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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.

The Phenoscape project attempts to formalize the description of evolutionary characters to make them interoperable and computable with the body of phenotype annotation being generated by model organism databases, and other biomedical research.

sciNote is an open source electronic lab notebook (ELN) that helps you manage your laboratory work and stores all your experimental data in one place. sciNote is specifically designed for life science students, researchers, lab technicians and group leaders.

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.

Tab2MAGE uses a flexible spreadsheet format for MIAME annotation of microarray experiments. Tab2MAGE spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.

mx is a Ruby/Rails code base with broad application in evolutionary biology, it includes general functionality for matrix handling, sequence management, ontology construction, specimen handling, taxonomic catalogs, taxonomic descriptions and more

Simulation of allele-specific RNA-seq data

The TIMTAM (Target Information Management Tracking And More) system implements a secure knowledgebase supporting the management, tracking, and analysis of experimental data associated with structural biology projects.

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.

Ruby Research Wiki (RRiki) can be used to keep notes and organize references for research. It uses a browser interface, an intuitive plain text formatting language (markdown), and facilities to cross-reference and hierarchically organize notes

A database schema and web application to archive, search, share, and download data of maximum body sizes of different taxonomic groups during the history of life on earth.

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.

The program fuses 2 sets of molecules. It tries different relative positions of molecules before binding them, so that there is no or minimal intersection in the resulting molecule. The atom to be fused in a molecule is labeled with an R symbol.

A client side browser implementation of Tom Ray's Tierra Artificial Life simulator (http://en.wikipedia.org/wiki/Tierra_(computer_simulation)).

soaPDB is a clean way to Search, Organize, and get e-mail Alerts for saved PDB (Protein Data Bank) queries