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A file format for exchanging computational models in systems biology
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.
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
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