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
- 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 - UbuntuScience/Astronomy
Biology
BioPerl
- a collection of Perl modules that are useful for programmers in bioinformatics/biology ClustalW
- Global multiple nucleotide or peptide sequence alignment ClustalX
- GUI for ClustalW
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. Insight Toolkit (ITK)
- an open-source software toolkit for performing registration and segmentation. Created to support the Visible Human Project.
More Biology applications - 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 VolMap
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 ChemDraw. xdrawchem
- 2D molecule drawing programs similar to ChemDraw. 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. 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
- 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 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
- 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.
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
- A collection of neuroscience related software integrated into Debian (and thus Ubuntu)
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. 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
LabVIEW for Linux (non-free) http://sine.ni.com/nips/cds/view/p/lang/en/nid/2541
Data acquisition
National Instruments GPIB drivers for Linux. http://www.ni.com/linux/gpib.htm
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. 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
UbuntuScience/Howto (still a work in progress....)
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
repository of ROOT packages
NeuroDebian of neuroscience-related software with backports for Debian and Ubuntu releases.
repository of ITK Packages
Daniel Leidert repository ( read)
Carlo Segre repository includes Ubuntu builds
Mailing Lists about Linux and Science
Related Wiki Pages
MOTU/Teams/Science is the MOTU team responsible for the upkeep of science packages within the Universe repository.
UbuntuSciencePackages is a list of packages that are in the official Ubuntu Repositories that scientists use.
UbuntuScienceMetaPackages discusses possible science metapackages
OpenFOAM - How to install OpenFOAM on Ubuntu.
Online Forums
Ubuntu Education & Science Forum
Some forum threads
Links
sourceforge - Scientific software on sourceforge.
DebianLinux.Net-Scientific Software - Links to science software.
freshmeat - Scientific software on freshmeat.
http://www.linuxlinks.com/Software/Scientific/ - Scientific Linux software.
gnome-files - scientific software - Scientific apps for gnome.
kde-apps.org- scientific software - Scientific apps for kde.
Free Science - FreeScience provides free scientific books and software.
Ubuntu Maverick for Research - Installation, pointers to many relevant programs on Ubuntu 10.10 for research (especially focused on PhD studies).
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.