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1. 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).

2. CompHEP

A package for evaluation of Feynman diagrams and integration over multi-particle phase space.

3. 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.

4. 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.

5. JabRef bibliography manager

JabRef is a graphical application for managing bibliographical databases. The main focus is on BibTeX databases, but other database formats will be supported as well. JabRef is distributed under the terms of the Gnu General Public License, runs on all platforms and requires java 1.4.

6. GAMESS

The General Atomic and Molecular Electronic Structure System is a freely availible general ab initio quantum chemistry package. Free graphics programs are also availible for downloading.

7. Maxima - a Computer Algebra System

Symbolic mathematics by the computer started out with the DOE/Macsyma project at MIT almost 50 years ago. Two of the spin-offs from the project are the Mathematica and the Maple suites. Since 1999 there is also a GNU-version of the Macsyma system, henceforth named Maxima. It is very powerful and slightly under-documented.

8. GROMACS

GROMACS is a very fast molecular dynamics code, which comes with lots of features like PME, a variety of cut-offs, non-equilibrium MD and more. The package includes also other algorithms like normal mode analysis and essential dynamics plus a wealth of analysis tools. It is supported by some of the leading trajectory viewers (VMD and gOpenMol). GROMACS is distributed under the GPL.

9. 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.

10. 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.

11. 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.

12. 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.

13. HMMER

Profile hidden Markov models for biological sequence analysis.

14. 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.

15. 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).

16. 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.

17. Scilab

Scilab is a scientific software package for numerical computations in a user-friendly environment. It features: Elaborate data structures (polynomial, rational and string matrices, lists, multivariable linear systems,...). Sophisticated interpreter and programming language with Matlab-like syntax. Hundreds of built-in math functions (new primitives can easily be added). Stunning graphics (2d, 3d, animation). Open structure (easy interfacing with Fortran and C via online dynamic link). Many built-in libraries: Linear Algebra (including sparse matrices, Kronecker form, ordered Schur,...). Control (Classical, LQG, H-infinity,...). Package for LMI (Linear Matrix Inequalities) optimization. Signal processing. Simulation (various ode's, dassl,...). Optimization (differentiable and non-differentiable, LQ solver). Scicos, an interactive environment for modeling and simulation of dynamical systems. Metanet (network analysis and optimization). Symbolic capabilities through Maple interface. Parallel Scilab.

18. Open Access: Should scientific articles be available online and free to the public?

Amanda Schaffer' Medical Examiner column in Slate magazine on the topic of the public library of science. Highly recommended.

19. OpenMap

Open Systems Mapping Technology - allows users to see and manipulate geospatial information.

20. Edwin H. Connell: Elements of Abstract and Linear Algebra

A free online textbook on abstract algebra with emphasis on linear algebra.

21. Nuclear Simulation Java Class Libraries

The class libraries here provide infrastructure for creating simulations of low energy nuclear physics experiments, as well as some useful working programs that do simple simulations and analysis of experiments performed with magnetic spectrographs.

22. jHepWork

Data analysis framework

23. Octave

GNU Octave is a high-level language, primarily intended for numerical computations.

24. GSL - The GNU Scientific Library, a free numerical library for C programmers

A free numerical library for scientific computing under the GNU General Public license.

25. The R Project for Statistical Computing

R is `GNU S' - A language and environment for statistical computing and graphics. R is similar to the award-winning S system, which was developed at Bell Laboratories by John Chambers et al. It provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, ...).

26. 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.

27. 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.

28. 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.

29. Free Science Resource

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

30. FELLA (Free Electron Laser Atomic, Molecular, and Optical Physics Program Package)

The software package FELLA has been written for basic research in atomic, molecular, and optical physics. The atomic physics programs treat the atomic electronic structure in Hartree-Fock-Slater approximation and the interaction of electrons with light of up to two colors. The molecular physics programs treat the x-ray absorption by laser-aligned molecules. An optical physics code describes the propagation of a laser and x-rays through a gaseous medium. Especially, FELLA has been inspired by the upcoming x-ray free electron lasers to study atoms and molecules in their light in combination with intense optical lasers. However FELLA is more general and has been used so far to study atoms and molecules in the light of third-generation synchrotrons.

31. 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.

32. LAM/MPI Parallel Computing

LAM/MPI is a high-quality open-source implementation of the Message Passing Interface specification, including all of MPI-1.2 and much of MPI-2. Intended for production as well as research use, LAM/MPI includes a rich set of features for system administrators, parallel programmers, application users, and parallel computing researchers.

33. JPIV Particle Image Velocimetry

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

34. IMTEK Mathematica Supplement (IMS)

The IMS is an open source Mathamtica Add-On providing more than 650 functions to Mathamtica: a nD fintie element environment, a circtuit simulator, model orde reduction, unstructured plotting and visualization. Many tutorials for simulation, Quamtum Mechanics and interfaces to VTK, HDL, Ansys, Tetgen, Triangle and more

35. ImageJ

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

36. FFTW

A fast, free C FFT library; includes real-complex, multidimensional, and parallel transforms. Benchmarked against many other FFTs.

37. Programs from Frenkel and Smit's book "Understanding Molecular Simulations"

Good starter code for MC and MD simulations

38. SourceForge - Science and Engineering

SourceForge is a web based service dedicated free hosting for opensource developers and their user base. Their site currently hosts over 90,000 open source projects which may be searched via multiple project parameters. Specific to the OpenScience focus, users can find over 7,000 projects under the science and engineering category.

39. Mersenne Twister

A very fast random number generator with a period of 2^19937-1

40. FCCU GNU/Linux Forensic Boot CD

FCCU GNU/Linux Forensic Bootable CD is a bootable CD based on KNOPPIX that contains a lot of tools suitable for computer forensic investigatins, including bash scripts. Its main purpose is to create images of devices prior to analysis, and it is used by the Belgian Federal Computer Crime Unit.

41. GAUL: Genetic Algorithm Utility Library

A Genetic Algorithm Routine Library

42. Vis5D

Vis5D is a system for interactive visualization of large 5-D gridded data sets such as those produced by numerical weather models.

43. GAP - Groups, Algorithms and Programming

GAP is a free system for computational discrete algebra.

44. MIT Photonic-Bands Home Page

free software for computation of photonic band structures

45. MOSCITO

MOSCITO is designed for molecular dynamics simulations of condensed phase systems defined by classical molecular mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS.

46. BioJava

Java tools for processing biological data

47. CLHEP

A Class Library for High Energy Physics

48. Celestia

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

49. Python and Scientific Computation

The home page for Scientific Computing with Python.

50. 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.