US-EC Workshop on Infrastructure Needs of Systems Biology

May 3-4, 2007
USDA Jean Mayer Human Nutrition Research Center on Aging
Tufts University Medical Center Campus
711 Washington Street
Boston, MA 02111

Co-chairs: Marvin Cassman (former Director of NIGMS)  and
Søren Brunak (Director for Biological Sequence Analysis, Technical University of Denmark)


The US-EC Task Force on Biotechnology Research is a long standing consultative mechanism between the U.S. Government and the European Union, which sponsors workshops that bring together leading US and European researchers to discuss topics of emerging interest on both sides of the Atlantic. The Task Force is co-chaired by Kathie L. Olsen, Deputy Director, National Science Foundation (NSF) and Christian Patermann, Research Directorate-General, EC.

Final Workshop

The final workshop report is available in Adobe Acrobat (PDF) format.

The agenda below includes links to the individual presentations of the invited speakers.


Thursday, May 3, 2007


Welcome and Introductions

  • Fred Heineken, NSF
  • Martha Steinbock, USDA
  • Søren Brunak, for the European Commission

Experimental Tools (Chair: Michael Ashburner)

  • Mathias Uhlen: “A human protein atlas&rdquo"
  • Stefan Hohmann: “Measurements for dynamic modeling&rdquo"
  • Michael Ashburner: “Ontologies for data integration”
10:30 Break

Databases (Chair: Rolf Apweiler)

  • Rolf Apweiler: “Enabling systems biology: development and implementation of proteomics standards and services”
  • Janet Thorton: “Towards a European bioinformatics infrastructure in the international context”
  • Alfonso Valencia: “The Biosapiens NoE experience in high-throughput genome annotation and the ENCODE pilot project case story”
12:30 Lunch

Modeling Applications (Chair: Pamela Silver)

  • Pamela Silver: “Can we design biological systems in a predictable manner?”
  • Frank Doyle: “Modeling and analysis challenges in biology: from genes to cells to systems”
  • Marcus Covert: “Model-driven discovery”
3:30 Break

Software Infrastructure (Chair: Mike Hucka)

  • Mike Hucka: “Standardization efforts for computational modeling in biology”
  • Gary Bader: “Pathway Commons: a public library of biological pathways”
  • Douglas Kell: “Loosely coupled bioinformatics workflows for systems biology”
7:30 Dinner at Les Zygomates Wine Bar Bistro

Friday, May 4, 2007

8:30 Discussions and Conclusions
12:00 Lunch
12:30 Discussions and Conclusions