Research Associate in Bioinformatics
Contact InformationDr. Oliver Ruebenacker
University of Connecticut Health Center
Center for Cell Analysis & Modeling
263 Farmington Avenue
Farmington, CT 06030-6406
Fax: 860- 679-1039
I am a member of the VCell team, developing software to turn biological knowledge into mathematical models. To use digitized biological knowledge available from public web databased to build and annotate models, I developed Systems Biology Linker (SyBiL) and Systems Biology Pathway Exchange (SBPAX), which allow to convert biological pathways, quantitative data and systems biological relationships to be turned into annotated cellular models that can be simulated with the Virtual Cell.The SBPAX project includes:
- Systems Biology Pathway Exchange Version 3 (SBPAX3), the latest version of SBPAX, which allows to build hierarchical structures of of systems biology terms (such as the Systems Biology Ontology (SBO)) and quantitative data. This allows to specify chemical properties, kinetc laws, kinetic parameters, and more. SBPAX3 is an extension to BioPAX Level 3 and proposal for inclusion in Level 4.
- Unit of Measurement Expressions (UOME), a scheme to specify almost any conceivable unit by reference to controlled vocabulary such as the Unit Ontology (UO), derivation from other units or by using a long and growing pre-defined list.
- Data Retrieval Interface Microdata (DRIMD), an HTML 5 Microdata specification to make database web interfaces navigatable by soft-ware agents without changing the appearance.