Tutorial 7

8/30 12:15 - 2:45, Hewlett 103

Retrieving Pathway Data for use in Kinetic Modeling

Oliver Ruebenacker, Ion Moraru and Michael Blinov

University of Connecticut Health Center.

Purpose provide a background and hands-on experience on how to retrieve pathway data from databases, visualize it, and use for modeling. Specifically, how to derive kinetic models of reaction networks using SyBiL - Systems Biology Linker (http://vcell.org/biopax).

The pathway databases contain enormous amount of data that can be used for modeling: 8 pathway databases accessible through Pathways Common (http://www.pathwaycommons.org) contain more than 418,000 interactions among 85,000 physical entities participating in 1,300 pathways. The direct use of this data for kinetic modeling is not always possible, in paprticular because of difference between data representation in databases and in models. The aims of the tutorial are:

  1. To provide an introduction to the definition and methods of ontology.
  2. To describe some ontologies used by biological communities: Gene Ontology (GO, http://www.geneontology.org), providing a controlled vocabulary to describe gene and gene product attributes; and BioPAX ontology (http://www.biopax.org) designed to serves as a data exchange format for biological pathway data.
  3. To describe pathway databases that can serve as the source of data for modelers., such as Reactome (http://reactome.org), Pathway Interaction Database (http://pid.nci.nih.gov/), and some others. Specifically, we will cover the ways to retrieve data, visualization modes, and supported data formats.
  4. To present difficulties that exists in one-to-one mapping between data and modeling exchange standards (BioPAX as a representataive of ontology, and SBML as a representative of markup languages.)
  5. To give hands-on experience with retrieving pathway data from databases, visualizing it, and using for modeling using SyBiL - Systems Biology Linker (http://vcell.org/biopax).
Tutorial material All registered participants will be provided with tutorial materials in electronic form in advance and hard-copy of tutorial materials on site. All participants will be provided with downloadable versions of the software well in advance, so they will have a chance to install SyBiL software that we will use during the tutorial.

  1. M. L. Blinov, O. Ruebenacker and I. I. Moraru (2008) Complexity and Modularity of Intracellular Networks - A Systematic Approach for Modeling and Simulation. IET Systems Biology, 2(5), 363-368.
  2. O. Ruebenacker, I. I. Moraru, J. C. Schaff and M. L. Blinov (2007) Kinetic Modeling Using BioPAX Ontology. Proceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine: 339-348.

Registration Registered attendees please register for this Tutorial.