BIOUML - OPEN SOURCE EXTENSIBLE WORKBENCH FOR SYSTEMS BIOLOGY

Summary Motivation: With the completion of several genomics initiatives, including the Human Genome Project, researchers are poised to begin the next phase of elucidating how living systems function. This step requires integrated software environment that spans the comprehensive range of capabilities. Results: BioUML – Biological Universal Modeling Language – is open source extensible Java workbench for systems biology. BioUML’s core is a meta model that provides an abstract layer for comprehensive formal description of wide range of biological and other complex systems. Content of databases on biological pathways (TRANSPATH, KEGG/pathways, GeneNet, GeneOntology) as well as SBML and CellML models can be expressed in terms of the meta model and used by BioUML workbench. Plug-in based architecture provides the workbench extensibility and possibility of seamless integration with other tools for systems biology. The workbench consists from Eclipse platform runtime that supports plug-ins registry and a set of plugins for database access, diagram editing, biological systems simulation and for integration with MATLAB and SBW/SBML. Availability: http://www.biouml.org