“UbuntuHelp:UbuntuScience”的版本间的差异

2007年11月21日 (三) 17:49的版本

文章出处:

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

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English

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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 UbuntuHelp: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

For information about the Ubuntu repositories see UbuntuHelp:Repositories. Clicking on the icon next a program should take you to information about the Ubuntu package.

Astronomy

• KStars - A virtual planetarium.

• XEphem - A very comprehensive ephemeris/planetarium. Old interface.

• Nightfall - An astronomy application for fun, education, and science.

• Stellarium - Stellarium is a free open source planetarium that shows a realistic sky in 3D, just like what you see with the naked eye, binoculars or a telescope.

• Google Earth - 3D earth viewing application includes a sky view.

More Astronomy applications - UbuntuHelp:UbuntuScience/Astronomy

Biology

• BioPerl - a collection of Perl modules that are useful for programmers in bioinformatics/biology
• also see BioJava and BioPython

• Tree View X - 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 - TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.

• Anchor(ITK)Insight Toolkit (ITK) - an open-source software toolkit for performing registration and segmentation. Created to support the Visible Human Project .
  • • unofficial debian packages

More Biology applications - UbuntuHelp:UbuntuScience/Biology

Biophysics

• Pymol - 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 - A 2D chemical structures editor.

• ghemical - A molecular modeling and computational chemistry package that provides molecular mechanics, semi-empirical (via MOPAC7), and ab initio (via MPQC) calculations.

• gdis - A molecular display program that supports OpenGL and POVRay rendering.

• OpenBabel - A chemical file format conversion program.

• Chemtool - 2D molecule drawing programs similar to Chem'Draw.

• xdrawchem - 2D molecule drawing programs similar to Chem'Draw.

• chemicalInventory - A free chemical inventory database using JChem for structure searching.

• mpqc - The Massively Parallel Quantum Chemistry Program. Ab initio quantum chemical computational package.

• Linux4Chemistry - List of Linux applications that may be useful for chemists.

• GROMACS - A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

Computer Science

Earth Sciences (Geology/Geography)

• Ubuntu:UbuntuGIS This is the page where suggestions and software lists for a professional "out of the box" Ubuntu based GIS workstation should be collected.

• GRASS - 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 - 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) - GMT is an open source collection of ~60 tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing Encapsulated Post'Script File (EPS) illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3-D perspective views.

• WW2D - Java based application similar to NASA World Wind or Google Earth software.

• Google Earth - 3D earth viewing application using satellite images (no cost but proprietary).

• Thuban - An interactive geographic data viewer.

• Survex - Cave surveying and mapping software.

• Therion - Cave surveying - 2D and 3D drawing software.

• Grads - Very fast graphics program for looking at meteorological data. Movies are very fast.

Ecology and Environmental Sciences

• Swarm - A conceptual framework for designing, describing, and conducting experiments on ABMs.

• Repast - The Recursive Porous Agent Simulation Toolkit.

• NetLogo - A Java-based programmable modeling environment for simulating natural and social phenomena.

• Simile - A proprietary ($$$) System Dynamics and object-based modeling and simulation software package similar to Stella, Model Maker, Vensim, etc. It is advertised as "Visual modeling software for the earth, environmental and life sciences". A free evaluation version, which limits the size of saved models, is available.

Econometrics

• Gretl - The GNU Regression, Econometric and Time-Series Library (gretl) is a package for econometric analysis.

Electronics

• Eagle - A printed circuit board design tool.

• oregano - Schematic capture, netlists, and spice for simulations.

• gEDA - GPL'd suite of Electronic Design Automation tools.

• Qucs - An integrated circuit simulator.

• Icarus Verilog - Icarus Verilog is a Verilog simulation and synthesis tool. It operates as a compiler, compiling source code writen in Verilog (IEEE-1364) into some target format.

Engineering Sciences

• QCad - A Computer Aided Design application. It is available in the universe repositories.

• CyCAS - A commercial Computer Aided Design application that runs on Linux. There is a public version available.

• Pro/ENGINEER - A commerical mechanical engineering and design CAD tool.

• A list of CAD software for Linux

Mathematics

• GDL - GNU Data Language is a high level language for numerical computations and data visualization similar to IDL (Interactive Data Language from Research Systems Inc.).

• UbuntuHelp:Octave - GNU Octave is a high-level language, primarily intended for numerical computations. (Similar to UbuntuHelp:MATLAB). Octave

• SciCraft - Addon to Octave, clones Simulink. Still in developement, blocks have to be written by the user. It is supposed to specialize in bioinformatics functions.

• Scilab - Another MATLAB-like application.

• SciCos - A free Simulink-like addon to Scilab.

• Maxima - A computer algebra system (xmaxima is its X interface).
  • • wxMaxima - A nice front end for Maxima.
    • The wxmaxima package doesn't work in Ubuntu 6.06. Please go to the UbuntuHelp: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 UbuntuHelp:LaTeX to render output

• GNU MP - GNU Multi-Precision arithmetic library. Useful if you need to use very big numbers in a C program.

• Anchor(GSL)GSL - The Gnu Scientific Library.

• OOStatistics - A statistics macro for OpenOffice Calc.

• freefem - 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
  • • UbuntuHelp:OpenFOAM has instructions on how to install OpenFOAM on Ubuntu.

• SciPy - An open source library of scientific tools for Python.
  • • SciPy CookBook
    • A wiki page similar to this one.

• F2PY - Fortran to Python interface generator provides a connection between Python and Fortran languages.

• GiNaC - 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.

• UbuntuHelp:Mathematica - A proprietary computer algebra system. Mathematica

• UbuntuHelp:Maple - A proprietary computer algebra system. Maple

• IDL - A proprietary data visualization & data analysis platform.

• UbuntuHelp:MATLAB - A proprietary numerical computing environment and programming language .Matlab

• PDL - Perl Data Language is a powerful data mathematics and data manipulation package for Perl.

• Mupad - A proprietary computer algebra system.

• Clucalc - A tool for 3D visualisations, Clifford algebras and scientific calculations.

• AUTO 2000 - Software for continuation and bifurcation problems in ordinary differential equations.

• GAP - Groups, Algorithms, Programming [1]- a System for Computational Discrete Algebra.

• Pari/GP [2]- designed for fast computations in number theory.

• Aribas[3]- an interactive interpreter for big integer arithmetic and multi-precision floating point arithmetic

• Yacas [4]- an easy to use, general purpose Computer Algebra System, a program for symbolic manipulation of mathematical expressions.

Statistics

• R - for statistical computing and graphics.
  • • JGR - Java GUI for R.
    • RKWard - 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 - 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 - 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 - An OpenGL-based program developed to illustrate the effects of special relativity on the appearance of moving objects.

• JaxoDraw - A UbuntuHelp:Java program for drawing Feynman diagrams.

• Anchor(ROOT)ROOT - An object oriented data analysis framework.

• HepForge - A website hosting high energy physics (HEP) software development projects - ie. Sourceforge for (HEP). HepForge Projects

More Physics applications - UbuntuHelp:UbuntuScience/Physics

Tools

• BIKA - A laboratory information management system (LIMS) built on top of Zope and Plone, and coded in Python.

• Fityk - 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 - "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 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 - 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 - 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 - 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 - A minimal GNOME front end to GNUPlot.
    • gnuplot tips (not so Frequently Asked Questions).

• grace - A 2D WYSIWYG plotting tool that exports to JPEG, PNG, EPS, PDF, and SVG. Also does curve fitting.

• PGPLOT - Fortran- or C-callable graphics subroutine package for making scientific graphs.

• RLPlot - 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 - A scientific application for data analysis and technical graphics. Attempts to be a "Microcal Origin" clone.

• Qtiplot - A 2D/3D, Qt based plotting tool that attempts to be another "Origin" clone.

• LabPlot - Another Qt based 2D/3D GUI plotting tool that also does curve fitting, supports many data formats, UbuntuHelp:LaTeX labeling, GSL GSL functions, and statistics.

• Veusz - A scientific plotting package written in Python.

• Gri - A scientific graphics language.

• Matplotlib - a cross platform 2d plotting library for Python. For instructions on compliling from source see the MatPlotLibHowTo.

• PyX - Python graphics package for the creation of postscript and PDF files - useful for graphing.

• MayaVi - An easy to use scientific data visualizer.

• Paraview - An application designed with the need to visualize large data sets in mind.

• kst - A plotting and data viewing program.

• Lybniz - A simple function graph plotter (graphic calculator), in Python and GTK. Ubuntu .deb avaliable.

• Zhu3D - Interactive 3D plotting program using OpenGL.

Plot Digitizers

• Plot Digitizer - A Java program used to digitize scanned plots of functional data.

• g3data - A program for extracting data from graphs.

• Engauge Digitizer - 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 - A free image processing system.

Vector Drawing Tools

• Xfig - A diagram and figure creation tool. Can import GIF, JPEG, and EPS figures and can export to Postscipt, UbuntuHelp:LaTeX, and bitmap files.

• Skencil - An excellent vector drawing package. Especially useful for creating and annotating existing postscript figures. Numerous plugins are available, most notably a UbuntuHelp:LaTeX plugin. Can import many different formats.

• Tgif - Another excellent postscript drawing program. Most suitable for black and white postscript figures.

• Inkscape - Excellent vector drawing program. Uses SVG format by default, but can write to EPS, PDF and UbuntuHelp:LaTeX with PSTricks macros, among other formats.

• Dia - A "Visio" like diagram tool. Especially useful for simple circuits and flowcharts.

• Ipe - A drawing editor for creating figures in PDF or (encapsulated) Postscript format. Incorporates UbuntuHelp:LaTeX code quite well.

• jPicEdt - Java based drawing program which can generate UbuntuHelp: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.

Word Processing Tools

• UbuntuHelp: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

• UbuntuHelp:Lyx - A WYSIWYM (What You See Is What You Mean) UbuntuHelp:LaTeX frontend. Lyx

• Anchor(Kile) Kile - A UbuntuHelp:LaTeX-frontend for KDE, with support for syntax highlighting and convenient palettes for all standard mathematical symbols and text formatting. It also provides easy access to forward and inverse search facilities.

• eqe - Allows you to write equations in UbuntuHelp:LaTeX and drag and drop them into other applications.

• OOoLatex - A set of Open'Office macros designed to integrate UbuntuHelp:LaTeX equations.

• Conglomerate - 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 - Like Kile Kile but loads faster.

• TeXmacs - A WYSIWIG scientific text editor.
  • • doubles as an interface for computer algebra systems like [Maxima], UbuntuHelp:Maple, mupad, axiom, giac, GTybalt, Macaulay 2, pari, yacas.
    • can also be used as a front end for [R], UbuntuHelp:Octave, [GNUplot], [Xfig], [Dr. Geo], [Eukleides], [Qcl].

• preview-latex - (almost) turns emacs into a WYSIWYG-UbuntuHelp:LaTeX-frontend.
  • • Can also be used in lyx.

• latex2html , tth and hevea for converting UbuntuHelp:LaTeX to html.

• [5] - A small Pidgin (see UbuntuHelp:GaimHowto) plugin that allows you to insert UbuntuHelp:LaTeX formulas into IM conversations.

• UbuntuHelp: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. MiKTeX Tools

Bibliographic Tools

• Bibtex - A program and file format for bibliographies in UbuntuHelp:LaTeX documents.
  • • A comprehesive Bibtex manual

• Pybliographer - A tool for managing bibliographic databases. Pybliographer is the graphical interface.

• Jabref - A Java-based BibTeX bibliography manager that can be used in conjunction with Lyx.

• KBibTeX - A BibTeX editor for KDE.

• Ubuntu:Bibus - Bibus is a bibliographic database. Bibus works with Open'Office.org 2.0. Bibus

• Bibutils - Collection of command line tools for bibliography format convertion. Format examples: BiBTeX, RIS, End'Note, COPAC, ISI, Pub'Med...

• Referencer - Referencer is a Gnome application to organize documents or references, and ultimately generate a BibTeX bibliography file. Features include: Automatic metadata retrieval; smart web links; import from BibTeX, Reference Manager and EndNote; tagging.

• Tellico - 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 - A Gnome application for organizing your book collections. It allows to sort entries along any field (author, year, etc.), and to retrieve book information from Internet.

• cb2Bib - The cb2Bib is a tool for rapidly extracting unformatted, or unstandardized, biblographic references from email alerts, journal Web pages, and PDF files.
  • • The cb2Bib reads the clipboard text contents and process it against a set of predefined patterns. If this automatic detection is successful, cb2Bib formats the clipboard data according to the structured BibTeX reference standard.
    • Otherwise, if no predefined format pattern is found or if detection proves to be difficult, manual data extraction is greatly simplified by cb2Bib. In most cases, such manual data extraction will provide with a new, personalized pattern to be included within the predefined pattern set for future automatic extractions.
    • Once the bibliographic reference is correctly extracted, it is added to a specified BibTeX database file. Optionally, article PDF files, if available, are renamed to its citeID and moved to a desired directory as a personal article library.

Distributed Computing

• openmosix - Turns a network of ordinary computers into a supercomputer.

• BOINC - 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.

• UbuntuHelp:FoldingAtHome - A protein folding simulation run by the Stanford University.

Ubuntu Packages

Science Section

6.06, 6.10, 7.04, 7.10.

Mathematics Section

6.06, 6.10, 7.04, 7.10,

TeX Section

6.06, 6.10, 7.04, 7.10.

Alternatives to Proprietary Scientific Software

See UbuntuHelp:UbuntuScience/AlternativesToProprietarySoftware

Hardware

• Labview for linux (non-free) [6]

Data acquisition

• National Instruments GPIB drivers for linux. [7]
• Comedi - Open source drivers, tools and libraries. comedi

Computer controlled systems

• RTAI - Real-Time Application Interface is a hard real-time extension to the Linux kernel. [8]

• EPICS - A set of Open Source software tools, libraries and applications to create distributed soft real-time control systems for scientific instruments such as a particle accelerators, telescopes and other large scientific experiments. [9]

Other information

Other Linux Distributions for Scientists

• Quantian - A Knoppix / Debian variant tailored to numerical and quantitative analysis.

• Debian-Med - Debian-Med is a "Custom Debian Distribution" for medical practice and research.
  • • debian-med metapackages are in Ubuntu(Universe): to list them type: apt-cache search debian-med

• Scientific Linux - Linux release put together by Fermilab and CERN based on RH

• Madrake4Chemistry - Mandrake Linux for chemistry

• TUn!x - A new project especially designed for the Technical University of Vienna. See also: http://informatik.tuwien.ac.at/tunix

• Poseidon Linux - A Brazilian distribution designed for academic and scientific use.

• _dvd_knoppixmake_sci.htm Xplora - A Knoppix/Debian based DVD which aims to make science accessible for schools.

• CAELinux - A liveDVD linux for Computer Aided Engineering.

Unofficial Ubuntu/Debian repositories with science software

• repository of ROOT ROOT packages
• Yaroslav Halchenko repository
• repository of ITK ITK Packages
• Teemu Ikonen repository

• Daniel Leidert repository ( read)

• Carlo Segre repository

• 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

• UbuntuHelp:OpenFOAM - How to install Open'FOAM on Ubuntu.

• UbuntuHelp:UbuntuScience/Astronomy

• UbuntuHelp:UbuntuScience/Biology

• UbuntuHelp:UbuntuScience/Physics

• UbuntuHelp: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
• [10] - 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 - Sollection 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.

Books