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. 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).

3. Avogadro

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers a flexible rendering engine and a powerful plugin architecture.

4. 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).

5. Jmol

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. It includes a web browser applet that can be integrated into web pages, a standalone Java application that runs on the desktop, and a development tool kit that can be integrated into other Java applications.

6. RapidMiner

RapidMiner (formerly YALE) is an open-source data mining solution. Applications of RapidMiner cover a wide range of real-world data mining tasks.

7. JChemPaint

A Java program for drawing of 2D chemical structures

8. KNIME

KNIME, pronounced [naim], is a modular data exploration platform that enables the user to visually create data flows (often referred to as pipelines), selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models.

9. The Molecular Workbench Software

The Molecular Workbench is a set of tools that can be used to compute and visualize the motion of ensembles of atoms and molecules. The motion of each entity is estimated using classical dynamics and applicable forces, including van der Waals potentials, Coulomb interactions, harmonic approximations to bonds, external fields, effective hydrophobic/hydrophilic forces, as well as boundaries and bond formation/breaking rules. Meso-scale objects and their interactions based on the Gay-Berne model are supported. The resulting ensembles can illustrate energy conservation, gas laws, pressure, phase transitions, chemical bonding, chemical reactions, Maxwell velocity distribution, osmosis, electrolysis, electrophoresis, liquid crystals, polymers, protein folding, molecular recognition, and more. Molecular Workbench also provides an authoring environment that can be used to easily create, visualize, annotate, contextualize, cross-link and distribute molecular dynamics models. Students can use the software to explore a vast range of preexisting models, or to develop models of their own.

10. FreePOOMA C++ Numerical Library

FreePOOMA is a C++ library supporting element-wise, data-parallel, and stencil-based physics computations using one or more processors. The library automatically handles all interprocessor communication, obviating the need for any explicit communication code. The library supports high-level syntax close to mathematical or algorithmic syntax (like Fortran 95), easing the conversion from algorithms to code.

11. 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.

12. 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.

13. The CP2K project homepage

CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.

14. catool

catool is a cross-platform GPL tool for the analysis of internal combustion engine pressure data. It calculates parameters such as IMEP, MFB, Pmax, Knock pressure and calculates cycle statistics. Data can be imported in CSV or AVL IFile format and exported as CSV, MATLAB or AVL IFile.

15. Ghemical

Ghemical is a computational chemistry software package released under the GNU GPL. Ghemical can do all-atoms molecular mechanics (there is an experimental Tripos 5.2-like force field for organic molecules), and reduced protein models.

16. Chemsuite Project

Chemsuite is a set of programs intended to provide to chemists an alternative to commercial chemistry office suites.

17. Weka

Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.

18. Lybniz

Lybniz is an easy to use mathematical function graph plotter using pyGTK. It is sutable for use as a graphing calculator or in education

19. Blitz++ library

Blitz++ is a C++ class library for scientific computing which provides performance on par with Fortran 77/90. It uses template techniques to achieve high performance. The current versions provide dense arrays and vectors, random number generators, and small vectors and matrices.

20. Seismic Unix (SU) home page

Seismic Unix aka SU - Open Source Seismic Processing package for Unix/ Linux - Source Download - Documentation - Graphical interfaces are available (TKSU and I_SU)

21. Celestia

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

22. Free Science Resource

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

23. 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.

24. OpenFVM

OpenFVM is a general open source three-dimensional CFD solver (for Linux and Windows). It uses the unstructured finite volume method to simulate non-isothermal transient flow. Gmsh is used for pre- and post- processing.

25. BKchem

BKchem is free chemical drawing program with many features, written in python.

26. Raster3D

Raster3D is a set of tools for generating high quality raster images of proteins or other molecules.

27. 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.

28. Code Aster

Code Aster is a genaral purpose FEA code. It has the ability to solve problems in non-linear thermo-mechanics, coupled fluid-structure dynamics, sismic/non-linear explicit dynamics, contacts, and visco-plasticity.

29. Chemtool

Chemtool is a program for drawing organic molecules easily and store them as an Postscript, X-Bitmap, LaTeX and XFig file.

30. 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

31. 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.

32. 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.

33. AGM Build

A molecular builder and conformational editor. AGM Build can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. Features: * Geometry editing * Lattice building * Building of chain molecules (for example proteins) * Chains with predetermined conformations * Charges and atom types according to selected Force Field

34. Open Natural Language Processing Projects

linguistic analysis software

35. GAMGI

The General Atomistic Modelling Graphic Interface. GAMGI aims to be useful for: 1) the scientific community working in Atomistic Modelling, that needs a graphic interface to build input data and to view and analyse output data, calculated with Ab-Initio and Molecular Mechanics programs; 2) the scientific community at large, studying Chemistry, Physics, Materials Science, Geology, etc., that needs a graphic interface to view and analyse atomic structural information and to prepare images for presentations in classes and seminars; 3) teaching chemistry and physics in secondary schools and universities, even inviting students to install and run GAMGI at home; 4) science promotion, in schools, exhibitions and science museums.

36. 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).

37. PGOPHER

PGOPHER is a general purpose program for simulating and fitting rotational spectra. PGOPHER will handle linear molecules and symmetric and asymmetric tops, including effects due to unpaired electrons and nuclear spin. The program can handle many sorts of transitions, including Raman, multiphoton and forbidden transitions. It can simulate multiple species and states simultaneously, including special effects such as perturbations and state dependent predissociation. Fitting can be to line positions or band contours.

38. V_Sim

V_Sim visualizes atomic structures such as crystals, grain boundaries, etc. V_Sim can use information from files in binary d3 format, in ascii, or in "xyz" format.

39. 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.

40. Gpiv

Gpiv is a graphic user interface program for recording and analyzing images obtained from a fluid flow that has been seeded with tracer particles by the so-called Particle Image Velocimetry technique (PIV). The program allows to have a quick overview of the parameter settings of all processes, easily changing them, executing the processes and visualizing their results in an interactive way.

41. 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.

42. OOFEM

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

43. 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.

44. 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.

45. SAGA

SAGA -- The System for an Automated Geo-scientific Analysis is a free Geographical Information System (GIS). The SAGA API supports grid data like digital terrain models and satellite images, vector data, and tables. This API makes it easy to implement new algorithms and exempts the developer from hassle programming overhead like user-interface design or file-io. SAGA comes with a big collection of SAGA-Modules, in areas of terrain- analysis, geo-statistics, image processing and process simulation.

46. iBabel cheminformatics and molecule viewer

This is an Applescript Studio application that provides a front-end for a variety of Cheminformatics tools. To date these include file conversion (between a vast range of chemical file formats), SMARTS-based substructure searching, similarity searching, list manipulation, overlaying using OpenBabel, a 2D viewer using JChempaint, a 3D molecule viewer using Jmol, binaries for which are now included in the iBabel application. Full description as a PDF file or in CDK news.

47. EasyChem

EasyChem is a program designed to draw chemical molecules, written under Linux and using Gtk+ 2. Focus is on press-quality final drawings, drawing very easily ornaments (non-bonding electron pairs, ...) and exporting to EPS/PDF formats with LaTeX fonts (Computer Modern).

48. Crystal orbital algebraic diagrammatic construction

The CO-ADC program suite has been designed to calculate band structures of semiconducting and insulating crystals. Thereby, the electron correlations are accounted for on ab initio level using the crystal orbital algebraic diagrammatic construction (CO-ADC) scheme. The software comprises an independent band Lanczos code for real- symmetric, complex-symmetric, and complex-Hermitian matrices.

49. 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.

50. 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.

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