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1. 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.

2. RapidMiner

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

3. 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

4. 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.

5. 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).

6. Open Visualization Data Explorer

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

7. 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.

8. 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.

9. XBS

XBS is a simple but very useful program for plotting ball-and-sticks models of molecules or crystals under the X Window system.

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. Garlic

Garlic is a free molecular visualization program written for unix and unix clones.

12. sl++

The Scientific Library is a C++ object oriented library specializing in linear algebra (although it contains other components as well).

13. xeo

xeo is a free (GPL) open project management for nanostructures using Java

14. 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.

15. Walldrawer

Walldrawer - an easy alternative to on-site wall drawing for archaeology. This software aims at putting together the tools needed to produce scaled, rectified, drawing-like pictures from digital photographs in archaeological excavations. This software was developed in Java using Java Advanced Imaging toolkit, but at the moment development is stopped. Functionality is not 100% however try using it, it is worth.

16. 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.

17. Babel

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

18. C++ Simulators of Turing and Post Machines

These C++ programs simulate nondeterministic / deterministic multitape Turing & Post machines, universal Turing machines, and Turing machines with faults, failures and recovery.

19. 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.

20. 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.

21. QMOL

Qmol is a program for viewing molecular structures and animating molecular trajectories.

22. VASP Data Viewer

A free, open source 3D viewer for molecular charge distributions.

23. 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)

24. 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.

25. 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.

26. 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.

27. 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.

28. 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.

29. jHepWork

Data analysis framework

30. BKchem

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

31. Raster3D

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

32. 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.

33. 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.

34. 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.

35. 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.

36. LabJ

LabJ (a.k.a Electronic Laboratory Notebook, ELN, Laboratory Journal) assists in planning chemical reactions and stores chemical information. Open Source, but it requires ISIS Desktop package from MSI.

37. Chemtool

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

38. 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).

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

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

40. 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.

41. 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.

42. PyMOL

PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.

43. NA_WorkSheet

The NA_WorkSheet is a collective aggregation of algorithms coded in Java that implements various Numerical Analysis solutions/techniques in one easy to use opensource tool. The app. may be used for graphing, root finding, differentiation, integration, interpolation, linear systems solving, and matrix operations.

44. 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).

45. CLHEP

A Class Library for High Energy Physics

46. Chemsuite Project

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

47. Celestia

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

48. 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.

49. JChemPaint

A Java program for drawing of 2D chemical structures

50. 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.