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The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.

A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are...

Atlas is a suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequecing (WECS) data.

Simulation of allele-specific RNA-seq data

Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.

The SPELL gene expression explorer searches multiple datasets for related gene expression patterns. Hibbs MA, et al. Exploring the functional landscape of gene expression: Directed search of large microarray compendia. Bioinformatics, 2007.

Simulator of virtual animals made up of biological neural networks for research in the Computational Neuroscience field.

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.