ChEBI and genome scale metabolic reconstructions

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Neil Swainston

Technology Education

Introduction ,[object Object],[object Object],[object Object],[object Object]

Genome-scale metabolic reconstructions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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MIRIAM ,[object Object],[object Object],[object Object],[object Object],[object Object]

MIRIAM annotation <species metaid="id_1" name="D-Glucose"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#id_1"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI:17634"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species>

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Why ChEBI? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

SBML Annotation Wizard ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

SBML Annotation Wizard ,[object Object],[object Object]

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Kinetic modelling project overview Enzyme kinetics Quantitative metabolomics Quantitative proteomics SBML Model (single pathway) Parameters (K M , k cat ) Variables (metabolite, protein concentrations) PRIDE MeMo SABIO-RK Web service Web service Web service MeMo-RK

Mapping experimental data to models ,[object Object],[object Object],[object Object],[object Object]

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ChEBI and genome scale metabolic reconstructions

1. ChEBI and genome-scale metabolic reconstructions Neil Swainston Manchester Centre for Integrative Systems Biology 2 nd ChEBI User Group Workshop, EMBL-EBI, Hinxton, UK 23 June 2010

3. Genome-scale metabolic reconstructions

6. Systems Biology Markup Language

9. MIRIAM annotation <species metaid="id_1" name="D-Glucose"> <annotation> <rdf:RDF> <rdf:Description rdf:about="#id_1"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI:17634"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species>

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24. Kinetic modelling project overview Enzyme kinetics Quantitative metabolomics Quantitative proteomics SBML Model (single pathway) Parameters (K M , k cat ) Variables (metabolite, protein concentrations) PRIDE MeMo SABIO-RK Web service Web service Web service MeMo-RK

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31. ChEBI and genome-scale metabolic reconstructions Neil Swainston Manchester Centre for Integrative Systems Biology 2 nd ChEBI User Group Workshop, EMBL-EBI, Hinxton, UK 23 June 2010

ChEBI and genome scale metabolic reconstructions

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