psamm.fastcore – Fastcore (approximate consistent subset)

Fastcore module implementing the fastcore algorithm

This is an implementation of the algorithms described in [Vlassis14]. Use the functions fastcore() and fastcc() to easily apply these algorithms to a MetabolicModel.

exception psamm.fastcore.FastcoreError

Indicates an error while running Fastcore

class psamm.fastcore.FastcoreProblem(*args, **kwargs)

Represents a FastCore extension of a flux balance problem.

Accepts the same arguments as FluxBalanceProblem, and an additional epsilon keyword argument.

Parameters:
  • model – MetabolicModel to solve.
  • solver – LP solver instance to use.
  • epsilon – Flux threshold value.
find_sparse_mode(core, additional, scaling, weights={})

Find a sparse mode containing reactions of the core subset.

Return an iterator of the support of a sparse mode that contains as many reactions from core as possible, and as few reactions from additional as possible (approximately). A dictionary of weights can be supplied which gives further penalties for including specific additional reactions.

flip(reactions)

Flip the specified reactions.

is_flipped(reaction)

Return true if reaction is flipped.

lp10(subset_k, subset_p, weights={})

Force reactions in K above epsilon while minimizing support of P.

This program forces reactions in subset K to attain flux > epsilon while minimizing the sum of absolute flux values for reactions in subset P (L1-regularization).

lp7(reaction_subset)

Approximately maximize the number of reaction with flux.

This is similar to FBA but approximately maximizing the number of reactions in subset with flux > epsilon, instead of just maximizing the flux of one particular reaction. LP7 prefers “flux splitting” over “flux concentrating”.

psamm.fastcore.fastcc(model, epsilon, solver)

Check consistency of model reactions.

Yield all reactions in the model that are not part of the consistent subset.

Parameters:
  • model – MetabolicModel to solve.
  • epsilon – Flux threshold value.
  • solver – LP solver instance to use.
psamm.fastcore.fastcc_consistent_subset(model, epsilon, solver)

Return consistent subset of model.

The largest consistent subset is returned as a set of reaction names.

Parameters:
  • model – MetabolicModel to solve.
  • epsilon – Flux threshold value.
  • solver – LP solver instance to use.
Returns:

Set of reaction IDs in the consistent reaction subset.
psamm.fastcore.fastcc_is_consistent(model, epsilon, solver)

Quickly check whether model is consistent

Return true if the model is consistent. If it is only necessary to know whether a model is consistent, this function is fast as it will return the result as soon as it finds a single inconsistent reaction.

Parameters:
  • model – MetabolicModel to solve.
  • epsilon – Flux threshold value.
  • solver – LP solver instance to use.
psamm.fastcore.fastcore(model, core, epsilon, solver, scaling=100000.0, weights={})

Find a flux consistent subnetwork containing the core subset.

The result will contain the core subset and as few of the additional reactions as possible.

Parameters:
  • model – MetabolicModel to solve.
  • core – Set of core reaction IDs.
  • epsilon – Flux threshold value.
  • solver – LP solver instance to use.
  • scaling – Scaling value to apply (see [Vlassis14] for more information on this parameter).
  • weights – Dictionary with reaction IDs as keys and values as weights. Weights specify the cost of adding a reaction to the consistent subnetwork. Default value is 1.
Returns:

Set of reaction IDs in the consistent reaction subset.