Modeling without Borders: Creating and Annotating VCell Models Using the Web

Biological research is becoming increasingly complex and data-rich, with multiple public databases providing a variety of resources: hundreds of thousands of substances and interactions, hundreds of ready to use models, controlled terms for locations and reaction types, links to reference materials (data and/or publications), etc. Mathematical modeling can be used to integrate this complex data and create quantitative, testable predictions based on the current state of knowledge of a biological process. Data retrieval, visualization, flexible querying, and model annotation for future reuse, are some of the important requirements for modeling-based research in the modern age. Here we describe an approach that we implement within the popular Virtual Cell (VCell) modeling and simulation framework in order to help connect the modeling community with the web of machine-processable systems biology knowledge. A new software application, called SyBiL (Systems Biology Linker), has been designe...

• Type: Conference
• Year: 2010
• Where: ISBRA
• Authors: Michael L. Blinov, Oliver Ruebenacker, James C. Schaff, Ion I. Moraru
• Keywords: Bioinformatics, Data And/or Publications, ISBRA 2010, Modeling Community, Systems Biology Knowledge