“UbuntuHelp:UbuntuScience”的版本间的差异
来自Ubuntu中文
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{{From|https://help.ubuntu.com/community/UbuntuScience}} | {{From|https://help.ubuntu.com/community/UbuntuScience}} | ||
{{Languages|UbuntuHelp:UbuntuScience}} | {{Languages|UbuntuHelp:UbuntuScience}} | ||
| − | + | 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>> | |
| − | + | Those installed by default are in Main (officially supported) Ubuntu repository. | |
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| − | https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircle.png - installed by default in Ubuntu < | + | |
| − | https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=IconKubuntuCircle.png - installed by default in Kubuntu < | + | |
| − | https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=edubuntu.png - installed by default in Edubuntu < | + | |
| − | https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=UbuntuGrey.png - Main (officially supported) Ubuntu repository, not installed by default < | + | |
| − | https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Universe (community maintained) repository < | + | |
| − | https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - Multiverse (non-free) repository < | + | |
For information about the Ubuntu repositories see [[UbuntuHelp:Repositories|Repositories]]. Clicking on the icon next a program should take you to information about the Ubuntu package. | For information about the Ubuntu repositories see [[UbuntuHelp:Repositories|Repositories]]. Clicking on the icon next a program should take you to information about the Ubuntu package. | ||
=== Astronomy === | === Astronomy === | ||
| − | * [http://edu.kde.org/kstars/ KStars] [http://packages.ubuntu.com/kstars | + | * [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.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] - | + | * [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 | + | * [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. | + | * [http://earth.google.com/ Google Earth] [http://packages.ubuntu.com/googleearth-package {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png}}] - 3D earth viewing application includes a sky view. |
''More Astronomy applications'' - [[UbuntuHelp:UbuntuScience/Astronomy|UbuntuScience/Astronomy]] | ''More Astronomy applications'' - [[UbuntuHelp:UbuntuScience/Astronomy|UbuntuScience/Astronomy]] | ||
=== 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). | + | * [ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ ClustalW] [http://packages.ubuntu.com/clustalw {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png}}] - Global multiple nucleotide or peptide sequence alignment |
| − | * [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. | + | * [ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ ClustalX] [http://packages.ubuntu.com/clustalw {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png}}] - GUI for ClustalW |
| − | * | + | * [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.cs.mu.oz.au/~gavinb/projects/itk.php unofficial | + | * [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)] [http://packages.ubuntu.com/insighttoolkit {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.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'' - [[UbuntuHelp:UbuntuScience/Biology|UbuntuScience/Biology]] | ''More Biology applications'' - [[UbuntuHelp:UbuntuScience/Biology|UbuntuScience/Biology]] | ||
=== Biophysics === | === 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://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.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 | * [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 === | === 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.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://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://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://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://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://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.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.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.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. | + | * [http://www.gromacs.org GROMACS] [http://packages.ubuntu.com/gromacs {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. |
| − | + | * [http://www.chemdoodle.com ChemDoodle] - A chemical structure environment. More than just another program for drawing molecules (although it does that easily), it's a brand new application for interacting with chemical data and creating chemical art. | |
=== Earth Sciences (Geology/Geography) === | === Earth Sciences (Geology/Geography) === | ||
| − | + | * [http://grass.itc.it GRASS] [http://packages.ubuntu.com/grass {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Geographic Resources Analysis Support System Commonly referred to as GRASS, is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/map production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many government agencies and environmental consulting companies. | |
| − | * [http://grass.itc.it GRASS] [http://packages.ubuntu.com/grass https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - Geographic Resources Analysis Support System Commonly referred to as GRASS, is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/map production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many government agencies and environmental consulting companies. | + | * [http://qgis.org/ QGIS] [http://packages.ubuntu.com/qgis {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Quantum GIS (QGIS) supports shapefile viewing and editing, spatial data storage with [[UbuntuHelp:PostgreSQL|PostgreSQL]]/PostGIS, projection on-the-fly, map composition, and a number of other features via a plugin interface. |
| − | * [http://qgis.org/ QGIS] [http://packages.ubuntu.com/qgis https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - Quantum GIS (QGIS) supports shapefile viewing and editing, spatial data storage with 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://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 | + | * [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://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://earth.google.com/ Google Earth] [http://packages.ubuntu.com/googleearth-package {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png}}] - 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://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://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://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. | * [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 {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Geographic objects support for [[UbuntuHelp:PostgreSQL|PostgreSQL]]. | ||
=== Ecology and Environmental Sciences === | === Ecology and Environmental Sciences === | ||
* [http://www.swarm.org/wiki/Main_Page Swarm] - A conceptual framework for designing, describing, and conducting experiments on ABMs. | * [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://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://ccl.northwestern.edu/netlogo/ NetLogo] - A Java-based programmable modeling environment for simulating natural and social phenomena. | ||
| − | * [http://www.simulistics.com/ Simile] - A proprietary ($$$) System Dynamics and object-based modeling and simulation software package similar to Stella, Model Maker, Vensim, etc. | + | * [http://www.simulistics.com/ Simile] - A proprietary ($$$) 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. |
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=== Physics === | === Physics === | ||
| − | * [http://wwwasd.web.cern.ch/wwwasd/cernlib/ Cernlib] [http://packages.ubuntu.com/cernlib https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png] - A suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the chemical and biological sciences. | + | * [http://wwwasd.web.cern.ch/wwwasd/cernlib/ Cernlib] [http://packages.ubuntu.com/cernlib {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - A suite of data analysis tools and libraries created for use in physics experiments, but also with applications to other fields such as the chemical and biological sciences. |
| − | * [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://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|Java]] program for drawing Feynman diagrams. | * [http://jaxodraw.sourceforge.net JaxoDraw] - A [[UbuntuHelp:Java|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/ 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'' - [[UbuntuHelp:UbuntuScience/Physics|UbuntuScience/Physics]] | ''More Physics applications'' - [[UbuntuHelp:UbuntuScience/Physics|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 ]. | |
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| − | [http://packages.ubuntu.com/feisty/science/ | + | |
| − | [http://packages.ubuntu.com/gutsy/science/ | + | |
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== Alternatives to Proprietary Scientific Software == | == Alternatives to Proprietary Scientific Software == | ||
See [[UbuntuHelp:UbuntuScience/AlternativesToProprietarySoftware|UbuntuScience/AlternativesToProprietarySoftware]] | See [[UbuntuHelp:UbuntuScience/AlternativesToProprietarySoftware|UbuntuScience/AlternativesToProprietarySoftware]] | ||
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* EPICS - A set of Open Source software tools, libraries and applications to create distributed soft real-time control systems for scientific instruments such as a particle accelerators, telescopes and other large scientific experiments. [http://www.aps.anl.gov/epics/index.php] | * EPICS - A set of Open Source software tools, libraries and applications to create distributed soft real-time control systems for scientific instruments such as a particle accelerators, telescopes and other large scientific experiments. [http://www.aps.anl.gov/epics/index.php] | ||
== Other information == | == Other information == | ||
| − | === | + | * [[UbuntuHelp:UbuntuScience/Howto|UbuntuScience/Howto]] (still a work in progress....) |
| + | === Other Linux Distributions for Scientists === | ||
| + | * [http://scubuntu.meraka.org.za/wiki Scubuntu] - The aim of the Scubuntu project is to develop a flavour of Ubuntu Linux for use by scientists. | ||
* [http://dirk.eddelbuettel.com/quantian.html Quantian] - A Knoppix / Debian variant tailored to numerical and quantitative analysis. | * [http://dirk.eddelbuettel.com/quantian.html Quantian] - A Knoppix / Debian variant tailored to numerical and quantitative analysis. | ||
| − | |||
| − | |||
* [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 | ||
| − | * [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://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://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.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. | * [http://www.caelinux.com/CMS/ CAELinux] - A liveDVD linux for Computer Aided Engineering. | ||
=== Unofficial Ubuntu/Debian repositories with science software === | === Unofficial Ubuntu/Debian repositories with science software === | ||
| − | * [http://mirror.phy.bnl.gov/debian-root/ repository] of [[ROOT ROOT]] packages | + | * [http://mirror.phy.bnl.gov/debian-root/ repository] of [[UbuntuHelp:[ROOT|ROOT]]] packages |
* [http://lists.debian.org/debian-science/2005/08/msg00001.html Yaroslav Halchenko] [http://www.onerussian.com/debian/ repository] | * [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://www.cs.mu.oz.au/~gavinb/projects/itk.php repository] of [[UbuntuHelp:[ITK|ITK]]] Packages |
* [http://lists.debian.org/debian-science/2005/08/msg00133.html Teemu Ikonen] [http://mentors.debian.net/debian repository] | * [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]) | * Daniel Leidert [http://debian.wgdd.de/debian/ repository] ( [http://debian.wgdd.de/repository read]) | ||
| − | * [http://lists.debian.org/debian-science/ | + | * [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] | * [http://scientificcomputing.net/ Balbir Thomas] [http://scientificcomputing.net/debian/packages/ repository] | ||
=== Mailing Lists about Linux and Science === | === Mailing Lists about Linux and Science === | ||
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=== Related Wiki Pages === | === Related Wiki Pages === | ||
* Ubuntu:MOTU/Teams/Science is the Ubuntu:MOTU team responsible for the upkeep of science packages within the Universe repository. | * 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 | + | * Ubuntu:UbuntuSciencePackages is a list of packages that are in the official Ubuntu Repositories that scientists use. |
* Ubuntu:UbuntuScienceMetaPackages discusses possible science metapackages | * Ubuntu:UbuntuScienceMetaPackages discusses possible science metapackages | ||
* [[UbuntuHelp:OpenFOAM|OpenFOAM]] - How to install Open''''''FOAM on Ubuntu. | * [[UbuntuHelp:OpenFOAM|OpenFOAM]] - How to install Open''''''FOAM on Ubuntu. | ||
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* [http://freescience.info Free Science] - Free''''''Science provides free scientific books and software. | * [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.jlab.org/~semenov/rlinks/soft.html Physics Related Software Manuals/Links]. | ||
| − | * [http://www.educypedia.be/ Educypedia] - | + | * [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.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://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://sal.iatp.by/ SAL] (Scientific Applications on Linux) is a collection of information and links to software that will be of interest to scientists and engineers. Not updated since 2001. | ||
* [http://scibuntu.sourceforge.net/ Scibuntu] - A script to install scientific tools. | * [http://scibuntu.sourceforge.net/ Scibuntu] - A script to install scientific tools. | ||
| − | |||
---- | ---- | ||
| − | + | [[category:CategoryScience]] | |
[[category:UbuntuHelp]] | [[category:UbuntuHelp]] | ||
2010年5月20日 (四) 00:34的最新版本
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点击翻译: |
English |
请不要直接编辑翻译本页，本页将定期与来源同步。 |
Legend:
- installed by default in Ubuntu <
>
- installed by default in Kubuntu <
>
- installed by default in Edubuntu <
>
- Main (officially supported) Ubuntu repository, not installed by default <
>
- Universe (community maintained) repository <
>
- 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.
目录
Astronomy
- KStars 模板:Https://help.ubuntu.com/community/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 模板: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.
- Google Earth 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - 3D earth viewing application includes a sky view.
More Astronomy applications - UbuntuScience/Astronomy
Biology
- BioPerl 模板: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 BioJava and BioPython
- ClustalW 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - Global multiple nucleotide or peptide sequence alignment
- ClustalX 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - GUI for ClustalW
- Tree View X 模板: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).
- Tree-puzzle 模板: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)>>Insight Toolkit (ITK) 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - 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 模板: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
- 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 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A 2D chemical structures editor.
- ghemical 模板: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.
- gdis 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A molecular display program that supports OpenGL and POVRay rendering.
- OpenBabel模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A chemical file format conversion program.
- Chemtool模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - 2D molecule drawing programs similar to Chem'Draw.
- xdrawchem 模板:Https://help.ubuntu.com/community/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 模板: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.
- Linux4Chemistry - List of Linux applications that may be useful for chemists.
- GROMACS 模板: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.
- 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)
- GRASS 模板: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.
- QGIS 模板: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.
- ncview - A very fast program for viewing netCDF files (a standard widely used in meteorology, climate and oceanography).
- Generic Mapping Tools (GMT) 模板: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.
- WW2D - Java based application similar to NASA World Wind or Google Earth software.
- Google Earth 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - 3D earth viewing application using satellite images (no cost but proprietary).
- Thuban 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - An interactive geographic data viewer.
- Survex 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Cave surveying and mapping software.
- Therion 模板:Https://help.ubuntu.com/community/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.
- PostGIS 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Geographic objects support for PostgreSQL.
Ecology and Environmental Sciences
- Swarm - A conceptual framework for designing, describing, and conducting experiments on ABMs.
- Repast - The Recursive Porous Agent Simulation Toolkit.
- NetLogo - A Java-based programmable modeling environment for simulating natural and social phenomena.
- Simile - A proprietary ($$$) System Dynamics and object-based modeling and simulation software package similar to Stella, Model Maker, Vensim, etc. It is advertised as "Visual modeling software for the earth, environmental and life sciences". A free evaluation version, which limits the size of saved models, is available.
Physics
- Cernlib 模板: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.
- Lightspeed 模板: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.
- 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
- 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
7.04, 7.10, 8.04, 8.10, 9.04 .
Alternatives to Proprietary Scientific Software
See UbuntuScience/AlternativesToProprietarySoftware
Hardware
- Labview for linux (non-free) [1]
Data acquisition
- National Instruments GPIB drivers for linux. [2]
- Comedi - Open source drivers, tools and libraries. comedi
Computer controlled systems
- RTAI - Real-Time Application Interface is a hard real-time extension to the Linux kernel. [3]
- EPICS - A set of Open Source software tools, libraries and applications to create distributed soft real-time control systems for scientific instruments such as a particle accelerators, telescopes and other large scientific experiments. [4]
Other information
- UbuntuScience/Howto (still a work in progress....)
Other Linux Distributions for Scientists
- Scubuntu - The aim of the Scubuntu project is to develop a flavour of Ubuntu Linux for use by scientists.
- Quantian - A Knoppix / Debian variant tailored to numerical and quantitative analysis.
- 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
- repository of [[UbuntuHelp:[ROOT|ROOT]]] packages
- Yaroslav Halchenko repository
- repository of [[UbuntuHelp:[ITK|ITK]]] Packages
- Teemu Ikonen repository
- Daniel Leidert repository ( read)
- Carlo Segre repository includes Ubuntu builds
- Balbir Thomas repository
Mailing Lists about Linux and Science
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
Ubuntu Education & Science Forum Some forum threads
- Are there any scientists-biologists out there using Ubuntu?
- Ubuntu Science Metapackage
- Scientific Software options for Ubuntu
- Scientific Ubuntu, installing OpenFOAM CFD software
- How To install ELMER Multiphysics software
Links
- DebianScience
- sourceforge - Scientific software on sourceforge.
- DebianLinux.Net-Scientific Software - Links to science software.
- freshmeat - Scientific software on freshmeat.
- Linux App finder - Science/Engineering Section
- DesktopLinux.com Linux software - Science Section
- [5] - Scientific linux software.
- gnome-files - scientific software - Scientific apps for gnome.
- kde-apps.org- scientific software - Scientific apps for kde.
- Free Science - Free'Science provides free scientific books and software.
- Physics Related Software Manuals/Links.
- Educypedia - Collection of links about scientific and educational material.
- The Openscience Project - Dedicated to writing and releasing free and Open Source scientific software.
- Open Bioinformatics - A non profit, volunteer run organization focused on supporting open source programming in bioinformatics.
- 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.
- Scibuntu - A script to install scientific tools.
