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1. SwisTrack: Multi-Object Video Tracking Software

SwisTrack allows for tracking multiple objects such as insects or robots from a video stream provided by a file or directly from a camera. SwisTrack's user interface allows adjusting parameters on the flight, and thus allow to find an optimal tracking configuration choosing from a suite of already implemented algorithms for segmentation and filtering in an intuitive fashion. Contributing code to SwisTrack is made easy as tracking core and GUI share an XML description of available tracking modes and its parameters.

2. GFortran

Gfortran is the name of the GNU Fortran 95 project, developing a free Fortran 95 compiler for GCC, the GNU Compiler Collection. The gfortran development effort uses an open development environment in order to attract a larger team of developers and to ensure that gfortran can work on multiple architectures and diverse environments.

3. OpenSim - a dynamic 3D robotics simulator for AI research

A robotics simulator that utilizes a constrained rigid-body (Newtonian) solver to simulate multiple mobile robots and manipulator systems, including sensors. Intended for robotics/AI researchers. Currently includes various sensor simulations and inverse kinematics solvers for redundant serial-chain manipulators.

4. The Chemistry Development Kit (CDK)

e CDK classes are Java utitility classes for ChemoInformatics and Computational chemistry, written in Java. They are developed constantly developed parallel to other projects that make use of them. They are a complete re-write of the CompChem classes that were the basis of JChemPaint, a Java Editor for 2D chemical structures, and of JMDraw, a Java package for the graphical layout of 2D chemical structures.

5. DUBSI 1.0, a Simulink blockset

The Dutchroll Blockset for Simulink (DUBSI), version 1.0, is a generic blockset with a number of useful Simulink blocks. Included are several source signals, switches, new To Workspace blocks, variable gains, rotations, a useful Moving Average filter and a 'soft limiter', plus detailed HTML documentation. It is available as free download under the Dutchroll Open Source Software License (DOSSL), version 1.0, which has been accepted as valid Open Source license by Sourceforge.

6. Maxima

Maxima is a system for the manipulation of symbolic and numerical expressions, including differentiation, integration, Taylor series, Laplace transforms, ordinary differential equations, systems of linear equations, polynomials, and sets, lists, vectors, matrices, and tensors. Maxima yields high precision numeric results by using exact fractions, arbitrary precision integers, and variable precision floating point numbers. Maxima can plot functions and data in two and three dimensions. Also has a graphical interface built in wxWidgets called wxMaxima (http://andrejv.github.com/wxmaxima/).

7. Fast C++ matrix library with optional interfaces to LAPACK and ATLAS

Armadillo is a C++ linear algebra library (matrix and vector maths) aiming towards a good balance between speed and ease of use. It's distributed under a license that is useful in both commercial and open-source contexts. This library is useful if C++ has been decided as the language of choice (due to speed and/or integration capabilities), rather than another language like Matlab or GNU Octave. Armadillo uses a delayed evaluation approach in order to combine several operations into one and reduce (or eliminate) the need for temporaries. This is accomplished through extensive use of recursive templates and template meta-programming. Furthermore, it optionally provides interfaces to LAPACK and ATLAS functions.

8. Celestia

A free 3D space simulator that lets you travel through the solar system and beyond to over 100,000 stars.

9. Nova

Nova is a free Integrated Observational Environment for astronomers. It combines an Ephemeris functionality with the capability of controlling modern "goto"Telescopes and popular CCD cameras.

10. OOFEM

is an object oriented, parallel, multiphysics finite element code system for solving mechanical, transport and fluid mechanics problems.

11. NeoBio - Bioinformatics algorithms in Java

NeoBio is a Java class library of Computational Biology Algorithms. The first version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.

12. JNumeric: Numerical Python for Jython

Provides the functionality for Jython that Numerical Python does for Python (CPython). As the Numerical Python documentation states, it is "...a collection of extension modules to provide high-performance multidimensional numeric arrays to the Python programming language." JNumeric provides the same functionality as the core of Numeric module and aims to provide all of the standard extensions to Numeric module (FFT, LinearAlgebra, RandomArray).

13. Open Visualization Data Explorer

IBM's famous volume renderer that does much much more.

14. GMT - Generic Mapping Tools

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. GMT supports ~30 map projections and transformations and comes with support data such as coastlines, rivers, and political boundaries. GMT is developed and maintained by Paul Wessel and Walter H. F. Smith with help from a global set of volunteers, and is supported by the National Science Foundation. It is released under the GNU General Public License.

15. Emergent

Emergent (a major rewrite of PDP++) is a comprehensive simulation environment for creating complex, sophisticated models of the brain and cognitive processes using neural network models. These same networks can also be used for all kinds of other more pragmatic tasks, like predicting the stock market or analyzing data. It includes a full GUI environment for constructing networks and the input/output patterns for the networks to process, and many different analysis tools for understanding what the networks are doing. It has a new tabbed-browser style interface with full 3D graphics (via OpenGL and Open Inventor/Coin3D), and powerful new GUI programming tools and data processing and analysis capabilities.

16. Free Science Resource

A Free Science Info Site (mainly books, software, links)

17. Babel

Babel is a program designed to interconvert a number of file formats currently used in molecular modeling.

18. Gretl

Gretl (Gnu Regression, Econometrics and Time-series Library) is a cross-platform software package for econometric analysis, written in the C programming language. It is is free, open-source software. You may redistribute it and/or modify it under the terms of the GNU General Public License (GPL).

19. Ensembl Genome Server

Ensembl is a joint project between EMBL-EBI and the Sanger Centre to develop a software system which produces and maintains automatic annotation on eukaryotic genomes.

20. Bioperl

The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.

21. Swarm

Swarm is a software package for multi-agent simulation of complex systems.

22. Saros

Saros is a research project to enable distributed pair programming (also called remote pair programming) in the Java IDE Eclipse. Saros supports real-time collaboration by two and more peers and adds many features to increase awareness and presence regarding the whereabouts of each peer.

23. OpenFOAM

The OpenFOAM (Field Operation and Manipulation) software package can simulate anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics, electromagnetics and the pricing of financial options.

24. FreeGIS

Free GIS Software and Free Geo-Data

25. Nature Magazine's Open Access Debate

The Internet is profoundly changing how scientists work and publish. New business models are being tested by publishers, including open access, in which the author pays and content is free to the user. This ongoing web focus will explore current trends and future possibilities. Each week, the website will publish specially commissioned insights and analysis from leading scientists, librarians, publishers and other stakeholders, as well as key links, and articles from our archive.

26. Aciqra

Aciqra is an open source virtual planetarium which tracks the locations of planets, the sun and moon along with Earth's shadow and displays the phases of the moon and planets in realtime. The program also includes several widgets which give it added functionality including Epidermidis graphing, planet location lister, an Eclipse finder and a conjunction engine.

27. BioCatalogue - the Life Sciences Web Service Registry

The BioCatalogue is a registry of biological Web Services. The BioCatalogue website is freely accessible to the world as it is searchable and indexable to search engines. It provides an open platform for biological Web Services registration, annotation and monitoring.

28. HFLOAT

The HUGE-FLOAT package. It's for computations with very long (huge!) floating point numbers. With hfloat you can compute pi to several million digits.

29. Quantum GIS (QGIS)

Quantum GIS (QGIS) is a user friendly Open Source Geographic Information System (GIS) that runs on Linux, Unix, Mac OSX, and Windows. QGIS supports vector, raster, and database formats. QGIS is licensed under the GNU General Public License. QGIS lets you browse and create map data on your computer. It supports many common spatial data formats (e.g. ESRI ShapeFile, geotiff). QGIS supports plugins to do things like display tracks from your GPS. QGIS is Open Source software and its free of cost.

30. AcouSTO (Acoustics Simulation TOol)

AcouSTO (Acoustics Simulation TOol) is an open source Boundary Element Method (BEM) solver for the Kirchhoff-Helmholtz Integral Equation (KHIE). The code is released under GPL v3.0.

31. Salome

SALOME is a free software that provides a generic platform for Pre and Post-Processing for numerical simulation. It is based on an open and flexible architecture made of reusable components available as free software. It is open-source (LGPL), and you can download both the sourcecode and the executables from this site. Salome Platform: * Supports interoperability between CAD modeling and computation software (CAD-CAE link) * Makes easier the integration of new components on heterogeneous systems for numerical computation * Sets the priority to multi-physics coupling between computation software * Provides a generic user interface, user-friendly and efficient, which helps to reduce the costs and delays of carrying out the studies * Reduces training time to the specific time for learning the software solution which has been based on this platform * All functionalities are accessible through the programmatic integrated Python console

32. OpenScientist

OpenScientist is an integration of open source products working together to do scientific visualization and data analysis ; in particular for high energy physics (HEP).

33. K3DSurf

K3DSurf is a program for visualizing and manipulating multidimensional surfaces by using Mathematical equations. It's also a "modeler" for POV-Ray in the area of parametric surfaces. It features 3D, 4D, 5D, and 6D HyperObjects visualization, full support for all functions (like the C language), support for mouse events in the drawing area, animation and morph effects, Povscript and mesh file generation, and support for VRML2 and OBJ files. More than 100 examples are provided.

34. SAGE

SAGE is free open source math software that supports research and teaching in algebra, geometry, number theory, cryptography, numerical computation, and related areas. Both the SAGE development model and the technology in SAGE itself is distinguished by an extremely strong emphasis on openness, community, cooperation, and collaboration: we are building the car, not reinventing the wheel. The overall goal of SAGE is to create a viable free open source alternative to Maple, Mathematica, Magma, and MATLAB.

35. Gabedit

Gabedit is a graphical interface to Gaussian, Molcas and Molpro computational chemistry packages running locally or on a remote server. It includes a 3D molecule editor and viewer. Most major molecular file formats are supported and graphics can be exported in many formats.

36. OpenFlower - Open Source CFD Software

OpenFlower (FLOW solvER) is a C++ open source CFD code mainly intended to solve the turbulent incompressible Navier-Stokes equations with a LES approach. It can deal with arbitrary complex 3D geometries with its finite volume approach (multi-elements meshes are accepeted).

37. Stellarium

Stellarium is an open source desktop planetarium for Linux/Unix, Windows and MacOSX. It renders the skies in realtime using OpenGL, which means the skies will look exactly like what you see with your eyes, binoculars, or a small telescope. Stellarium is very simple to use, which is one of its biggest advantages: it can easily be used by beginners.

38. JPIV Particle Image Velocimetry

JPIV is a software package for Particle Image Velocimetry (PIV). The program is open source and platform independent.

39. PhyloSort

A Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.

40. GRASS GIS

GRASS GIS (Geographic Resources Analysis Support System) is an open source, free Geographical Information System (GIS) with raster, topological vector, image processing, and visualization functionality.

41. Open Natural Language Processing Projects

linguistic analysis software

42. Taverna Workbench and Server

Taverna is an open source domain independent Workflow Management System a suite of tools used to design and execute scientific workflows. Taverna has been created by the myGrid project and funded through the OMII-UK. Taverna has a guaranteed funding till 2014. The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool that for a quick execution of workflows from a terminal without the overheads of the GUI. Taverna allows for the automation of experimental methods through the use of a number of different (local or remote) services from a very diverse set of domains biology, chemistry and medicine to music, meteorology and social sciences. Effectively, Taverna allows a scientist with limited computing background and limited technical resources and support to construct highly complex analyses over public and private data and computational resources, all from a standard PC, UNIX box or Apple computer.

43. Open Source Seismic Interpretation System

OpendTect is an open source seismic interpretation software system for processing, visualizing and interpreting multi-volume seismic data, and for fast-track development of innovative interpretation tools. Optionally OpendTect can be extended with (closed source) commercial plugins.

44. IRAF

Image Reduction and Analysis Facility

45. CAE Linux

A Linux distribution designed specifically for computer aided engineering. Based on the open-source CAE Salom & Code_Aster software, you can load STEP / IGES geometry in Salom and start partitionning and meshing your problem in just 5 minutes.

46. Madagascar

Madagascar is an open-source software package for geophysical data processing and reproducible numerical experiments. Its mission is to provide a convenient and powerful environment and a convenient technology transfer tool for researchers working with digital image and data processing. The technology developed using the Madagascar project management system is transferred in the form of recorded processing histories, which become "computational recipes" to be verified, exchanged, and modified by users of the system.

47. Elmer

Elmer is an Open Source Finite Element Software for Multiphysical Problems. Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM).

48. Quantum-Espresso

Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).

49. myExperiment

myExperiment makes it easy to find, use and share scientific workflows and other Research Objects, and to build communities.

50. jHepWork

Data analysis framework