.

* [http://openbabel.sourceforge.net/ OpenBabel][http://packages.ubuntu.com/openbabel https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - A chemical file format conversion program.

* [http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html Chemtool][http://packages.ubuntu.com/chemtool https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - 2D molecule drawing programs similar to Chem''''''Draw.

* [http://xdrawchem.sourceforge.net/ xdrawchem] [http://packages.ubuntu.com/xdrawchem https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - 2D molecule drawing programs similar to Chem''''''Draw.

* [http://www.chemicalinventory.org chemicalInventory] - A free chemical inventory database using JChem for structure searching.

* [http://www.mpqc.org/ mpqc] [http://packages.ubuntu.com/mpqc https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - The Massively Parallel Quantum Chemistry Program. ''Ab initio'' quantum chemical computational package.

* [http://www.redbrick.dcu.ie/~noel/linux4chemistry/linux4chemistry.py Linux4Chemistry] - List of Linux applications that may be useful for chemists.

* [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.

=== Computer Science ===

=== 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://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 PostgreSQL/PostGIS, projection on-the-fly, map composition, and a number of other features via a plugin interface.

* [http://meteora.ucsd.edu/~pierce/ncview_home_page.html ncview] - A very fast program for viewing netCDF files (a standard widely used in meteorology, climate and oceanography).

* [http://gmt.soest.hawaii.edu/ Generic Mapping Tools (GMT)] [http://packages.ubuntu.com/gmt https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - GMT is an open source collection of ~60 tools for manipulating geographic and Cartesian data sets (including filtering, trend  fitting, gridding, projecting, etc.) and producing Encapsulated Post''''''Script File (EPS) illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3-D perspective views.

* [http://ww2d.csoft.net/index.php?title=Introduction WW2D] - Java based application similar to NASA World Wind or Google Earth software.

* [http://earth.google.com/ Google Earth] - 3D earth viewing application using satellite images (no cost but proprietary).

* [http://thuban.intevation.org/ Thuban] [http://packages.ubuntu.com/thuban https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - An interactive geographic data viewer.

* [http://www.survex.com/ Survex] [http://packages.ubuntu.com/survex https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - Cave surveying and mapping software.

* [http://therion.speleo.sk/ Therion] [http://packages.ubuntu.com/therion https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - Cave surveying - 2D and 3D drawing software.

* [http://grads.iges.org/grads/head.html Grads] - Very fast graphics program for looking at meteorological data. Movies are very fast.

=== Ecology and Environmental Sciences ===

* [http://www.swarm.org/wiki/Main_Page Swarm] - A conceptual framework for designing, describing, and conducting experiments on ABMs.

* [http://repast.sourceforge.net/ Repast] - The Recursive Porous Agent Simulation Toolkit.

* [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.

=== 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'd 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 writen 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 Computer Aided Design application. It is available in the universe repositories.

* [http://www.cycas.de/ CyCAS ] - A commercial Computer Aided Design application that runs on Linux. There is a public version available.

* [http://www.ptc.com/appserver/mkt/products/home.jsp?k=403  Pro/ENGINEER] - A commerical mechanical engineering and design CAD tool.

* [http://www.tech-edv.co.at/lunix/CADlinks.html A list of CAD software for Linux]

=== Mathematics ===

* [http://gnudatalanguage.sourceforge.net/ GDL] - 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]] [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]]). [http://www.octave.org/ Octave]

* [http://www.scicraft.org/ 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.

* [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 addon 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]] 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]] 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]] has instructions on how to install 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]] - A proprietary computer algebra system. [http://www.mathematica.com Mathematica]

* [[UbuntuHelp: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]] - A proprietary numerical computing environment and programming language .[http://www.mathworks.com/ Matlab]

* [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] [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] [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][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] [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.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 ===

* [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://lightspeed.sourceforge.net/ Lightspeed] [http://packages.ubuntu.com/lightspeed https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - An OpenGL-based program developed to illustrate the effects of special relativity on the appearance of moving objects.

* [http://jaxodraw.sourceforge.net JaxoDraw] - A [[UbuntuHelp:Java]] program for drawing Feynman diagrams.

* [[Anchor(ROOT)]][http://root.cern.ch ROOT] - An object oriented data analysis framework.

* [http://www.hepforge.org/ HepForge] - A website hosting high energy physics (HEP) software development projects - ie. Sourceforge for (HEP).  [http://www.hepforge.org/projects HepForge Projects]

''More Physics applications'' - [[UbuntuHelp:UbuntuScience/Physics]]

=== Tools ===

*  [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 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 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 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 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 ] - 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, [[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. For instructions on compliling from source see the MatPlotLibHowTo.

* [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 avaliable.

* [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/g3data 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 Postscipt, [[UbuntuHelp: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: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:LaTeX]] with PSTricks macros, among other formats.

* [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:LaTeX]] code quite well.

* [http://jpicedt.sourceforge.net/ jPicEdt] - Java based drawing program which can generate [[UbuntuHelp: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:LaTeX]].

==== Word Processing Tools ====

* [[UbuntuHelp: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]] https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A WYSIWYM (What You See Is What You Mean) [[UbuntuHelp:LaTeX]] frontend. [http://www.lyx.org/ Lyx]

* [[Anchor(Kile)]] [http://kile.sourceforge.net/ Kile] https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A [[UbuntuHelp: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/ eqe] - Allows you to write equations in [[UbuntuHelp:LaTeX]] and drag and drop them into other applications.

* [http://ooolatex.sourceforge.net/ OOoLatex] - A set of Open''''''Office macros designed to integrate [[UbuntuHelp:LaTeX]] equations.

* [http://www.conglomerate.org/ Conglomerate] https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - An XML editor, to create DocBook or similar formats.

* [http://www.gnomefiles.org/app.php/Pytexipng/ Pytexipng] - A LaTeX formula converter to png images using a nice GTK gui. Pytexipng can convert a 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] https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Like [[Kile Kile]] but loads faster.

* [http://www.texmacs.org/ TeXmacs] https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png  - A WYSIWIG scientific text editor.
*** doubles  as an interface for computer algebra systems like [Maxima], [[UbuntuHelp:Maple]],  mupad,  axiom, giac,  GTybalt, Macaulay 2, pari, yacas.
*** can also be used as a front end for [R], [[UbuntuHelp: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:LaTeX]]-frontend.
*** [http://wiki.lyx.org/LyX/InstantPreview Can also be used in lyx].

* [http://www.latex2html.org/ latex2html] https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png , [http://hutchinson.belmont.ma.us/tth/ tth]https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png and [http://pauillac.inria.fr/~maranget/hevea/ hevea] https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=UbuntuGrey.png for converting [[UbuntuHelp:LaTeX]] to html.

* [http://sourceforge.net/projects/pidgin-latex/] - A small Pidgin (see [[UbuntuHelp:GaimHowto]]) plugin that allows you to insert [[UbuntuHelp:LaTeX]] formulas into IM conversations.

* [[UbuntuHelp: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: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:LaTeX]] documents.
*** [http://www.tug.org/tex-archive/info/bibtex/tamethebeast/ttb_en.pdf A comprehesive 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] - A Java-based BibTeX bibliography manager that can be used in conjunction with Lyx.

* [http://www.unix-ag.uni-kl.de/~fischer/kbibtex/ 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] - 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]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]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, biblographic 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]] - A protein folding simulation run by the Stanford University.


== Ubuntu Packages  ==

===== Science Section =====

[http://packages.ubuntu.com/dapper/science/  6.06],
[http://packages.ubuntu.com/edgy/science/  6.10],
[http://packages.ubuntu.com/feisty/science/  7.04],
[http://packages.ubuntu.com/gutsy/science/  7.10].

===== Mathematics Section =====

[http://packages.ubuntu.com/dapper/math/  6.06],
[http://packages.ubuntu.com/edgy/math/  6.10],
[http://packages.ubuntu.com/feisty/math/  7.04],
[http://packages.ubuntu.com/gutsy/math/  7.10],

===== TeX Section =====

[http://packages.ubuntu.com/dapper/tex/  6.06],
[http://packages.ubuntu.com/edgy/tex/  6.10],
[http://packages.ubuntu.com/feisty/tex/  7.04],
[http://packages.ubuntu.com/gutsy/tex/  7.10].

== Alternatives to Proprietary Scientific Software ==

See [[UbuntuHelp:UbuntuScience/AlternativesToProprietarySoftware]]

== 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. [http://www.comedi.org/ comedi]

=== Computer controlled systems ===

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

* 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 Linux Distributions for Scientists ===

* [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

* [http://groundstate.ca/mdk4chem Madrake4Chemistry] - Mandrake Linux for chemistry

* [http://pluto.htu.tuwien.ac.at TUn!x] - A new project especially designed for the Technical University of Vienna. See also: http://informatik.tuwien.ac.at/tunix 

* [http://poseidon.furg.br/ Poseidon Linux ] - A Brazilian distribution designed for academic and scientific use.

* [http://www.xplora.org/ww/en/pub/xplora/library/software/xplora<u>_dvd_knoppix</u>make_sci.htm Xplora] - A Knoppix/Debian based DVD which aims to make science accessible for schools.

* [http://www.caelinux.com/CMS/ CAELinux] - A liveDVD linux for Computer Aided Engineering.

=== Unofficial Ubuntu/Debian repositories with science software ===

* [http://mirror.phy.bnl.gov/debian-root/ repository] of [[ROOT ROOT]] packages
* [http://lists.debian.org/debian-science/2005/08/msg00001.html Yaroslav Halchenko] [http://www.onerussian.com/debian/ repository]
* [http://www.cs.mu.oz.au/~gavinb/projects/itk.php repository] of [[ITK ITK]] Packages
* [http://lists.debian.org/debian-science/2005/08/msg00133.html Teemu Ikonen] [http://mentors.debian.net/debian repository]

* Daniel Leidert [http://debian.wgdd.de/debian/ repository] ( [http://debian.wgdd.de/repository read])

* [http://lists.debian.org/debian-science/2005/08/msg00008.html Carlo Segre] [http://fermi.phys.iit.edu/debian/ repository]

* [http://scientificcomputing.net/ Balbir Thomas] [http://scientificcomputing.net/debian/packages/ repository]

=== Mailing Lists about Linux and Science ===

* [https://lists.ubuntu.com/mailman/listinfo/ubuntu-motu-science Ubuntu MOTU Science mailing list]

* [http://lists.debian.org/debian-science/ debian-science mailing list ]


=== Related Wiki Pages ===

* Ubuntu:MOTU/Teams/Science is the Ubuntu:MOTU team responsible for the upkeep of science packages within the Universe repository.

* Ubuntu:UbuntuSciencePackages is a list of packages that are in the official Ubuntu Repositories  that scientists use.

* Ubuntu:UbuntuScienceMetaPackages discusses possible science metapackages

* [[UbuntuHelp:OpenFOAM]] - How to install Open''''''FOAM on Ubuntu.

* [[UbuntuHelp:UbuntuScience/Astronomy]]

* [[UbuntuHelp:UbuntuScience/Biology]]

* [[UbuntuHelp:UbuntuScience/Physics]]

* [[UbuntuHelp:UbuntuScience/AlternativesToProprietarySoftware]]

=== Online Forums ===

[http://www.ubuntuforums.org/forumdisplay.php?f=169 Ubuntu Education & Science Forum]

Some forum threads

* [http://www.ubuntuforums.org/showthread.php?t=29919 Are there any scientists-biologists out there using Ubuntu?]

* [http://ubuntuforums.org/showthread.php?p=329324 Ubuntu Science Metapackage]

* [http://www.ubuntuforums.org/showthread.php?t=150310 Scientific Software options for Ubuntu]

* [http://ubuntuforums.org/showthread.php?t=156298 Scientific Ubuntu, installing OpenFOAM CFD software]

* [http://www.ubuntuforums.org/showthread.php?t=161490 How To install ELMER Multiphysics software]

=== Links ===

* [http://wiki.debian.net/?DebianScience DebianScience]

* [http://sourceforge.net/softwaremap/trove_list.php?form_cat=97 sourceforge] - Scientific software on sourceforge.

* [http://debianlinux.net/science.html DebianLinux.Net-Scientific Software] - Links to science software.

* [http://freshmeat.net/browse/97/ freshmeat] - Scientific software on freshmeat.

* [http://linuxappfinder.com/category1.php?cat1=Scientific%20amp%20Engineering Linux App finder - Science/Engineering Section]

* [http://www.desktoplinux.com/directory/Application_software/Scientific/ DesktopLinux.com Linux software - Science Section]
* [http://www.linuxlinks.com/Software/Scientific/] - Scientific linux software.

* [http://www.gnomefiles.org/category.php?cat_id=6 gnome-files - scientific software] - Scientific apps for gnome.

* [http://www.kde-apps.org/index.php?xcontentmode=280&PHPSESSID=24670ac4d0dfebdc067bdf158b01ac44 kde-apps.org- scientific software] - Scientific apps for kde.

* [http://freescience.info Free Science] - Free''''''Science provides free scientific books and software.

* [http://www.jlab.org/~semenov/rlinks/soft.html Physics Related Software Manuals/Links].

* [http://www.educypedia.be/ Educypedia] - Sollection of links about scientific and educational material.

* [http://www.openscience.org/blog/?page_id=44 The Openscience Project] - Dedicated to writing and releasing free and Open Source scientific software.

* [http://www.open-bio.org Open Bioinformatics] - A non profit, volunteer run organization focused on supporting open source programming in bioinformatics.

* [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.


=== Books ===


----
[[category:CategoryDocumentation]] [[category:CategoryScience]]

[[category:UbuntuHelp]]