Skip to Search
Skip to Navigation
Skip to Content

University of Connecticut Health Center - Know Better Care Richard D. Berlin
Center for Cell Analysis & Modeling

CCAM Staff

Oliver Ruebenacker

Research Associate in Bioinformatics


Contact Information
Dr. Oliver Ruebenacker
University of Connecticut Health Center
Center for Cell Analysis & Modeling
263 Farmington Avenue
Farmington, CT 06030-6406
Phone: 860-679-3706
Fax: 860- 679-1039
Email:oruebenacker@uchc.edu

Research Interests

I am a member of the VCell team, developing software to turn biological knowledge into mathematical models. To use digitized biological knowledge available from public web databased to build and annotate models, I developed Systems Biology Linker (SyBiL) and Systems Biology Pathway Exchange (SBPAX), which allow to convert biological pathways, quantitative data and systems biological relationships to be turned into annotated cellular models that can be simulated with the Virtual Cell.

The SBPAX project includes:
  • Systems Biology Pathway Exchange Version 3 (SBPAX3), the latest version of SBPAX, which allows to build hierarchical structures of of systems biology terms (such as the Systems Biology Ontology (SBO)) and quantitative data. This allows to specify chemical properties, kinetc laws, kinetic parameters, and more. SBPAX3 is an extension to BioPAX Level 3 and proposal for inclusion in Level 4.
  • Unit of Measurement Expressions (UOME), a scheme to specify almost any conceivable unit by reference to controlled vocabulary such as the Unit Ontology (UO), derivation from other units or by using a long and growing pre-defined list.
  • Data Retrieval Interface Microdata (DRIMD), an HTML 5 Microdata specification to make database web interfaces navigatable by soft-ware agents without changing the appearance.

 

ruebenacker

CCAM Events Calendar

Director

Dr. Leslie Loew
les@volt.uchc.edu
860-679-3568

Deputy-Director

Dr. Ann Cowan
acowan@nso2.uchc.edu
860-679-1449

Administrative Contact

Karen Zucker
zucker@nso2.uchc.edu
Center for Cell Analysis & Modeling
Phone: 860- 679-1452
Fax: 860-679-1039
Selected Publications

Modeling without Borders: Creating and Annotating VCell Models Using the Web Michael L. Blinov, Oliver Ruebenacker, James C. Schaff and Ion I. Moraru Lecture Notes in Computer Science, 2010, Volume 6053 (2010)

Oliver Ruebenacker, Michael Blinov: Using views of Systems Biology Cloud: application for model building Theory in Biosciences, Volume 130, Number 1, 45-54 (2010).

Michael L Blinov, Oliver Ruebenacker, Ion I Moraru: Integrating BioPAX pathway knowledge with SBML models IET Syst. Biol., 2009, Vol. 3, Iss. 5, pp. 317– 328 (2009).

Michael L Blinov, Oliver Ruebenacker, Ion I Moraru: Complexity and Modularity of Intracellular Networks - A Systematic Approach for Modeling and Simulation IET Systems Biology, 2(5), 363-368 (2008)

Oliver Ruebenacker, Ion I Moraru, James C Schaff, Michael L Blinov: Kinetic Modeling Using BioPAX Ontology IEEE International Conference on Bioinformatics and Biomedicine, 2007, Proceedings, pages 339-348.

Oliver Ruebenacker: Weakly interacting Bose gases in the fluctuation region PhD thesis, University of Massachusetts at Amherst, MA, US (2005), advisor: Nikolay Prokof’ev.

Nikolay Prokof‘ev, Oliver Ruebenacker, Boris Svistunov: Weakly interacting Bose gas in the vicinity of the normal-fluid-superfluid transition Phys. Rev. A Volume 69, Issue 5, 053625 (2004).

Nikolay Prokof‘ev, Oliver Ruebenacker, Boris Svistunov: Critical Point of a Weakly Interacting Two-Dimensional Bose Gas Phys. Rev. Lett. 87, 160601 (2001).

Oliver Ruebenacker: Hole Dynamics in a two-dimensional quantum anti-ferromagnet Diplom thesis, University of Karlsruhe, Germany, 2000, advisors: Peter Woelfle, Nikolay Prokof‘ev.


Professional Activities

Elected BioPAX Editor by the BioPAX community

Chair of the BioPAX Pathways and Models Workgroup and the SBPAX Workgroup

Invited Expert at the Health Care and Life Sciences Interest Group at the World Wide Web Consortium