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Legend:

IconsPage/ubuntu.png - installed by default in Ubuntu
IconsPage/kubuntu.png - installed by default in Kubuntu
IconsPage/edubuntu.png - installed by default in Edubuntu
IconsPage/ubuntu_grey.png - Main (officially supported) Ubuntu repository, not installed by default
IconsPage/community.png - Universe (community maintained) repository
IconsPage/important.png - Multiverse (non-free) repository

Those installed by default are in Main (officially supported) Ubuntu repository. For information about the Ubuntu repositories see Repositories. Clicking on the icon next a program should take you to information about the Ubuntu package.

Astronomy

  • KStars http://packages.ubuntu.com/kstars - A virtual planetarium.

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

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

  • Stellarium http://packages.ubuntu.com/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 http://packages.ubuntu.com/googleearth-package - 3D earth viewing application includes a sky view.

More Astronomy applications - UbuntuScience/Astronomy

Biology

  • BioPerl http://packages.ubuntu.com/bioperl - a collection of Perl modules that are useful for programmers in bioinformatics/biology

  • ClustalW http://packages.ubuntu.com/clustalw - Global multiple nucleotide or peptide sequence alignment

  • Tree View X http://packages.ubuntu.com/treeviewx - 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 http://packages.ubuntu.com/tree-puzzle - TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.

  • Insight Toolkit (ITK) http://packages.ubuntu.com/insighttoolkit - an open-source software toolkit for performing registration and segmentation. Created to support the Visible Human Project.

More Biology applications - UbuntuScience/Biology

Biophysics

  • Pymol http://packages.ubuntu.com/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 VolMap

Chemistry

  • GChemPaint http://packages.ubuntu.com/gchempaint - A 2D chemical structures editor.

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

  • gdis http://packages.ubuntu.com/gdis - A molecular display program that supports OpenGL and POVRay rendering.

  • OpenBabelhttp://packages.ubuntu.com/openbabel - A chemical file format conversion program.

  • Chemtoolhttp://packages.ubuntu.com/chemtool - 2D molecule drawing programs similar to ChemDraw.

  • xdrawchem http://packages.ubuntu.com/xdrawchem - 2D molecule drawing programs similar to ChemDraw.

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

  • mpqc http://packages.ubuntu.com/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 http://packages.ubuntu.com/gromacs - 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 http://packages.ubuntu.com/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 http://packages.ubuntu.com/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) http://packages.ubuntu.com/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 PostScript 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 http://packages.ubuntu.com/googleearth-package - 3D earth viewing application using satellite images (no cost but proprietary).

  • Thuban http://packages.ubuntu.com/thuban - An interactive geographic data viewer.

  • Survex http://packages.ubuntu.com/survex - Cave surveying and mapping software.

  • Therion http://packages.ubuntu.com/therion - Cave surveying - 2D and 3D drawing software.

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

  • PostGIS http://packages.ubuntu.com/postgis - 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.

Neuroscience

  • NeuroDebian http://neuro.debian.net/pkglists/pkgs-by_release-ubuntu_11.04_%22natty_narwhal%22_%28natty%29.html - A collection of neuroscience related software integrated into Debian (and thus Ubuntu)

Physics

  • Cernlib http://packages.ubuntu.com/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 http://packages.ubuntu.com/lightspeed - 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.

  • 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

Alternatives to Proprietary Scientific Software

See UbuntuScience/AlternativesToProprietarySoftware

Hardware

Data acquisition

Computer controlled systems

  • RTAI - Real-Time Application Interface is a hard real-time extension to the Linux kernel. http://www.rtai.org/

  • EPICS - A set of Open Source software tools, libraries and applications to create distributed soft real-time control systems for scientific instruments such as a particle accelerators, telescopes and other large scientific experiments. http://www.aps.anl.gov/epics/index.php

Other information

Other Linux Distributions for Scientists

  • Ubuntu sci - The aim of the Ubuntusci 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.

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

  • CAELinux - A live DVD Linux for Computer Aided Engineering.

Unofficial Ubuntu/Debian repositories with science software

Mailing Lists about Linux and Science

Online Forums

Ubuntu Education & Science Forum

Some forum threads


CategoryScience

UbuntuScience (last edited 2013-12-14 11:58:25 by knome)