Predator

Seed extraction in metabolic networks.

installation

pip install predator

Solving modes

Complete scope

Activating all metabolites. This is the default mode, if no targets are provided.

Examples:

python -m predator data.sbml
python -m predator data.sbml --visualize data.png --export data.lp --no-topological-injection

Target scope

This is an optimized solving mode, used if targets are provided, using --targets/-t or --targets-file/-tf.

The optimization rely on the use of Strongly Connected Components.

Examples:

python -m predator data.sbml -t protein_1
python -m predator data.sbml -t protein_1 protein_2 --forbidden-seeds protein_3 --targets-are-forbidden --start-seeds protein_42

Pareto front exploration

Using asprin, it enumerates the pareto front solutions over the following constraints:

• minimization of seeds
• maximization of targets
• minimization of targets that are also seeds (if flag --targets-are-forbidden/-taf is given)

If --greedy flag is given, the whole graph will be treated in one step. It is not expected to scale over large graphs, but may provide slightly different answers.

Example:

python -m predator data.sbml -t protein_1 --pareto

TODO

• union et intersection des solutions
  • implem pour la recherche search_seeds_activate_all
  • implem pour la recherche search_seeds_activate_targets_iterative
  • implem pour la recherche search_seeds_activate_targets_greedy
  • implem pour la recherche search_pareto_front
  • implem pour la recherche search_pareto_targets_iterative

release cycle

Releases made with zest.releaser:

pip install zest.releaser[recommended]  # install the manager
fullrelease  # make a new release