ThermOptiCS

ThermOptiCS(model, core, tol, TICs, Dir, doTOCC, timeLimit)

Thermodynamically feasible context-specific model building.

USAGE:

[Model,bCoreRxns,TICs,Dir] = ThermOptiCS (model,core,tol)

INPUTS:

• model – COBRA model structure for which act as the GSMM

• core – Reaction IDs which are defined to be core (These reactions will be present in the final model)

• tol – Tolerance value (User defined non-zero value).

OPTIONAL INPUTS:

• TICs – TICs of the ‘model’ (output from ThermOptEnumMILP)

• Dir – Direction of the TICs (output from ThermOptEnumMILP)

• doTOCC – Boolean value. 1: ThermOptCC will be run on the model and blocked

  reactions will be removed

  0: ThermOptCC will not be run on the model (This

  requires the input model to be thermodynamically-flux consistent)

• timeLimit – Upper time limit in seconds to solve the minReac optimization problem (Default: 120s)

OUTPUTS:

• Model – Context-specific model

• bCoreRxns – Core reactions that are thermodynamically blocked (or infeasible)

• TICs – List of all the Thermodynamically infeasible cycles in the given input model

• Dir – The flux directions for reactions in the corresponding TICs

findConsistentIDS_TOCS(model, core, TICmat, rev2irrev, tol)

Identifies the thermodynamically consistent IDs for the given input of irreversible reaction model

USAGE:

reacInd = findConsistentIDS_TOCS (model,core,TICmat,rev2irrev,tol)

INPUTS:

• model – COBRA model structure with irreversible reactions only

• core – Reaction IDs for which thermodynamic consistency has to be verified

• TICmat – Matlab matrix with information on TICs in the model

• rev2irrev – Mapping between the reversible reactions to its corresponding irreversible reactions

• tol – Minimum positive number defined as non-zero

OUTPUTS:

• reacInd – Indices of reactions that are identified to be thermodynamically consistent

• x – The solution obtained after solving the MILP optimization problem

findMinNetwork(model, core, P, TICmat, rev2irrev, tol, x0, timeLimit)

Identifies the thermodynamically consistent minimal network

USAGE:

IDS = findMinNetwork (model,core,P,TICmat,rev2irrev,tol,x0,timeLimit)

INPUTS:

• model – COBRA model structure with irreversible reactions only

• core – Reaction IDs for which thermodynamic consistency has been verified

• TICmat – Matlab matrix with information on TICs in the model

• rev2irrev – Mapping between the reversible reactions to its corresponding irreversible reactions

• tol – Minimum positive number defined as non-zero

• x0 – Inital feasible point for the MILP problem

• timeLimit – timeLimit for solving the minNetwork MILP problem

OUTPUTS:

IDS – Indices of reactions in the minimal network