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A database and a web front end for physiologic data on animal feeding, developed with PostgreSQL and Django at NESCent (http://www.nescent.org) for Mammalian Feeding Working Group (http://www.feedexp.org).
Current development of the codebase is on Github at http://github.com/NESCent/feedingdb.
Text2Genome is a set of scripts to extract nucleotide sequences from scientific articles and to map them to genomes and genes using a local alignment algorithm (BLAST/BLAT)
PowerTalk automatically speaks Microsoft PowerPoint presentations. For presenters who find speaking difficult, audiences containing people with visual impairments and fun educational uses. Uses synthesised computer speech provided with Windows
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A web-based system for upoading, managing, sharing, and analyzing bioinformatic data. The system is primarily written in python, and runs on both linux and MacOs.
Tools to perform metabolic control analyses on biochemical network models in SBML format. Allows computation of first and second order response coefficients, elasticities, first order control coefficients and first order spectral response coefficients.
Brian is a new simulator for spiking neural networks available on almost all platforms. The motivation for this project is that a simulator should not only save the time of processors, but also the time of scientists.
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A Python library bringing together utilities I've written over the years for work in bioinformatics and biostatistics, which should be generally applicable outside these fields as well. Focuses on string processing, DBI, and math.
PepT-IDE is a protein analysis tool that is used for multiple sequence alignment, 3D visualization and displaying protein contact maps for protein sequences and structures. It also has feedback communication between the different views of the protein.
openSputnik is a robust distributed platform for massive scale precalculation of genetic and genomic data using contemporary bioinformatics methods. Annotated DNA, RNA and protein sequences are stored as binary objects in a variery of relational database
Python library to convert networks from/to many different formats, like the ones used in Pajek, Cytoscape and other popular graph formats like GML. It also includes support to integrate experimental data to the netowork.
Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.
CC8Works is a Web-based software system for managing and documenting a cross of eight existing inbred mouse lines to yield hundreds to thousands of recombinant inbred lines that will become a permanent genetic resource for biomedical research.