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* [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.
=== Computer Science ===
=== Computer Science ===
=== Earth Sciences (Geology/Geography) ===
=== Earth Sciences (Geology/Geography) ===
* Ubuntu:UbuntuGIS This is the page where suggestions and software lists for a professional "out of the box" Ubuntu based GIS workstation should be collected.
* Ubuntu:UbuntuGIS This is the page where suggestions and software lists for a professional "out of the box" Ubuntu based GIS workstation should be collected.
* [http://grass.itc.it GRASS] [http://packages.ubuntu.com/grass {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Geographic Resources Analysis Support System Commonly referred to as GRASS, is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/map production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many government agencies and environmental consulting companies.
* [http://grass.itc.it GRASS] [http://packages.ubuntu.com/grass {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Geographic Resources Analysis Support System Commonly referred to as GRASS, is a Geographic Information System (GIS) used for geospatial data management and analysis, image processing, graphics/map production, spatial modeling, and visualization. GRASS is currently used in academic and commercial settings around the world, as well as by many government agencies and environmental consulting companies.
* [http://qgis.org/ QGIS] [http://packages.ubuntu.com/qgis {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Quantum GIS (QGIS) supports shapefile viewing and editing, spatial data storage with PostgreSQL/PostGIS, projection on-the-fly, map composition, and a number of other features via a plugin interface.
* [http://qgis.org/ QGIS] [http://packages.ubuntu.com/qgis {{https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png}}] - Quantum GIS (QGIS) supports shapefile viewing and editing, spatial data storage with [[UbuntuHelp:PostgreSQL|PostgreSQL]]/PostGIS, projection on-the-fly, map composition, and a number of other features via a plugin interface.
* [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 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://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.
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* [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.
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* [http://www.graphiteone-cad.com/en/index.htm Graphiteone] - 3D and 2D commercial mechanical engineering CAD. Version 1.3: Free for personal use only. Version 2.0: With Parasolid-Kernel from UGS, Evaluationlicence for one month available.
* [http://www.graphiteone-cad.com/en/index.htm Graphiteone] - 3D and 2D commercial mechanical engineering CAD. Version 1.3: Free for personal use only. Version 2.0: With Parasolid-Kernel from UGS, Evaluationlicence for one month available.
* [http://www.geuz.org/gmsh/ Gmsh] an automatic 3D finite element grid generator with a built-in CAD engine and post-processor.
* [http://www.geuz.org/gmsh/ Gmsh] an automatic 3D finite element grid generator with a built-in CAD engine and post-processor.
* [http://www.oofem.org/en/oofem.html OOFem] a free finite element code with object oriented architecture for solving mechanical, transport and fluid mechanics problems.
* [http://www.collabcad.com CollabCAD] - 3D and 2D commercial mechanical engineering CAD/CAM based on open source software . Freeware-Version available.
* [http://www.collabcad.com CollabCAD] - 3D and 2D commercial mechanical engineering CAD/CAM based on open source software . Freeware-Version available.
* [http://www.varicad.com Varicad] - Modern 3D and 2D commercial mechanical engineering CAD. Cheap CATIA, Pro/E - LIGHT. Trialversion for one month available.
* [http://www.varicad.com Varicad] - Modern 3D and 2D commercial mechanical engineering CAD. Cheap CATIA, Pro/E - LIGHT. Trialversion for one month available.

2009年11月17日 (二) 20:55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 <
> Those installed by default are in Main (officially supported) Ubuntu repository. For information about the Ubuntu repositories see Repositories. Clicking on the icon next a program should take you to information about the Ubuntu package.

Astronomy

More Astronomy applications - UbuntuScience/Astronomy

Biology

More Biology applications - UbuntuScience/Biology

Biophysics

Chemistry

Computer Science

Earth Sciences (Geology/Geography)

Ecology and Environmental Sciences

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

Econometrics

Electronics

Engineering Sciences

  • QCad 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A 2D-Computer Aided Design application similar AutoCAD. It is available in the universe repositories.
  • CyCAS - A commercial Computer Aided Design application for architects. There is a public version available.
  • ARCAD - A commercial Computer Aided Design application for architects.
  • BRL-CAD - A Open Source 3D-CAD program. It is a Constructive Solid Geometry (CSG) solid modeling system with over 20 years development and production use by the U.S. military.
  • Varkon 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Open Source 3D- (parametric) and 2D-Developmentplatform for a CAD program. It is available in the universe repositories.
  • Salome - A Open Source software suite including Pre-/Post processing Tools: 3D-CAD, Mesher, FEM-Software
  • Free-CAD - Modern Open Source 3D-Solid CAD. FreeCAD will aim directly to mechanical engineering, product design and related features (like Catia, and Solid-Works). Early state of Development.
  • gCAD3D - A 3D-surface-CAD/CAM. Program is freeware.
  • Graphiteone - 3D and 2D commercial mechanical engineering CAD. Version 1.3: Free for personal use only. Version 2.0: With Parasolid-Kernel from UGS, Evaluationlicence for one month available.
  • Gmsh an automatic 3D finite element grid generator with a built-in CAD engine and post-processor.
  • OOFem a free finite element code with object oriented architecture for solving mechanical, transport and fluid mechanics problems.
  • CollabCAD - 3D and 2D commercial mechanical engineering CAD/CAM based on open source software . Freeware-Version available.
  • Varicad - Modern 3D and 2D commercial mechanical engineering CAD. Cheap CATIA, Pro/E - LIGHT. Trialversion for one month available.
  • Webersys - 3D and 2D commercial mechanical engineering CAD/CAM. Trialversion for one month available.
  • MEDUSA - 2D/3D commercial mechanical engineering CAD. Free for personal use only.
  • Pro/ENGINEER - A 3D-commercial mechanical engineering and design CAD tool.
  • A list of CAD software for Linux
  • XFoil is a program to design and/or calculate airfoils. See this forum thread on how to install it.

Mathematics

Statistics

Medicine

Physics

More Physics applications - UbuntuScience/Physics

Tools

Fortran Compilers

Plotting Tools

Plot Digitizers

Image Processing Tools

Vector Drawing Tools

Word Processing Tools

Bibliographic Tools

Distributed Computing

Ubuntu Packages

Science Section

7.04, 7.10, 8.04, 8.10, 9.04 .

Mathematics Section

7.04, 7.10, 8.04, 8.10, 9.04 .

TeX 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) [2]

Data acquisition

  • National Instruments GPIB drivers for linux. [3]
  • 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. [4]
  • 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. [5]

Other information

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.
  • 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