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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 program has been written having in mind to create an useful tool to evaluate the Motor Evoked Potentials (MEPs) generated by Transcranial Magnetic Stimulation (TMS) and recorded with the program "Signal" (version 2.xx).
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.
BushMan is a web interface and a quality assurance tool for biological sequence assembly.
It is a small application that helps process chromatograms, and it assembles using Phred and Phrap. It produces a FASTA formatted consensus sequence.
PARs is a bioinformatics tool for the analysis of cis-regulatory DNA sequences. Composed of two parts: a suite of sequence analysis algorithms for predicting cis-binding sites in DNA sequences and a GUI for visualisation and exploration of the results.
Biological Annotation Tool is a general-purpose high speed environment for manipulating biological sequence annotations in multiple input and output formats. A plugin-style API permits much extensibility.
Cellogica is a cellular logic analysis tool. It incorporates sequential logic and finite state machine to elucidate the relationship between transcription factors and corresponding gene expression.
DNAID software is a tool for assessing confidence in biological identifications made by comparing DNA sequences. It allows DNA sequences to be placed within a taxonomy and determines confidence in matches of a query sequence to each taxon.
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.
Pymerase is a tool intended to generate a python object model, relational database, and an object-relational model connecting the two. However it has been extended to also output webpages and can be easily extended to output whatever else you might like.
jrgp is a strong-typed Genetic Programming system, which features a graphical interface (gool) to setup and run GP-problems and a tool (fs-d) that greatly simplifies the definition of a GP-problem.