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PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
TMAJ is software for Tissue MicroArrays (TMA's). Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.
MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection
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Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices using Dynamic Time Warping with a one-to-one (bijective) smooth warp-function. It is ideal for the chromatographic alignment of complex mass spectrometry proteomics data.
This library is a lightweight implementation of genetic algorithm, contains the most popular types of chromosomes and the basic algorithms for selection, elitism, crossing and mutation.
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Metmask has moved to github http://github.com/hredestig/metmask
Metmask is a tool written in python for managing chemical identifiers for metabolomics experiments. It can incorporate identifiers from local textfiles, several online databases, query PubChem and record all found associations in a local sqlite database.
This tool is designed to solve generalized pattern matching problem, by which we only find a set of sub-patterns, ignoring the gaps in between the sub-patterns. This tool is extremely fast and also has good tolerance to errors.
The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!
h2:www is an easily extendable online interface for bioinformatical command-line tools, providing convenient project-oriented working facilities for multiple users.
Taverna is *no longer* hosted on SourceForge, but has moved to the Apache Software Foundation: https://taverna.apache.org
These pages and mailing list archives are provided for *archival purposes* for older Taverna 1.x releases.
See https://taverna.apache.org/download/ for the latest releases from Apache Taverna.
QSAR is a project that aims to build a GUI that enables people to build quantitative structure activity (or property) relationship models. It will use parts of CDK (cdk.sf.net), JOELib (joelib.sf.net), R (www.r-project.org) and other projects.
vcif is an open source software for validation of Crystallographic Information Files. It supports lexical, parser and dictionary validation (DDL 1 and 2 are fully supported, DDLm draft partially supported)
This project implements an algorithm for segmenting protein sequences into smaller meaningful blocks. The method is based on the pure statistical approach and it uses an analogy between proteins and natural language.