1^st Beilstein ESCEC Symposium 2003

Functional characterization of enzymes and the subsequent computational analysis and modelling of the cellular metabolism and the interaction of cells within tissues and organs led to the foundation of a new branch within the life sciences, called systems biology. At this time, data from metabolic simulations show broad value ranges with high uncertainty because the accessible experimental data have been generated under non-standardized experimental conditions. The results from functional characterizations of enzymes are usually determined by individual laboratory-specific application and implementation of the experimental design. Thus, successful biological analysis requires comparable and reliable data from both enzyme and physiological interactions collected under standardized experimental conditions. However, as long as the quality of the in-put as well as the out-going modelling data can not be improved, the chances of success for this young discipline to escape from the verbally overused -omics-sciences are poor.

The standardization of the above mentioned experimental conditions – or rather “recommendations” – firstly needs broad discussions within the scientific community which hopefully will lead to some common acceptance so that each researcher will carry out his/her experiments in accord with these quasi-standards. The Beilstein-Institut supports this standardization process by hosting the 1st ESCEC workshop and it is also willing to organize and present the following meetings as long as this is appropriate. At such time as a self-sufficient working group has formed, the Institut would look to modify its role and support this work in other ways.

This first meeting will address the following questions:

• are any standards used in the field of functional characterization of enzymes?
  
  
• are there any standard procedures or instructions for experimental conditions?
  
  
• is it possible to define laboratory procedures for common use?
  
  
• do current repositories for enzyme characterization data meet the demands of users?
  
  
• which data types for metabolic simulations are necessary?
  
  
• are there any demands for the transfer of standardized experimental data to journals or databases?

Opening Remarks and Greetings
Carsten Kettner, Beilstein-Institut, Frankfurt am Main, Germany

System Biology and the Setting of Standards for Life
Hans Westerhoff, Vrije Universität, Amsterdam, The Netherlands

Application of Proteomics in Pharmaceutical Industry
Hanno Langen, Hoffmann-La Roche AG, Basel, Switzerland

Integration of Chemical and Genomic Knowledge in KEGG
Minoru Kanehisa, Kyoto University, Japan

Extending Enzyme Classification with Metabolic and Kinetic Data: Some Difficulties to be Resolved
Keith Tipton, Trinity College, Dublin, Ireland

The HUPO Proteomics Standards Initiative
Rolf Apweiler, EMBL Outstation - European Bioinformatics Institute, Cambridge, UK

Enzyme Data Requirements for Kinetic and Structural Modelling Example
David Fell, Oxford Brookes University, Oxford, UK

Methods for Design of Optimal Experiments with Application to Parameter Estimation in Enzyme Catalytic Processes
Ekaterina Kostina, University of Heidelberg, Germany

Broad-Range Metabolite Analysis: Integration into Genomic Programs
Alisdair Fernie, MPI for Molecular Plant Physiology, Golm, Germany

Determination of Enzyme Activities by Mass Spectrometry – Benefits and Limitations
Hartmut Schlüter, Charité – Humboldt-University, Berlin, Germany
Berlin

Studying Enzyme Kinetics by Progress Curve Analysis
Hermann-Georg Holzhütter, Charité – Humboldt University, Berlin, Germany

Structural Modelling of Biochemical Systems: What can we Determine with Minimal Enzymological Information?
Mark Poolman, Oxford Brookes University, Oxford, UK

Enzymes, Pathway Modelling and Metabolite Databases
Stefan Schuster, University of Jena, Germany

Beyond Mechanism: Enzyme Kinetics in the Context of Systems Biological Modelling
Jan-Hendrik Hofmeyr, University of Stellenbosch, South Africa

JWS Online Cellular Systems Modelling and the Silicon Cell
Jacky L. Snoep, University of Stellenbosch, South Africa

Controlled Vocabularies and Ontologies in Enzymology
Kyrill N. Degtyarenko, EMBL Outstation - European Bioinformatics Institute, Cambridge, UK

Profiles of Molecular Function – Genomic Enzymology
Thomas S. Leyh, The Albert Einstein College of Medicine, Bronx, New York, USA

Resource Sharing and Data Exchange: SBW and SBML
Herbert Sauro, Kegg Graduate Institute, Claremont, USA

Experimental Enzyme Data as Presented in BRENDA
Dietmar Schomburg, CUBIC (Cologne University Bioinformatics Centre), Köln, Germany

Enhanced Graphical Representation of Metabolic Networks
Detlev Krömker, University of Frankfurt/Main, Germany

Are We Talking about the Same Thing?
Richard Cammack, King's College London, UK

Numerical Optimization Methods for Enzyme Networks
Pedro Mendes, Virginia Bioinformatics Institute, Virginia Tech Blacksburg, USA