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ChEBI and genome scale metabolic reconstructions

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Neil Swainston
Neil Swainston
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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
Introduction ,[object Object],[object Object],[object Object],[object Object]
Genome-scale metabolic reconstructions
Genome-scale metabolic reconstructions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Systems Biology Markup Language ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Systems Biology Markup Language
Limitations ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
MIRIAM ,[object Object],[object Object],[object Object],[object Object],[object Object]
MIRIAM annotation <species metaid=&quot;id_1&quot; name=&quot;D-Glucose&quot;> <annotation> <rdf:RDF> <rdf:Description rdf:about=&quot;#id_1&quot;> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource=&quot;urn:miriam:obo.chebi:CHEBI:17634&quot;/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species>
For example… ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
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]
Why ChEBI? ,[object Object],[object Object],[object Object],[object Object]
Why ChEBI? ,[object Object],[object Object],[object Object],[object Object],[object Object]
SuBliMinaL
Autofill ,[object Object],[object Object],[object Object]
Why ChEBI? ,[object Object],[object Object],[object Object]
 
Reaction balancing ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Reaction balancing in SuBliMinaL
Interfacing with cheminformatics ,[object Object],[object Object],[object Object],[object Object],[object Object]
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]
 
Conclusions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Thanks…
No Thanks…
Many Thanks…
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

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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
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  • 9. MIRIAM annotation <species metaid=&quot;id_1&quot; name=&quot;D-Glucose&quot;> <annotation> <rdf:RDF> <rdf:Description rdf:about=&quot;#id_1&quot;> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource=&quot;urn:miriam:obo.chebi:CHEBI:17634&quot;/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species>
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  • 22. Reaction balancing in SuBliMinaL
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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