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

  • Michael L. Blinov
  • Oliver Ruebenacker
  • James C. Schaff
  • Ion I. Moraru
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6053)


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 designed and developed for simultaneous querying of multiple systems biology knowledge bases and data sources, such as web repositories, databases, and user files, and converting the extracted and refined data into model elements. Integration of SyBiL as a component of VCell makes these capabilities easily available to a wide modeling community.


Biological databases mathematical modeling VCell data conversion 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Michael L. Blinov
    • 1
  • Oliver Ruebenacker
    • 1
  • James C. Schaff
    • 1
  • Ion I. Moraru
    • 1
  1. 1.Center for Cell Analysis and ModelingUniversity of Connecticut Health CenterFarmingtonUSA

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