gMCSpy.ProblemDefinitions module

buildDictionaryDossageNetwork(cobraModel: Model, forceLength: bool, compressedNodes: List[str], rxnToForce: List[str], verbose: int = 0, targetB: float = 0.001, cConstant: float = 0.001)

Builds the dictionary that defines the MILP problem to be solved by the MCS algorithm in a Regulatory network.

Parameters:

• modelStruct – Cobra Model, the metabolic model to be operated on. Only Cobra models generated by expanded network are supported.

• forceLength – boolean. If true, the length of the solution is forced to be off a given length each iteration, otherwise the length is not forced.

• targetB – float. Desired activity level of the metabolic task to be disrupted.

• cConstant – float. Used to activate w variable

• rxnToForce – list of strings. Reactions to be forced to be part of the solution. Empty by default.

If the bounds are left as None they are ment to be infinity (None = Infinity), so each solver can interpret it as it is defined.

Returns:

problemDict. Dictionary that defines the MILP problem to be solved by any solver defined in gMCSpy.

buildDictionaryFBA(cobraModel: Model)

Build FBA problem dictionary The basic idea of FBA is to use constraints based on the mass balance and stoichiometry of reactions to determine the steady-state fluxes through the metabolic network. The steady-state assumption assumes that the concentrations of metabolites do not change over time, which is reasonable for many metabolic systems.

buildDictionaryFBAWithDeletions(cobraModel: Model, gMCS: List[str] | None = None, isoformSeparator: str | None = None)

Build FBA problem dictionary The basic idea of FBA is to use constraints based on the mass balance and stoichiometry of reactions to determine the steady-state fluxes through the metabolic network. The steady-state assumption assumes that the concentrations of metabolites do not change over time, which is reasonable for many metabolic systems.

buildDictionaryMCSGeneProblem(cobraModel: Model, gDict: dict, matrixG: csc_matrix, relationships: dict, maxKOLength: int, numberNewGenesByKO: dict, minKOLength: int = 0, forceLength: bool = False, verbose: int = 0, targetB: float = 0.001, cConstant: float = 0.001, logPath: str | None = None)

Builds the dictionary that defines the MILP problem to be solved by the MCS algorithm.

Parameters:

• modelStruct – Cobra Model, the metabolic model to be operated on. Only Cobra models are supported.

• forceLength – boolean. If true, the length of the solution is forced to be off a given length each iteration, otherwise the length is not forced.

• targetB – float. Desired activity level of the metabolic task to be disrupted.

• cConstant – float. Used to activate w variable

• rxnToForce – list of strings. Reactions to be forced to be part of the solution. Empty by default.

If the bounds are left as None they are ment to be infinity (None = Infinity), so each solver can interpret it as it is defined.

Returns:

problemDict. Dictionary that defines the MILP problem to be solved by any solver defined in gMCSpy.

buildDictionaryMCSGeneTargetedProblem(cobraModel: Model, gDict: dict, matrixG: csc_matrix, relationships: dict, maxKOLength: int, numberNewGenesByKO: dict, geneSubset: list, targetKOs: list, minKOLength: int = 0, forceLength: bool = False, verbose: int = 0, targetB: float = 0.001, cConstant: float = 100)

Builds the dictionary that defines the MILP problem to be solved by the MCS algorithm.

Parameters:

• modelStruct – Cobra Model, the metabolic model to be operated on. Only Cobra models are supported.

• forceLength – boolean. If true, the length of the solution is forced to be off a given length each iteration, otherwise the length is not forced.

• targetB – float. Desired activity level of the metabolic task to be disrupted.

• cConstant – float. Used to activate w variable

• rxnToForce – list of strings. Reactions to be forced to be part of the solution. Empty by default.

If the bounds are left as None they are meant to be infinity (None = Infinity), so each solver can interpret it as it is defined.

Returns:

problemDict. Dictionary that defines the MILP problem to be solved by any solver defined in gMCSpy.

buildDictionaryMCSProblem(cobraModel: Model, forceLength: bool, rxnToForce: List[str], verbose: int = 0, targetB: float = 0.001, cConstant: float = 0.001)

Builds the dictionary that defines the MILP problem to be solved by the MCS algorithm.

Parameters:

• modelStruct – Cobra Model, the metabolic model to be operated on. Only Cobra models are supported.

• forceLength – boolean. If true, the length of the solution is forced to be off a given length each iteration, otherwise the length is not forced.

• targetB – float. Desired activity level of the metabolic task to be disrupted.

• cConstant – float. Used to activate w variable

• rxnToForce – list of strings. Reactions to be forced to be part of the solution. Empty by default.

If the bounds are left as None they are ment to be infinity (None = Infinity), so each solver can interpret it as it is defined.

Returns:

problemDict. Dictionary that defines the MILP problem to be solved by any solver defined in gMCSpy.

buildDictionaryMCSTargetedProblem(cobraModel: Model, forceLength: bool, rxnSubset: List[str], rxnKnockOut: List[str], verbose: int = 0, targetB: float = 0.001, cConstant: float = 0.001)

Builds the dictionary that defines the MILP problem to be solved by the MCS algorithm.

Parameters:

• modelStruct – Cobra Model, the metabolic model to be operated on. Only Cobra models are supported.

• forceLength – boolean. If true, the length of the solution is forced to be off a given length each iteration, otherwise the length is not forced.

• targetB – float. Desired activity level of the metabolic task to be disrupted.

• cConstant – float. Used to activate w variable

• rxnToForce – list of strings. Reactions to be forced to be part of the solution. Empty by default.

If the bounds are left as None they are ment to be infinity (None = Infinity), so each solver can interpret it as it is defined in each solver.

Returns:

problemDict. Dictionary that defines the MILP problem to be solved by any solver defined in gMCSpy.

buildDictionaryReactionsFBAWithDeletions(cobraModel: Model, reactions: List[str] | None = None)

Build FBA problem dictionary The basic idea of FBA is to use constraints based on the mass balance and stoichiometry of reactions to determine the steady-state fluxes through the metabolic network. The steady-state assumption assumes that the concentrations of metabolites do not change over time, which is reasonable for many metabolic systems.

buildDictionaryRegNetwork(cobraModel: Model, forceLength: bool, compressedNodes: List[str], rxnToForce: List[str], verbose: int = 0, targetB: float = 0.001, cConstant: float = 0.001)

Builds the dictionary that defines the MILP problem to be solved by the MCS algorithm in a Regulatory network.

Parameters:

• modelStruct – Cobra Model, the metabolic model to be operated on. Only Cobra models generated by expanded network are supported.

• forceLength – boolean. If true, the length of the solution is forced to be off a given length each iteration, otherwise the length is not forced.

• targetB – float. Desired activity level of the metabolic task to be disrupted.

• cConstant – float. Used to activate w variable

• rxnToForce – list of strings. Reactions to be forced to be part of the solution. Empty by default.

If the bounds are left as None they are ment to be infinity (None = Infinity), so each solver can interpret it as it is defined.

Returns:

problemDict. Dictionary that defines the MILP problem to be solved by any solver defined in gMCSpy.

readjustmentProblem(rules, gMIs)