Computational

gfit creates an interface between computational models and experimental data and provides tools for their analysis

Geom4J is a computational geometry library for Java. It contains implementation of the most important computational geometry data structures and algorithms coded in pure Java, designed for ease of use and optimized for performance.

The GridUnit project is a first effort to use the huge heterogeneity and distributed nature of Computational Grids to imporve the software testing process. It is an extension of the widelly adopted JUnit testing framework.


Platforms: Windows, Mac, Linux

Platform for parallel computation in the Amazon cloud, including machine learning ensembles written in R for computational biology and other areas of scientific research. Home to MR-Tandem, a hadoop-enabled fork of X!Tandem peptide search engine.


Platforms: Windows, Mac, Linux

The Instrument Element is a Grid/Cloud component that provides the computational/data Grid with an abstraction of real instruments, and Users with a more interactive interface to control them. More information: http://instrumentelem.sourceforge.net/


Platforms: *nix

JASA allows researchers in agent-based computational economics to write high-performance trading simulations using a number of different auction protocols. The software also provides base classes for implementing simple adaptive trading agents.


Platforms: Windows, Mac, Linux

This project is a Web Service based computational grid infrastructure written in Java. Once setup, it allows a user to submit job(s) to the grid to be scheduled for execution on the grid nodes.


Platforms: Windows, Mac, Linux

The FlashServer is a part of the MASSim project of the Computational Intelligence Group at the TU Clausthal, Germany and his main task is the visualization of the games as Flash videos. Currently the FS is not in use during the Multi-Agent Contest.


Platforms: *nix

A computational tool to design and annotate metabolic pathways from genome annotations


Platforms: Windows, Mac, Linux

The Moses Tool Suite is a collection of tools for visual modeling, simulation, analysis, synthesis, and visualization of computational systems.


Platforms: Windows, Mac, Linux

This project will include some tools to manage mysql replication and to help its integration in modern scientific computational GRID environment.


Platforms: Windows, Mac, Linux

The Open Modeling Interface and Environment (OpenMI) defines a standardized way to exchange data between computational models that run simultaneously. OpenMI aims to enhance process interaction representation in integrated environmental modelling.


Platforms: Windows, Mac, Linux

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'.


Platforms: Windows, Mac, Linux

A computational tool to discover location of promoter consensus sequences in bacterial genomes.


Platforms: Windows, Mac, Linux

The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.


Platforms: Mac, Solaris, Linux

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.


Platforms: Windows, Mac, Linux

This is a multi-threaded Java program that tries to maximise CPU utilization by separating and distributing the computational part of the work from the file reading and writing part by using separate threads.


Platforms: Windows, Mac, Linux

The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.


Platforms: Windows, Mac, Linux

The CCP1GUI project aims to develop a free, extensible Graphical User Interface to various computational chemistry codes developed by the worldwide academic community, with an emphasis on ab initio Quantum Chemistry codes.


Platforms: Windows, Mac, Linux

The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java.


Platforms: Windows, Mac, Linux