The Subliminal Toolbox: automating steps in the reconstruction of metabolic networks

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Neil Swainston

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Automation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Model annotations ,[object Object],[object Object],[object Object],[object Object],[object Object]

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Balance ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Balance carbon dioxide + 2-Acetolacetate  Pyruvate Ab = 0 A = b represents a vector of stoichiometries CO 2 + C 5 H 7 O 4 -  C 3 H 3 O 3 - Reactants Products Optional reactants Optional products CO2 C5H7O4 C3H3O3 H+ H20 H+ H20 CO2 C 1 5 -3 0 0 0 0 -1 O 2 4 -3 0 1 0 -1 -2 H 0 7 -3 1 2 -1 -2 0 charge 0 -1 1 1 0 -1 0 0 b min T 1 1 1 0 0 0 0 0

Balance ,[object Object],carbon dioxide + 2-Acetolacetate  2 Pyruvate + H + CO 2 + C 5 H 7 O 4 -  2 C 3 H 3 O 3 - + H + Reactants Products Optional reactants Optional products CO2 C5H7O4 C3H3O3 H+ H20 H+ H20 CO2 C 1 5 -3 0 0 0 0 -1 O 2 4 -3 0 1 0 -1 -2 H 0 7 -3 1 2 -1 -2 0 charge 0 -1 1 1 0 -1 0 0 b min T 1 1 1 0 0 0 0 0 b T 1 1 2 0 0 1 0 0

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Usage and availability ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

UniProt compartmentalisation UniProt curated information

PSORT compartmentalisation WoLF PSORT prediction

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The Subliminal Toolbox: automating steps in the reconstruction of metabolic networks

1. The Subliminal Toolbox: automating steps in the reconstruction of metabolic networks Neil Swainston Manchester Centre for Integrative Systems Biology 1st Conference on Constraint-based Reconstruction and Analysis Reykjavik, Iceland 24 June2011

4. Publicly available resources Formula, Charge, Structure GPR relationships Compartment data Sequence, Metadata Web services

5. Subliminal Toolbox

8. Balance carbon dioxide + 2-Acetolacetate  Pyruvate Ab = 0 A = b represents a vector of stoichiometries CO 2 + C 5 H 7 O 4 -  C 3 H 3 O 3 - Reactants Products Optional reactants Optional products CO2 C5H7O4 C3H3O3 H+ H20 H+ H20 CO2 C 1 5 -3 0 0 0 0 -1 O 2 4 -3 0 1 0 -1 -2 H 0 7 -3 1 2 -1 -2 0 charge 0 -1 1 1 0 -1 0 0 b min T 1 1 1 0 0 0 0 0

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15. Shorthand Converted to SBML, protonated, balanced and merged as before

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18. The Subliminal Toolbox: automating steps in the reconstruction of metabolic networks Neil Swainston Manchester Centre for Integrative Systems Biology 1st Conference on Constraint-based Reconstruction and Analysis Reykjavik, Iceland 24 June 2011

19. UniProt compartmentalisation

20. UniProt compartmentalisation UniProt curated information

21. PSORT compartmentalisation

22. PSORT compartmentalisation WoLF PSORT prediction

The Subliminal Toolbox: automating steps in the reconstruction of metabolic networks

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