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Mito-MAS-m is a simulator of the mitochondrial inner membrane and the enzymatic complexes embedded in it, implementing a coarse-grained (CG) model of the molecules using rigid structures and Dissipative Particules Dynamics (DPD) as motion equation.
Omnigraphs are a formal extension of hypergraphs with the ability of edges to connect to multiple nodes and edges. This project hosts the Ogre compilers.
Shellcalc (sc) is a lightweight and versatile reverse polish notation (RPN) calculator for the command-line. It implements access to the basic operations and many functions from the glibc math library.
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A MATLAB package to simulate sample paths of the solution of a Itô or Stratonovich stochastic differential equation (SDE), compute statistics and estimate the parameters from data.
A note of caution: SDE Toolbox is no more developed but it's still downloadable. Its inferential capabilities can be considered surpassed (at best). Actually the parameter estimation methods were already far from the state-of-art when the project began in 2007 (!). The considered implemented parametric and...
The Automatic Model Optimization Reference Implementation, AMORI, is a framework that integrates the modelling and the optimization processes by providing a plug-in interface for both. A genetic algorithm and Markov simulations are currently implemented.
OpenDiscreteDynamicProgrammingTemplate : founds optimal constrainted parameters of a discrete controls with second order optimization template replacing Hessian with directional derivatives and backpropagation for digital filter(as neural network)
This project about providing run-time support for developing Decentralized Autonomic Computing systems (Eclipse Innovation Grand). Currently the project contains a automatic guided vehicle (AGV) simulator and an editor and visualisation as eclipse plugin
MathMLSolver is a c++ library that is able to read MathML2.0 documents and string based mathematical expressions, to fill up an AST, solve them and dump the results into MathML again.
We present a maximum-likelihood method for examining the selection pressure and detecting positive selection in noncoding regions using multiple aligned DNA sequences.
Data mining tool for the extraction of spatio-temporal frequent patterns ("Trajectory patterns" or "T-patterns") from GPS-like trajectories of a set of moving objects. Work performed within the European project GeoPKDD - www.geopkdd.eu
Neurofitter is a parameter tuning package for electrophysiological neuron models. For more information please take a look at http://neurofitter.sourceforge.net
GeneIndex is a parallel program using MPI. It finds frequencies and positions of all words of a certain length in a DNA sequence. Large genome will be an ideal target of GeneIndex.
JavArch is a simple gate-level and above simulator. It is written in Java so it is portable and uses Java's builtin event-driven mechanisms to reflect how electronics actually work.
JUndo is a declarative object-oriented programming language with functional, and intensional programming characteristics. Applications include multi-level undo and sophisticated error recovery. See http://verdantium.blogspot.com/
Wattos is a collection of mostly Java programs for Structural Biology and NMR Spectroscopy. It's programs analyze, annotate, parse, archive, and disseminate experimental NMR data deposited by authors world wide into the PDB and BMRB.
Google() meets the Matrix. Red Piranha combines Lucene (Searching Ability), XML-RDF (ability to learn), Tomcat (for P2P Power) and Spring (Ease of use) to not only let you find anything, anywhere, but to actually understand what you are looking for.
R Tools for Biologists (RT4Bio) is a multi-functional package writen in R language developed in the Laboratory of Behavioral and Computational Ecology at State University of Montes Claros - MG - Brazil. Formerly known as RRJ.
VxmlSurfer is a modular, multi-platform, extensible VoiceXML 2.0 interpreter, geared to Web browsing as opposed to telephony. VxmlSurfer is currently used as a user interface for the HearSay non-visual Web browser.
APSGraph is a C++ object-oriented library for graph data and algorithms. The main objective of this library is to provide a maximum algorithms performance.