DEVELOPMENT OF DATABASE STRUCTURE FOR VIRTUAL CELL

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our existing database infrastructure design has been very stable. This design is a developmental database that allows collaborative development (model sharing) and change tracking throughout the lifetime of a model. This ambitious design facilitates model re-use and extensibility by one or more users without invalidating previous (intermediate) models or results. Features of the design include object ownership, version management, annotation, and simple publishing. XML is now used internally as an intermediate format (Virtual Cell Markup Language) for lightweight persistence (greatly increasing model load performance), client-side caching, and to provide language and platform independent communication. The Systems Biology Markup Language (SBML) allows a level of model interoperability among the existing modeling tools and model repositories and is actively supported by the Virtual Cell, both by contributing to the standard and by importing and exporting compliant models. Support for importing and exporting models in the CellML format has been provided.