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The program versusSNP is a flexible tool for mining SNPs between two close related genomes. First, we align all the orthologous genes and select SNPs, then the SNPs are separated into categories based on their mutation types.
Easy install web server for Genetic and Molecular Biological Laboratory so that PI can update lab homepage himself. Also serve as Lab database server that store DNAStrider plasmid , order tracking and mouse colony database.
BLOSpectrum tools provide programs to automatically classify proteins according to SCOP database. In order to achieve such a goal, they implements all the required information theory widgets on BLOSpectrum fingerprints.
Knime (http://www.knime.org) nodes for sequence bioinformatics. Sequime is an eclipse plug-in for the KNIME data mining platform, providing additional nodes for reading, processing and visualizing sequence information.
PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
PheMaDB is a web-based data management system to store and analyze OmniLog Phenotype Microarray data. The manuscript can be accessed here: http://www.biomedcentral.com/1471-2105/12/109. Chang WE et al. BMC Bioinformatics. 2011 Apr 20;12(1):109.
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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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.
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.
SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.
Software developed under MATLAB R14 environment.
It's aim is to make the modeling of bacterial inactivation system and adjust a simulator to obtain new data of the experiment or validate the one that has been obtained at the laboratory.
h2:www is an easily extendable online interface for bioinformatical command-line tools, providing convenient project-oriented working facilities for multiple users.
WhichGenes is a web-based bioinformatics tool. It allows the user to extract lists of genes from multiple sources in order to use them for further experiments.