The MCISB employs 9.5 multidisciplinary people who share an office and lab. They follow an iterative and integrative approach to develop an annotated, kinetic model of yeast metabolism. To integrate experimental data with models, they utilize unique, public identifiers for molecules from databases like ChEBI and UniProt. They have developed tools like KineticsWizard to help experimentalists capture identifier data. Their annotated yeast model follows MIRIAM standards to unambiguously identify over 2000 molecules with database references.

7. Computers don’t like names … because they are non-unique / ambiguous / imprecise / etc.

8. (3R,4R,5S,6S)-6-(hydroxymethyl) oxane-2,3,4,5-tetrol Biochemists like names a little too much… Glucose Glc Anhydrous dextrose Cerelose 2001 Traubenzucker Staleydex 95M

13. But names are still important

17. SBML annotation <species id=”glc&quot; name=&quot;D-Glucose&quot;> <annotation> <rdf:li rdf:resource=&quot;urn:miriam:obo.chebi:CHEBI:17634&quot;/> </annotation> </species>

19. KineticsWizard

20. Project overview Enzyme kinetics Quantitative metabolomics Quantitative proteomics SBML Model Parameters (K M , K cat ) Variables (metabolite, protein concentrations) PRIDE XML MeMo SABIO-RK Web service Web service Web service MeMo-RK Web service

24. CellDesigner plugins …eventually

28. Einfach Klasse!

29. Modelling infrastructure

30. Taverna http://taverna.sourceforge.net

31. Taverna

32. Modelling life-cycle workflows

33. Model construction Input: list of ORFs Output: SBML file 1. Get reaction info 3. Create species 2. Create compartments 4. Create reactions Get annotations

34. Model construction

36. SABIO-RK web service

37. Model parameterisation

39. COPASI web service Design and Architecture of Web Services for Simulation of Biochemical Systems. Dada JO, Mendes P. Data Integration in the Life Sciences, Manchester, UK (2009).

40. Model calibration

43. Thanks…