1. 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).

2. 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.

3. 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).

4. 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

5. RapidMiner

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

6. 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.

7. 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.

8. 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.

9. 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.

10. Celestia

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

11. 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.

12. 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.

13. BPKIT

BPKIT is a toolkit of block preconditioners for the iterative solution of linear systems. The most effective general purpose and black-box type of preconditioners are available, including block SSOR, block tridiagonal ILU, and the block extension of point ILU with level-of-fill. Any of these "global" preconditioners may be coupled with one of a large collection of "local" preconditioners for approximately or exactly inverting or solving with the diagonal or pivot blocks. These include a number of approximate inverse techniques.

14. sl++

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

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. 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

17. Open Visualization Data Explorer

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

18. 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.

19. Chemsuite Project

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

20. 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.

21. 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).

22. JChemPaint

A Java program for drawing of 2D chemical structures

23. 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.

24. 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.

25. 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.

26. 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.

27. XBS

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

28. 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.

29. Chemtool

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

30. Garlic

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

31. 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).

32. 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.

33. Geopsy & Dinver: processing of ambient vibration recordings

Geopsy and Dinver are distributed in Sesarray package initiated during European project SESAME (2004). Geopsy is a graphical user interface and a core library to handle seismic signals (especially long ones). Signals can be displayed and processed (filter, fft, taper, merge, ...). Additionally, various specialized modules are provided for processing ambient vibration recordings. Dinver is a graphical environment and a core library for stochastic inversion problems (Conditional Neighbourhood Algorithm). Again, the structure is modular. The first module being developed for the inversion of dispersion curves and associated objects.

34. 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.

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. 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.

37. 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.

38. 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.

39. 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)

40. 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.

41. 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.

42. 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.

43. 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.

44. 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.

45. 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.

46. 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.

47. 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.

48. 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.

49. 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

50. 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.

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