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TiMAT2 contains tools for low and high level genomic tiling microarray analysis using the Affymetrix, NimbleGen, and Agilent platforms. It is designed for processing single and multi chip data sets from ChIP-Chip, RNA difference, and aCGH experiments.
Java GUI to analyze one (or more, in batch mode) datasets with several feature selection methods at the same time and also performing an "ensemble" analysis. It can be easily extended to include any feature selection algorithm.
XMPP Web Services for Java (XWS4J) is an implementation of machine to machine communication over XMPP. The communicated content is encoded in XML, according to customized definitions of input and output in W3C XML Schemata.
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Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)
CIP-FOSS will serve as a common entry page for Free and Open Source Software developed at the International Potato Center (CIP), Lima, Peru (http://www.cipotato.org).
The system is designed for the automated analysis of high throughput sequencing data. At present Aped is focused on the analysis of data derived from Sanger and 454 sequencing. Additional functionality exists for SAGE and taxonomic profiling.
BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project.
The Hanalyzer is a tool designed to help biologists explain results observed in genome-scale experiments and to generate new hypotheses. It combines information extraction, semantic data integration, reasoning, and visualization.
Our software can test for HLA allele and amino-acid differences between two populations. It examines zygosity, tests for strongest association, interaction & linkage disequilibrium among amino acid epitopes.
Mathematics, Chemistry and Bio-informatics semantic knowledge editor and simulation environment. It should serve as interactive science learning program or science classroom notebook and workshop.
User friendly PDB (Protein Data Bank) file editor with graphic user interface for protein crystallographers to expedite selective parallel edit / data extraction / analysis of their PDB files
http://ewi.utwente.nl/~biorange/rshell - The RShell project is a plugin for the Taverna workflow system. It enables one to execute R scripts within the Taverna workflow system. The RShell processor is built on the RServe project. For more info:
FreeLIMS is a Laboratory Information Management System ( LIMS ). Manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights. FreeLIMS is Open Source and Free.
Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.
The Flow Cytometry Laboratory Information Management System (FlowLIMS) is a web-based software system that gives users the ability to create and manage experiment protocols for the DiVa and FACScan flow cytometers
ProteinShader is a molecular visualization tool that can produce illustrative renderings of proteins that approximate what an artist might create using pen and ink. This free platform-independent program is written in Java and OpenGL Shading Language.