||<>|| Legend: {{attachment:IconsPage/ubuntu.png}} - installed by default in Ubuntu <
> {{attachment:IconsPage/kubuntu.png}} - installed by default in Kubuntu <
> {{attachment:IconsPage/edubuntu.png}} - installed by default in Edubuntu <
> {{attachment:IconsPage/ubuntu_grey.png}} - Main (officially supported) Ubuntu repository, not installed by default <
> {{attachment:IconsPage/community.png}} - Universe (community maintained) repository <
> {{attachment:IconsPage/important.png}} - Multiverse (non-free) repository <
> Those installed by default are in Main (officially supported) Ubuntu repository. For information about the Ubuntu repositories see [[Repositories]]. Clicking on the icon next a program should take you to information about the Ubuntu package. == Astronomy == * [[http://edu.kde.org/kstars/|KStars]] [[http://packages.ubuntu.com/kstars|{{attachment:IconsPage/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|{{attachment:IconsPage/community.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]] [[http://packages.ubuntu.com/googleearth-package|{{attachment:IconsPage/important.png}}]] - 3D earth viewing application includes a sky view. ''More Astronomy applications'' - [[UbuntuScience/Astronomy]] == Biology == * [[http://www.bioperl.org|BioPerl]] [[http://packages.ubuntu.com/bioperl|{{attachment:IconsPage/community.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://www.clustal.org/clustal2/|ClustalW]] [[http://packages.ubuntu.com/clustalw|{{attachment:IconsPage/important.png}}]] - Global multiple nucleotide or peptide sequence alignment * [[http://www.clustal.org/clustal2/|ClustalX]] [[http://packages.ubuntu.com/clustalw|{{attachment:IconsPage/important.png}}]] - GUI for ClustalW * [[http://darwin.zoology.gla.ac.uk/%7Erpage/treeviewx/index.html|Tree View X]] [[http://packages.ubuntu.com/treeviewx|{{attachment:IconsPage/community.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|{{attachment:IconsPage/community.png}}]] - TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. * <>[[http://www.itk.org/|Insight Toolkit (ITK)]] [[http://packages.ubuntu.com/insighttoolkit|{{attachment:IconsPage/community.png}}]] - 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'' - [[UbuntuScience/Biology]] == Biophysics == * [[http://pymol.sourceforge.net/|Pymol]] [[http://packages.ubuntu.com/pymol|{{attachment:IconsPage/community.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|{{attachment:IconsPage/community.png}}]] - A 2D chemical structures editor. * [[http://www.uku.fi/%7Ethassine/ghemical/|ghemical]] [[http://packages.ubuntu.com/ghemical|{{attachment:IconsPage/community.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|{{attachment:IconsPage/community.png}}]] - A molecular display program that supports OpenGL and POVRay rendering. * [[http://openbabel.sourceforge.net/|OpenBabel]][[http://packages.ubuntu.com/openbabel|{{attachment:IconsPage/community.png}}]] - A chemical file format conversion program. * [[http://ruby.chemie.uni-freiburg.de/~martin/chemtool/chemtool.html|Chemtool]][[http://packages.ubuntu.com/chemtool|{{attachment:IconsPage/community.png}}]] - 2D molecule drawing programs similar to Chem''''''Draw. * [[http://xdrawchem.sourceforge.net/|xdrawchem]] [[http://packages.ubuntu.com/xdrawchem|{{attachment:IconsPage/community.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|{{attachment:IconsPage/community.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|{{attachment:IconsPage/community.png}}]] - A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. * [[http://www.chemdoodle.com|ChemDoodle]] - A chemical structure environment. More than just another program for drawing molecules (although it does that easily), it's a brand new application for interacting with chemical data and creating chemical art. == Earth Sciences (Geology/Geography) == * [[http://grass.itc.it|GRASS]] [[http://packages.ubuntu.com/grass|{{attachment:IconsPage/community.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|{{attachment:IconsPage/community.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|{{attachment:IconsPage/community.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]] [[http://packages.ubuntu.com/googleearth-package|{{attachment:IconsPage/important.png}}]] - 3D earth viewing application using satellite images (no cost but proprietary). * [[http://thuban.intevation.org/|Thuban]] [[http://packages.ubuntu.com/thuban|{{attachment:IconsPage/community.png}}]] - An interactive geographic data viewer. * [[http://www.survex.com/|Survex]] [[http://packages.ubuntu.com/survex|{{attachment:IconsPage/community.png}}]] - Cave surveying and mapping software. * [[http://therion.speleo.sk/|Therion]] [[http://packages.ubuntu.com/therion|{{attachment:IconsPage/community.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. * [[http://postgis.refractions.net/|PostGIS]] [[http://packages.ubuntu.com/postgis|{{attachment:IconsPage/community.png}}]] - Geographic objects support for PostgreSQL. == 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. == Neuroscience == * [[http://neuro.debian.net|NeuroDebian]] [[http://neuro.debian.net/pkglists/pkgs-by_release-ubuntu_11.04_%22natty_narwhal%22_%28natty%29.html|{{attachment:IconsPage/community.png}}]] - A collection of neuroscience related software integrated into Debian (and thus Ubuntu) == Physics == * [[http://wwwasd.web.cern.ch/wwwasd/cernlib/|Cernlib]] [[http://packages.ubuntu.com/cernlib|{{attachment:IconsPage/community.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|{{attachment:IconsPage/community.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 [[Java]] program for drawing Feynman diagrams. * <>[[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]] * [[http://www.mcstas.org/|McStas]] - A neutron scattering instrument Monte Carlo simulation package, which simulates neutron spectrometers and beam lines. ''More Physics applications'' - [[UbuntuScience/Physics]] = Ubuntu Packages: Science Section = [[http://packages.ubuntu.com/feisty/science/|7.04]], [[http://packages.ubuntu.com/gutsy/science/|7.10]], [[http://packages.ubuntu.com/heron/science/|8.04]], [[http://packages.ubuntu.com/intrepid/science/|8.10]], [[http://packages.ubuntu.com/jaunty/science/| 9.04 ]]. [[http://packages.ubuntu.com/karmic/science/| 9.10 ]]. [[http://packages.ubuntu.com/lucid/science/| 10.04 ]]. = Alternatives to Proprietary Scientific Software = See [[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 = * [[UbuntuScience/Howto]] (still a work in progress....) == Other Linux Distributions for Scientists == * [[http://ubuntusci.meraka.org.za|Ubuntu sci]] - The aim of the Ubuntu^sci^ project is to develop a flavour of Ubuntu Linux for use by scientists. * [[http://dirk.eddelbuettel.com/quantian.html|Quantian]] - A Knoppix / Debian variant tailored to numerical and quantitative analysis. * [[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___dvd_knoppix__make_sci.htm|Xplora]] - A Knoppix/Debian based DVD which aims to make science accessible for schools. * [[http://www.caelinux.com/CMS/|CAELinux]] - A live DVD 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://neuro.debian.net|NeuroDebian]] of neuroscience-related software with backports for Debian and Ubuntu releases. * [[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/2008/12/msg00033.html|Carlo Segre]] [[http://debian-xray.iit.edu|repository]] includes Ubuntu builds * [[http://scientificcomputing.net/|Balbir Thomas]] [[http://scientificcomputing.net/debian/packages/|repository]] * [[UbuntuScience/PythonXY| PythonXY for Ubuntu]] == 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 * [[OpenFOAM]] - How to install Open''''''FOAM on Ubuntu. * [[UbuntuScience/Astronomy]] * [[UbuntuScience/Biology]] * [[UbuntuScience/Physics]] * [[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.myoutsourcedbrain.com/2010/11/ubuntu-maverick-for-phd-students.html|Ubuntu Maverick for Research]] - Installation, pointers to many relevant programs on Ubuntu 10.10 for research (especially focused on PhD studies). * [[http://www.jlab.org/~semenov/rlinks/soft.html|Physics Related Software Manuals/Links]]. * [[http://www.educypedia.be/|Educypedia]] - Collection 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. ---- CategoryScience