Informatics In The Manchester Centre For Integrative Systems Biology

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Neil Swainston

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Informatics in the Manchester Centre for Integrative Systems Biology ,[object Object],[object Object],[object Object],[object Object]

The MCISB ,[object Object],[object Object],[object Object],[object Object]

Definition of the problem ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Informatics challenges ,[object Object],[object Object],[object Object],[object Object],[object Object]

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

(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

Solution ,[object Object],[object Object],[object Object],[object Object]

Solution ,[object Object],[object Object],[object Object],[object Object],[object Object]

But names are still important ,[object Object],[object Object],[object Object]

Models ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Models ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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

Solution on the experimental side ,[object Object],[object Object],[object Object]

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

But… ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

And… ,[object Object],[object Object],[object Object],[object Object]

So… ,[object Object],[object Object],[object Object],[object Object]

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

Model parameterisation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Model calibration ,[object Object],[object Object],[object Object],[object Object],[object Object]

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).

Conclusion ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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Informatics In The Manchester Centre For Integrative Systems Biology

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

10.

11.

12.

13. But names are still important

14.

15.

16.

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

18.

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

21.

22.

23.

24. CellDesigner plugins …eventually

25.

26.

27.

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

35.

36. SABIO-RK web service

37. Model parameterisation

38.

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

41.

42.

43. Thanks…

44.

Informatics In The Manchester Centre For Integrative Systems Biology

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