Reconstruction

Reconstruction

• Demeter
  • Suite
  • Src
• Modelgeneration
  • Modelproperties
  • Stoichconsistency
  • Massbalance
  • Modelverification
  • Fluxconsistency
• Rbionet
  • Gui
• Refinement
  • Gprlogic
• Comparison
  • Modelborgifier
• Metaboreport
  • Other
• Fastgapfill
  • Auxillaryfiles
• Growthexpmatch

Function list

gapFind(model, findNCgaps, verbFlag)

Identifies all blocked metabolites (anything downstream of a gap) in a model. MILP algorithm that finds gaps that may be missed by simple inspection of the S matrix. To find every gap in a model, change the rxn bounds on all exchange reactions to allow uptake of every metabolite.

USAGE:

[allGaps, rootGaps, downstreamGaps] = gapFind (model, findNCgaps, verbFlag)

INPUT:

model – a COBRA model

OPTIONAL INPUTS:

• findNCgaps – find no consupmption gaps as well as no production gaps (default false)

• verbFlag – verbose flag (default false)

OUTPUTS:

• allGaps – all gaps found by GapFind

• rootGaps – all root no production (and consumption) gaps

• downstreamGaps – all downstream gaps

Based on Kumar, V. et al. BMC Bioinformatics. 2007 Jun 20;8:212.

testPathway(model, MetIn, MetOut, AdditionalMetsInorOut, ObjectiveOption)

Allows the user to see if given one metabolite A, downstream metabolite B can be made made. Additional sinks can be added for co-factors if needed A –>–>–>–>–> B

USAGE:

[Flux, FBAsolution, model] = testPathway (model, MetIn, MetOut, AdditionalMetsInorOut, ObjectiveOption)

INPUTS:

• model – COBRA model structure

• MetIn – The input metabolite(s) (A)

• MetOut – The output metabolite (B)

OPTIONAL INPUTS:

• AdditionalMetsInorOut – Additional metabolites for which sinks will be added

• ObjectiveOption – Boolean:

  • 1 = objective will be production of B (default)

  • 0 = use objective in model

OUTPUTS:

• Flux – The rate of B production

• FBAsolution – Solution to the FBA problem

• model – COBRA model with sinks in it