Virtual Cell at UConn



BioPAX at Virtual Cell: Publications

 

  1. Manual.
  2. O. Ruebenacker, I. I. Moraru, J.C. Schaff, and M. L. Blinov (2009) Integrating BioPAX knowledge with SBML models. To appear in IET Systems Biology. (pdf).
  3. 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 (pdf).
  4. 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 (pdf).

BioPAX at Virtual Cell: Presentations

 

  1. Poster: O. Ruebenacker, I. I. Moraru and M. L. Blinov (2009) Latest from the Data Integration Frontier: Using Pathway Data to Build and annotate Systems Biology Model . Presented at the 3rd q-bio meeting, Santa Fe, NM, July 30-Aug 2, 2009.
  2. Flyer: O. Ruebenacker, I. I. Moraru and M. L. Blinov (2009) Using BioPAX Pathways for SBML Models with SyBiL. Flyer presented at the Biophysical Society Meeting, Boston, MA, February-March 2009.
  3. Tutorial: M. L. Blinov, O. Ruebenacker, I. I. Moraru (2009) Bridging data and modeling communities. Presentation at NRCAM meeting, February 23rd, 2009.
  4. Tutorial: O. Ruebenacker, "Bridging data and modeling communities. Ontologies of cellular networks, pathway databases and pathway data retrieval tools" (pdf). Presented at the 2nd q-bio conference, August 6th, 2008, Santa Fe, NM.
  5. Poster: I.I. Moraru, Oliver Ruebenacker, M.L. Blinov "Towards unifying systems biology - using pathway data in BioPAX format for SBML simulators. Presented at the 2008 ICSB, August 2008, Gotenburgh, Sweden.
  6. Poster: "Modeling Complex Networks: Integrating Rules (BioNetGen) and Data Mining (BioPAX Ontology) into the Virtual Cell Framework" by M. L. Blinov, I. I. Moraru, O. Ruebenacker, J. C. Schaff, A. Lakshminarayana, F. Gao, and L. M. Loew. Presented at 2007 ICSB meeting, October 2007, Long Beach, CA

Web-resources that use BioPAX

  1. General description of BioPAX format