We use R (www.r-project.org) in order to generate a greater specificity and sensitivity of protein identification by Mass Spectrometry. These functions are implemented as add-on packages to the open source GPL software R.
runsbml - Pathway Simulation Tool emulates the dynamics of biological pathways by calculating concentrations of biochemical compounds at different times and conditions.
This is a collection of utilities and other nifty code items developed by Thought River for use in internal projects, and made available here for public use.
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qsims simulates quantum dynamics with an (almost) arbitrary time-dependent Hamiltonian. qsims uses a Chebychev polynomial expansion of the Schrodinger propagator, and the pseudospectral method developed by R. Kosloff.
sheep is an open source rigid body dynamics engine written in modern, strictly portable C++. It features collisions between hierarchies of convex polyhedra (using the SWIFT library), resting contacts handling and an extensible set of joints.
The Synaptic Simulator is a program which simulates models of single neuronal synapses and compartments, complex constructs of such models. Furthermore the program is able to regain parameters by fitting simulated results with experimental data.
MEDDAC is the seeding point for designing a new approach to Operating System design itself. It is an Open Source project with roots in mainframe design and development the author began in 1979. Monitor Editor Disassembler Decompiler Assembler Compiler
REMD toolkit is designed as a C++ framework to build a replica-exchange molecular dynamics (REMD) program, suitable for solving the multiple-minima problem that prevents accurate estimation of thermodynamical properties.
toxic is a modern, physically correct global illumination renderer aiming to produce photorealistic images and animations. A number of plug-ins are under development to allow using toxic with various open source and commercial 3D modeling packages.
Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.
a C++ template container implementation of k-dimensional space sorting based on the kd-tree data structure. THIS PROJECT HAS MOVED TO ALIOTH.DEBIAN.ORG
The fst2v5d package converts data stored in the Canadian RPN Standard File (FST) format into Vis5D format. FST files, commonly used to store meteorological data, are scanned by fst2v5d to generate both 4D fields and independent topography input files.
OpenSim - Open Simulator. Primarily a 3D simulator for multiple indoor and outdoor mobile robots. Includes 3D real-time rendering (via OSG) and a physics engine (via ODE). Current emphasis is on manipulators.
ODE for Java is a binding between C dynamics library ODE (Open Dynamics Engine, http://ode.org) and Java. Separate packages provide among other things a Java3D integration and thus a scenegraph representation of selected ODE objects.
Damocles is a game engine programmed in C++.(Opengl/SDL) ||| OS:Linux / Windows ||| 3 main modules in Damocles: ||| Damocles : 3D engine |||Junior : Physic and Mathematics engine ||| Unik : Network engine (Only for Windows version for the moment)
6Vertex is an Objective C/Cocoa application (and standard C functions) for computing and visualizing matrix models generated with the 6-vertex model for computing boundary shapes and phase transition shapes for differently weighted vertices.
pSmunli is another opensource Physics SiMUlatioN LIbrary in 3D environment. To perform more realistic simulation on your application(such as game and scientific simulation). It supports OpenGL and DirectX.
X-Bc (formerly: xbc) is a graphical user interface to the command line calculator bc. All Inputs and Outputs stays visible for editing and comparing. Functionality: trigonometry, number-theory, exponential funcs, scientific constants, primenumbers ...
Computational modelling is a interdisciplinary field spanning many techniques and programming languages. AgenTools is a project dedicated to establishing increased modularity in scientific computing packages and a portal linking to other existing project
Random number generator, and random number seed generator classes for C++. Includes abstract base classes and derived generators. Cross platform compatible.
GAST-Viz is a toolkit allowing for the creation of OpenGL atomistic simulation applications using discrete element modeling methods. A number of sample applications are included.