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1. Protomol: ProtoMol is a high-performance framework in c++ for rapid prototyping of novel algorithms for molecular dynamics and related applications. Its flexibility is achieved primarily through the use of inheritance and design patterns (object-oriented programming). Performance is obtained by using templates that enable generation of efficient code for sections critical to performance (generic programming). The framework encapsulates important optimizations that can be used by developers, such as parallelism in the force computation. Its design is based on domain analysis of numerical integrators for molecular dynamics (MD) and of fast solvers for the force computation, particularly due to electrostatic interactions. Several new and efficient algorithms are implemented in ProtoMol. Finally, it is shown that ProtoMol's sequential performance is excellent when compared to a leading MD program, and that it scales well for a moderate number of processors. Binaries and source codes for Windows, Linux, Solaris, IRIX, HP-UX, and AIX platforms are available under open source license at http://protomol.sourceforge.net.
2. PyGeo: a Dynamic 3d geometry laboratory: PyGeo is a dynamic geometry laboratory and toolkit. PyGeo may be used to explore the most basic concepts of Euclidean geometry at an introductory level, including by elementary schools students and their teachers. But is particularly suitable for exploring more advanced geometric topics - such as projective geometry and the geometry of complex numbers The intent is to bring a rich visual experience to the study of both synthetic and analytic geometry.
3. 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.
4. Babel: Babel is a program designed to interconvert a number of file formats currently used in molecular modeling.
5. Science Magazine's article on the NIH Public Access Policy: Elias Zerhouni covers the NIH Public Access Policy in this article in Science magazine
6. BioBike: A platform for knowledge-based computational biology. Written in Lisp, downloadable or accessible through our web servers.
7. 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.
8. 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).
9. Python and Scientific Computation: The home page for Scientific Computing with Python.
10. Swarm: Swarm is a software package for multi-agent simulation of complex systems.
11. OOFEM: is an object oriented, parallel, multiphysics finite element code system for solving mechanical, transport and fluid mechanics problems.
12. Calculix: Finite element package which accepts Abaqus INP files. Includes pre- and post-processor
13. 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)
14. 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.
15. 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
16. 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.
17. 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).
18. Free Science Resource: A Free Science Info Site (mainly books, software, links)
19. XPPAut : PDE and ODE resolver plus bifurcation analysys tool: XPPAUT is a tool for solving differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations.
20. 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.
21. View3D: calculation of radiation view factors in 2D and 3D: View3D is a command-line tool for evaluating radiation view factors for scenes with complex 2D and 3D geometry. It uses an adaptive integration method to calculate the view factors between faces where there is partial obstruction from inbetween faces. This program can be used to calculate the view factors (aka shape factors/configuration factors/form factors) for radiant heat transfer in diffuse grey enclosures.
22. RemoteSensing.org: Open Source Remote Sensing Effort
23. 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.
24. Open Visualization Data Explorer: IBM's famous volume renderer that does much much more.
25. 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.
26. PostGIS: PostGIS adds support for geographic objects to the PostgreSQL object-relational database. In effect, PostGIS "spatially enables" the PostgreSQL server, allowing it to be used as a backend spatial database for geographic information systems (GIS), much like ESRI's SDE or Oracle's Spatial extension.
27. 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.
28. polyXmass: software for analyzing mass spectrometric data for polymers
29. Celestia: A free 3D space simulator that lets you travel through the solar system and beyond to over 100,000 stars.
30. 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.
31. 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.
32. ns-3: ns-3 is a discrete-event network simulator for Internet systems, targeted primarily for research and educational use. ns-3 is free software, licensed under the GNU GPLv2 license, and is publicly available for research, development, and use.
33. 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.
34. LabPlot: Data analysis and visualisation. A new KDE-based graphing / plotting package that looks very powerful.
35. Avida: Avida is an auto-adaptive genetic system designed primarily for use as a platform in Digital or Artificial Life research. In lay terms, Avida is a digital world in which self-replicating computer programs mutate and evolve. Avida allows the user to study questions and perform experiments in evolutionary dynamics and theoretical biology that are intractable in real biological systems.
36. 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.
37. PAML: Phylogenetic Analysis by Maximum Likelihood
38. 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.
39. JSpecView: JSpecView is a viewer for spectral data in the JCAMP-DX format.
40. 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.
41. NanoCAD: A freeware nanotech design system in Java
42. OpenSim: OpenSim is an open-source software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement. The software provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through multi-institutional collaboration.
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. 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
45. The Sleuth Kit: The Sleuth Kit and The Autopsy Forensic Browser are open source file system digital forensics tools that analyze NTFS, FAT, UFS, EXT2FS, and EXT3FS file systems.
46. PerlMol -- Perl Modules for Molecular Chemistry: PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that "simple things should be simple". It should be possible to write one-liners that use this toolkit to do meaningful "molecular munging".
47. cb2bib - From clipboard to BibTeX: A tool for extracting bibliographic references: From clipboard to BibTeX: A tool for rapidly extracting unformatted bibliographic references from email alerts, journal web pages, and PDF files. The cb2Bib facilitates the capture of single references from unformatted and non standard sources. Output references are written in BibTeX. Article files can be easily linked and renamed by dragging it onto the cb2Bib window. Additionally, it permits editing and browsing BibTeX files, searching references and the contents of linked files, and cite them into document editors.
48. ScientificPython: ScientificPython is a collection of Python modules that are useful for scientific computing.
49. software for calculation of diffraction patterns: Debyer takes a file with atom positions as input and can output X-ray and neutron diffraction patterns, the total scattering structure function, the pair distribution function (PDF), and related functions (RDF, reduced PDF). It can be used for comparison of molecular dynamics simulations or other models of atomistic structure of the material with X-ray and neutron powder diffraction experiments. The parallel version uses the MPI library.
50. WATEQ4F: A program for calculating speciation of major, trace, and redox elements in natural waters

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