特殊:Badtitle/NS100:UbuntuScience:修订间差异

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=== Biology ===
=== 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
* [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]
* 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://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.
* [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 ].
* [[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 ]
* [http://www.cs.mu.oz.au/~gavinb/projects/itk.php unofficial debian packages ]
''More Biology applications'' - [[UbuntuHelp:UbuntuScience/Biology|UbuntuScience/Biology]]
''More Biology applications'' - [[UbuntuHelp:UbuntuScience/Biology|UbuntuScience/Biology]]
=== Biophysics ===
=== Biophysics ===
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* [http://www.scicos.org/ SciCos] - A free Simulink-like addon to Scilab.
* [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://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.
* [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.
* 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
* 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://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.
* [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.
* [[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.
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* [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.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
* [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.
* [[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/ 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]
* [http://www.scipy.org/Cookbook SciPy CookBook]
*** A [http://www.scipy.org/Topical_Software wiki page] similar to this one.
* 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://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.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.
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==== Statistics ====
==== 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://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://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://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://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.
* [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 ===
=== 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.debian.org/devel/debian-med/ Debian-med] - A set of metapackages that Ubuntu inherits from Debian for medical practice and research.
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* [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://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://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://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://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://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://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.
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* [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.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.
* [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|Maple]],  mupad,  axiom, giac,  GTybalt, Macaulay 2, pari, yacas.
* 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].
* 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:LaTeX|LaTeX]]-frontend.
* [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|LaTeX]]-frontend.
** [http://wiki.lyx.org/LyX/InstantPreview Can also be used in lyx].
* [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|LaTeX]] to html.
* [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|LaTeX]] to html.
* [http://sourceforge.net/projects/pidgin-latex/] - A small Pidgin (see [[UbuntuHelp:GaimHowto|GaimHowto]]) plugin that allows you to insert [[UbuntuHelp:LaTeX|LaTeX]] formulas into IM conversations.
* [http://sourceforge.net/projects/pidgin-latex/] - A small Pidgin (see [[UbuntuHelp:GaimHowto|GaimHowto]]) plugin that allows you to insert [[UbuntuHelp:LaTeX|LaTeX]] formulas into IM conversations.
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==== Bibliographic  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|LaTeX]] documents.
* Bibtex https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=UbuntuGrey.png - A program and file format for bibliographies in [[UbuntuHelp:LaTeX|LaTeX]] documents.
** [http://www.tug.org/tex-archive/info/bibtex/tamethebeast/ttb_en.pdf A comprehesive Bibtex manual]
* [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://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://jabref.sourceforge.net/ Jabref] - A Java-based BibTeX bibliography manager that can be used in conjunction with Lyx.
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* [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://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.
* [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.
* 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.
* 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.
* 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  ====
==== Distributed Computing  ====
* [http://openmosix.sourceforge.net/ openmosix] - Turns a network of ordinary computers into a supercomputer.
* [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.
* [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.
* 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.
* [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.
* [[UbuntuHelp:FoldingAtHome|FoldingAtHome]] - A protein folding simulation run by the Stanford University.
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* [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.
* [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>
* 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

2007年12月6日 (四) 15:46的版本

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

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 UbuntuScience/Howto (Still a work in progress....)

Applications

Some applications that scientists use in Linux. Please add some more.

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
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

  • KStars IconsPage?action=AttachFile&do=get&target=edubuntu.png- A virtual planetarium.
  • XEphem - A very comprehensive ephemeris/planetarium. Old interface.
  • Nightfall - An astronomy application for fun, education, and science.
  • Stellarium 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.
  • Google Earth - 3D earth viewing application includes a sky view.

More Astronomy applications - UbuntuScience/Astronomy

Biology

  • BioPerl IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - a collection of Perl modules that are useful for programmers in bioinformatics/biology
  • also see BioJava and BioPython
  • Tree View X 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).
  • Tree-puzzle 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)Insight Toolkit (ITK) - an open-source software toolkit for performing registration and segmentation. Created to support the Visible Human Project .
  • unofficial debian packages

More Biology applications - UbuntuScience/Biology

Biophysics

  • Pymol IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - An open source visualization program. Reads many formats, including crystallographic map files
  • Coot - Superb tool for crystallographers
  • 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

  • GChemPaint IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A 2D chemical structures editor.
  • ghemical 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.
  • gdis IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A molecular display program that supports OpenGL and POVRay rendering.
  • OpenBabelIconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A chemical file format conversion program.
  • ChemtoolIconsPage?action=AttachFile&do=get&target=iconCircleUn.png - 2D molecule drawing programs similar to Chem'Draw.
  • xdrawchem IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - 2D molecule drawing programs similar to Chem'Draw.
  • chemicalInventory - A free chemical inventory database using JChem for structure searching.
  • mpqc IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - The Massively Parallel Quantum Chemistry Program. Ab initio quantum chemical computational package.
  • Linux4Chemistry - List of Linux applications that may be useful for chemists.
  • GROMACS 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.
  • GRASS 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.
  • QGIS 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.
  • ncview - A very fast program for viewing netCDF files (a standard widely used in meteorology, climate and oceanography).
  • Generic Mapping Tools (GMT) 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.
  • WW2D - Java based application similar to NASA World Wind or Google Earth software.
  • Google Earth - 3D earth viewing application using satellite images (no cost but proprietary).
  • Thuban IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - An interactive geographic data viewer.
  • Survex IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Cave surveying and mapping software.
  • Therion IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Cave surveying - 2D and 3D drawing software.
  • Grads - Very fast graphics program for looking at meteorological data. Movies are very fast.

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.

Econometrics

  • Gretl IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - The GNU Regression, Econometric and Time-Series Library (gretl) is a package for econometric analysis.

Electronics

  • Eagle IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - A printed circuit board design tool.
  • oregano IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Schematic capture, netlists, and spice for simulations.
  • gEDA IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - GPL'd suite of Electronic Design Automation tools.
  • Qucs IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - An integrated circuit simulator.
  • Icarus Verilog 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

  • QCad IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A Computer Aided Design application. It is available in the universe repositories.
  • CyCAS - A commercial Computer Aided Design application that runs on Linux. There is a public version available.
  • Pro/ENGINEER - A commerical mechanical engineering and design CAD tool.
  • A list of CAD software for Linux

Mathematics

  • 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.).
  • Octave IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - GNU Octave is a high-level language, primarily intended for numerical computations. (Similar to MATLAB). Octave
  • SciCraft - Addon to Octave, clones Simulink. Still in developement, blocks have to be written by the user. It is supposed to specialize in bioinformatics functions.
  • Scilab IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - Another MATLAB-like application.
  • SciCos - A free Simulink-like addon to Scilab.
  • Maxima IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A computer algebra system (xmaxima is its X interface).
  • wxMaxima 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 wxMaxima page in this wiki for a work around.
  • Here is a tutorial about using Te'Xmacs as a Maxima frontend
  • imaxima embeds a maxima session in emacs and uses LaTeX to render output
  • GNU MP 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)GSL IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - The Gnu Scientific Library.
  • OOStatistics - A statistics macro for OpenOffice Calc.
  • freefem IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A partial differential equation oriented language using Finite Element Method - 2D and 3D versions.
  • OpenFOAM - A former commercial computational fluid dynamics code that is now under GPL, see end of this page and
  • OpenFOAM has instructions on how to install OpenFOAM on Ubuntu.
  • SciPy IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - An open source library of scientific tools for Python.
  • SciPy CookBook
  • A wiki page similar to this one.
  • F2PY IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Fortran to Python interface generator provides a connection between Python and Fortran languages.
  • GiNaC IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - C++ library for symbolic computations.
  • 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.
  • Mathematica - A proprietary computer algebra system. Mathematica
  • Maple - A proprietary computer algebra system. Maple
  • IDL - A proprietary data visualization & data analysis platform.
  • MATLAB - A proprietary numerical computing environment and programming language .Matlab
  • PDL IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Perl Data Language is a powerful data mathematics and data manipulation package for Perl.
  • Mupad - A proprietary computer algebra system.
  • Clucalc - A tool for 3D visualisations, Clifford algebras and scientific calculations.
  • AUTO 2000 - Software for continuation and bifurcation problems in ordinary differential equations.
  • GAP - Groups, Algorithms, Programming [1]- a System for Computational Discrete Algebra.
  • Pari/GP [2]- designed for fast computations in number theory.
  • Aribas[3]- an interactive interpreter for big integer arithmetic and multi-precision floating point arithmetic
  • Yacas [4]- an easy to use, general purpose Computer Algebra System, a program for symbolic manipulation of mathematical expressions.

Statistics

  • R IconsPage?action=AttachFile&do=get&target=iconCircleUn.png- for statistical computing and graphics.
  • JGR - Java GUI for R.
  • RKWard IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - An easy to use, transparent front end to the R language.
  • Some R tutorials and examples.
  • R Graph Gallery - Collection of graphics that can be created using R. Includes the R commands used to create the graphics.

Medicine

  • Debian-med - A set of metapackages that Ubuntu inherits from Debian for medical practice and research.
  • Aeskulap - A medical image viewer.
  • GNUmed IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Medical practice software.
  • kradview - DICOM viewer.
  • OpenClinica - A web-based Clinical Data Management Software (CDMS) platform for managing multi-site clinical research studies.
  • openDICOM.NET - DICOM imaging software.

Physics

  • Cernlib 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.
  • Lightspeed 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.
  • JaxoDraw - A Java program for drawing Feynman diagrams.
  • Anchor(ROOT)ROOT - An object oriented data analysis framework.
  • HepForge - A website hosting high energy physics (HEP) software development projects - ie. Sourceforge for (HEP). HepForge Projects

More Physics applications - UbuntuScience/Physics

Tools

  • BIKA - A laboratory information management system (LIMS) built on top of Zope and Plone, and coded in Python.
  • FitykIconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A curve fitting and data analysis program, specialized in peak fitting.
  • Bumblebee - A system for managing instruments and other resources (e.g. analytical equipment) that must be shared between a number of users.
  • g3data 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

Plotting Tools

  • PLplot 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.
  • GNUplot 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.
  • plotdrop IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A minimal GNOME front end to GNUPlot.
  • gnuplot tips (not so Frequently Asked Questions).
  • graceIconsPage?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.
  • PGPLOT IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - Fortran- or C-callable graphics subroutine package for making scientific graphs.
  • RLPlot 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.
  • 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.
  • SciGraphica IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A scientific application for data analysis and technical graphics. Attempts to be a "Microcal Origin" clone.
  • Qtiplot - A 2D/3D, Qt based plotting tool that attempts to be another "Origin" clone.
  • LabPlot 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, LaTeX labeling, GSL GSL functions, and statistics.
  • Veusz - A scientific plotting package written in Python.
  • Gri IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A scientific graphics language.
  • Matplotlib 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.
  • PyX IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Python graphics package for the creation of postscript and PDF files - useful for graphing.
  • MayaVi IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - An easy to use scientific data visualizer.
  • Paraview - An application designed with the need to visualize large data sets in mind.
  • kst IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A plotting and data viewing program.
  • Lybniz IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A simple function graph plotter (graphic calculator), in Python and GTK. Ubuntu .deb avaliable.
  • Zhu3D - Interactive 3D plotting program using OpenGL.

Plot Digitizers

  • Plot Digitizer - A Java program used to digitize scanned plots of functional data.
  • g3data IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A program for extracting data from graphs.
  • Engauge Digitizer 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

  • ImageJ - Java-based image processing.
  • VIPS IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A free image processing system.

Vector Drawing Tools

  • Xfig 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, LaTeX, and bitmap files.
  • Skencil 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 LaTeX plugin. Can import many different formats.
  • Tgif IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Another excellent postscript drawing program. Most suitable for black and white postscript figures.
  • Inkscape IconsPage?action=AttachFile&do=get&target=iconCircle.png - Excellent vector drawing program. Uses SVG format by default, but can write to EPS, PDF and LaTeX with PSTricks macros, among other formats.
  • Dia IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A "Visio" like diagram tool. Especially useful for simple circuits and flowcharts.
  • Ipe IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A drawing editor for creating figures in PDF or (encapsulated) Postscript format. Incorporates LaTeX code quite well.
  • jPicEdt - Java based drawing program which can generate LaTeX, eepic and pstricks code from a user-friendly graphical interface.
  • LaTeXDraw - Java based drawing program which can generate and edit pstricks code for LaTeX.

Word Processing Tools

  • LaTeX 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. LaTeX
  • Lyx IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A WYSIWYM (What You See Is What You Mean) LaTeX frontend. Lyx
  • Anchor(Kile) Kile IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A LaTeX-frontend for KDE, with support for syntax highlighting and convenient palettes for all standard mathematical symbols and text formatting. It also provides easy access to forward and inverse search facilities.
  • eqe - Allows you to write equations in LaTeX and drag and drop them into other applications.
  • OOoLatex - A set of Open'Office macros designed to integrate LaTeX equations.
  • Conglomerate IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - An XML editor, to create DocBook or similar formats.
  • 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.
  • Texmaker IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Like Kile Kile but loads faster.
  • TeXmacs IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A WYSIWIG scientific text editor.
  • doubles as an interface for computer algebra systems like [Maxima], Maple, mupad, axiom, giac, GTybalt, Macaulay 2, pari, yacas.
  • can also be used as a front end for [R], Octave, [GNUplot], [Xfig], [Dr. Geo], [Eukleides], [Qcl].
  • preview-latex IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - (almost) turns emacs into a WYSIWYG-LaTeX-frontend.
  • Can also be used in lyx.
  • latex2html IconsPage?action=AttachFile&do=get&target=iconCircleM2.png , tthIconsPage?action=AttachFile&do=get&target=iconCircleM2.png and hevea IconsPage?action=AttachFile&do=get&target=UbuntuGrey.png for converting LaTeX to html.
  • [5] - A small Pidgin (see GaimHowto) plugin that allows you to insert LaTeX formulas into IM conversations.
  • 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 LaTeX. MiKTeX Tools

Bibliographic Tools

  • Bibtex IconsPage?action=AttachFile&do=get&target=UbuntuGrey.png - A program and file format for bibliographies in LaTeX documents.
  • A comprehesive Bibtex manual
  • Pybliographer IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A tool for managing bibliographic databases. Pybliographer is the graphical interface.
  • Jabref - A Java-based BibTeX bibliography manager that can be used in conjunction with Lyx.
  • KBibTeX 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. Bibus
  • Bibutils - Collection of command line tools for bibliography format convertion. Format examples: BiBTeX, RIS, End'Note, COPAC, ISI, Pub'Med...
  • 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.
  • TellicoIconsPage?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.).
  • AlexandriaIconsPage?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.
  • 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

  • openmosix - Turns a network of ordinary computers into a supercomputer.
  • BOINC 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.
  • 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.
  • FoldingAtHome - A protein folding simulation run by the Stanford University.

Ubuntu Packages

Science Section

6.06, 6.10, 7.04, 7.10.

Mathematics Section

6.06, 6.10, 7.04, 7.10,

TeX Section

6.06, 6.10, 7.04, 7.10.

Alternatives to Proprietary Scientific Software

See UbuntuScience/AlternativesToProprietarySoftware

Hardware

  • Labview for linux (non-free) [6]

Data acquisition

  • National Instruments GPIB drivers for linux. [7]
  • 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. [8]
  • 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. [9]

Other information

Other Linux Distributions for Scientists

  • Quantian - A Knoppix / Debian variant tailored to numerical and quantitative analysis.
  • Debian-Med - Debian-Med is a "Custom Debian Distribution" for medical practice and research.
  • debian-med metapackages are in Ubuntu(Universe): to list them type: apt-cache search debian-med
  • Scientific Linux - Linux release put together by Fermilab and CERN based on RH
  • Madrake4Chemistry - Mandrake Linux for chemistry
  • TUn!x - A new project especially designed for the Technical University of Vienna. See also: http://informatik.tuwien.ac.at/tunix
  • Poseidon Linux - A Brazilian distribution designed for academic and scientific use.
  • _dvd_knoppixmake_sci.htm Xplora - A Knoppix/Debian based DVD which aims to make science accessible for schools.
  • CAELinux - A liveDVD linux for Computer Aided Engineering.

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

Books