UbuntuHelp:UbuntuScience

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https://help.ubuntu.com/community/UbuntuScience

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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

- 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.

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)

• 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 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.

Econometrics

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

Electronics

• Eagle 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - A printed circuit board design tool.
• oregano 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Schematic capture, netlists, and spice for simulations.
• gEDA 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - GPL suite of Electronic Design Automation tools.
• Qucs 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - An integrated circuit simulator.
• Icarus Verilog 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Icarus Verilog is a Verilog simulation and synthesis tool. It operates as a compiler, compiling source code written in Verilog (IEEE-1364) into some target format.

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

• GDL 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png- 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 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - GNU Octave is a high-level language, primarily intended for numerical computations. (Similar to MATLAB). Octave
• SciCraft - Add-on to Octave, clones Simulink. Still in development, blocks have to be written by the user. It is supposed to specialize in bioinformatics functions.
• Scilab 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - Another MATLAB-like application.
• SciCos - A free Simulink-like add-on to Scilab.
• Maxima 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A computer algebra system (xmaxima is its X interface).
• wxMaxima 模板: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 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 模板: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)>>GSL 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - The Gnu Scientific Library.
• OOStatistics - A statistics macro for OpenOffice Calc.
• freefem 模板: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.
• 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 模板:Https://help.ubuntu.com/community/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 模板: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.
• GiNaC 模板:Https://help.ubuntu.com/community/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
• GeoGebra - A free and multi-platform dynamic mathematics software for schools that joins geometry, algebra and calculus. It received several international awards including the European and German educational software awards. Geogebra
• PDL 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Perl Data Language is a powerful data mathematics and data manipulation package for Perl.
• 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 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - a System for Computational Discrete Algebra.
• Pari/GP 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - designed for fast computations in number theory.
• Aribas模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - an interactive interpreter for big integer arithmetic and multi-precision floating point arithmetic
• Yacas 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - an easy to use, general purpose Computer Algebra System, a program for symbolic manipulation of mathematical expressions.

Statistics

• SPSS The propietary statistical reference package. Written in Java, since version 16 (currently 17) runs on Linux, although it has some problems with Compiz Fusion (Solution: sudo gedit /etc/environment. Add at the end: AWT_TOOLKIT="MToolkit". Save and restart).
• PSPP/PSPPIRE It is intended as a free replacement of the proprietary program SPSS. PSPPIRE is the PSPP GUI.
• R 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - for statistical computing and graphics.
• JGR - Java GUI for R.
• RKWard 模板:Https://help.ubuntu.com/community/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 模板:Https://help.ubuntu.com/community/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 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

Tools

• BIKA - A laboratory information management system (LIMS) built on top of Zope and Plone, and coded in Python.
• Fityk模板:Https://help.ubuntu.com/community/IconsPage?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 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - "g3data is used for extracting data from graphs. In publications graphs often are included, but the actual data is missing. g3data makes the extracting process much easier."

Fortran Compilers

• Intel Fortran Compiler 9.0 for noncommercial, nonacademic use. Please respect the license agreements. A step by step installation guide can be found here: http://www.ubuntuforums.org/showthread.php?t=89571 (Post by Chickenmonger)
• gfortran模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - The GNU Fortran 95 compiler.
• g95 - The goal of the g95 project is to create a free, open source Fortran 95 compiler and runtime libraries.

Plotting Tools

• PLplot 模板: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.
• GNUplot 模板: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.
• plotdrop 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A minimal GNOME front end to GNUPlot.
• gnuplot tips (not so Frequently Asked Questions).
• grace模板: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.
• PGPLOT 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - Fortran- or C-callable graphics subroutine package for making scientific graphs.
• RLPlot 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - RLPlot is a GUI based program for displaying scientific data in standard formats. It has full support for all error-bar types and it has greater flexibility with displaying colour and texture in charts than gnuplot (filled bar chart boxes are possible without any additional programs). Output is generated on the X display here further changes can be made to the graph using point and click methods. Images can be exported as scalable vector graphics (SVG) as well as EPS, WMF and TIFF formats.
• 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 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A scientific application for data analysis and technical graphics. Attempts to be a "Microcal Origin" clone.
• Qtiplot 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A 2D/3D, Qt based plotting tool that attempts to be another "Origin" clone.
• LabPlot 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Another Qt based 2D/3D GUI plotting tool that also does curve fitting, supports many data formats, UbuntuHelp:LaTeX labeling, [[UbuntuHelp:[GSL|GSL|[GSL|GSL]]] functions, and statistics.
• Veusz - A scientific plotting package written in Python.
• Gri 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A scientific graphics language.
• Matplotlib 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - a cross platform 2d plotting library for Python.
• PyX 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Python graphics package for the creation of Postscript and PDF files - useful for graphing.
• MayaVi 模板:Https://help.ubuntu.com/community/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 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A plotting and data viewing program.
• Lybniz 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A simple function graph plotter (graphic calculator), in Python and GTK. Ubuntu .deb available.
• Zhu3D - Interactive 3D plotting program using OpenGL.

Plot Digitizers

• Plot Digitizer - A Java program used to digitize scanned plots of functional data.
• g3data 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A program for extracting data from graphs.
• Engauge Digitizer 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - a Qt-based system including zoom and curve-tracing functionality, apparently (it seemed a little unintuitive on my first play with it).

Image Processing Tools

• ImageJ - Java-based image processing.
• VIPS 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A free image processing system.

Vector Drawing Tools

• Xfig 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A diagram and figure creation tool. Can import GIF, JPEG, and EPS figures and can export to Postscript, LaTeX, and bitmap files.
• Skencil 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - An excellent vector drawing package. Especially useful for creating and annotating existing Postscript figures. Numerous plugins are available, most notably a [[UbuntuHelp:LaTeX|LaTeX]] plugin. Can import many different formats.
• Tgif 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Another excellent Postscript drawing program. Most suitable for black and white Postscript figures.
• Inkscape 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircle.png - Excellent vector drawing program. Uses SVG format by default, but can write to EPS, PDF and [[UbuntuHelp:LaTeX|LaTeX]] with PSTricks macros, among other formats.
• Textext Inkscape extension to add editable LaTeX text objects to a document
• Dia 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A "Visio" like diagram tool. Especially useful for simple circuits and flowcharts.
• Ipe 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A drawing editor for creating figures in PDF or (encapsulated) Postscript format. Incorporates [[UbuntuHelp:LaTeX|LaTeX]] code quite well.
• jPicEdt - Java based drawing program which can generate [[UbuntuHelp:LaTeX|LaTeX]], eepic and pstricks code from a user-friendly graphical interface.
• LaTeXDraw - Java based drawing program which can generate and edit pstricks code for [[UbuntuHelp:LaTeX|LaTeX]].

Word Processing Tools

• [[UbuntuHelp:LaTeX|LaTeX]] - 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 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A WYSIWYM (What You See Is What You Mean) [[UbuntuHelp:LaTeX|LaTeX]] frontend. LyX
• <<Anchor(Kile)>> Kile 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A [[UbuntuHelp:LaTeX|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.
• ekee - Allows you to write equations in [[UbuntuHelp:LaTeX|LaTeX]] and drag and drop them into other applications.
• OOoLatex - A set of Open'Office macros designed to integrate [[UbuntuHelp:LaTeX|LaTeX]] equations.
• Conglomerate 模板:Https://help.ubuntu.com/community/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 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - Like [[UbuntuHelp:[Kile|Kile]]] but loads faster.
• TeXmacs 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A WYSIWYG 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 - (almost) turns Emacs into a WYSIWYG-[[UbuntuHelp:LaTeX|LaTeX]]-frontend.
• Can also be used in lyx.
• latex2html 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png, tth 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png and hevea 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=UbuntuGrey.png for converting [[UbuntuHelp:LaTeX|LaTeX]] to html.
• [1] - A small Pidgin (see Pidgin) plugin that allows you to insert [[UbuntuHelp:LaTeX|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 [[UbuntuHelp:LaTeX|LaTeX]]. MiKTeX Tools

Bibliographic Tools

• Bibtex - A program and file format for bibliographies in [[UbuntuHelp:LaTeX|LaTeX]] documents.
• A comprehensive Bibtex manual
• Pybliographer 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A tool for managing bibliographic databases. Pybliographer is the graphical interface.
• Jabref 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleM2.png - A Java-based BibTeX bibliography manager that can be used in conjunction with LyX.
• KBibTeX 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A BibTeX editor for KDE.
• Ubuntu:Bibus - Bibus is a bibliographic database. Bibus works with Open'Office.org 2.0. Bibus
• Bibutils - Collection of command line tools for bibliography format convertion. Format examples: BiBTeX, RIS, End'Note, COPAC, ISI, Pub'Med...
• Referencer 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - 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.
• Tellico 模板:Https://help.ubuntu.com/community/IconsPage?action=AttachFile&do=get&target=iconCircleUn.png - A KDE application for organizing your collections. It allows to add special tags to entries, and sort entries along any field (author, year, keywords, etc.).
• Alexandria 模板: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.
• cb2Bib - The cb2Bib is a tool for rapidly extracting unformatted, or unstandardized, bibliographic 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 模板: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.
• 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

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

• 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

• Ubuntu MOTU Science mailing list
• 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

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
• [6] - 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.

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