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Separate Full Network and Target mode

Current feature

Target or Full Network mode is automatically set, depending on whether a target (metabolites only) file is supplied or targets are provided on the command line. The only command to launch seed search is python -m seed2lp run

Target mode

When the target mode is used, the seed searching focus to the targets metabolite producibility on Reasoning or Hybrid search mode.
The FBA search mode doesn't take into account the targets, the only purpose of the FBA search mode is to ensure flux into the objective reaction.
The Hybrid search mode also ensure flux into the objective reaction, in addition to ensuring target producibility.

Full Network mode

When the Full Network mode is used, all network metabolites become targets and the Reasoning or Hybrid search mode focus the seed searching to ensure the productivity of all metabolites.
The FBA search mode doesn't take into account the targets, the only purpose of the FBA search mode is to ensure flux into the objective reaction.
The Hybrid search mode also ensure flux into the objective reaction, in addition to ensuring target producibility.

Objective reaction rule

For Hybrid and FBA search mode, the objective reaction cannot be selected. It is automatically found based on if there is "Biomass" into the reaction name, if not, if there is objectives set in the SBML file. If no objective found, the seed searching is stopped.

Desired feature

Target or Full Network will be launched separately and the target can be either reactions (to change objective for FBA or Hybrid search mode) or metabolites (to ensure some metabolites producibility for Reasoning or Hybrid seach mode).

Target mode

The target mode will be launch with the command python -m seed2lp target. A target file can be provided or not.

With target file

File composition

The file must be a text file, with one data per line. A data ca be

  • a metabolite: prefixed by "M_"
  • a reaction: prefixed by "R_" (at the beginning focus only on one objective reaction, then in another issue do multiple)
    • If there is no objective reaction objective, the same rules as "without target file" are applied

Without target file

If there is no target file provided, the tool will search on SBML file the objective reaction following these rules:

  • No reaction present on the objective list into the SBML file -> An error is raised
  • Multiple reactions or one reaction present on the objective list into the SBML file
    • None of the reactions have a coefficient to 1 -> An error is raised
    • One reaction has a coefficient to 1 -> the reaction is selected
    • Multiple reactions has a coefficient to 1 -> An error is raised *(for multiple reactions case)

Rules

Reasoning

The reasoning do not focus on objective reaction, only on metabolites. To ensure objective reaction flux present into the target file, it will also add the reactants of objective reaction to the target metabolite list. The seed searching focus to the target metabolites producibility.

Hybrid

The hybrid focus on the objective reaction and the metabolites. It will ensure flux on objective reaction and will also add the reactants of objective reaction to the target metabolite list.

FBA

The hybrid focus only the objective reaction, not on the metabolites. It will ensure flux on objective reaction.

Full Network mode

The full network mode will be launch with the command python -m seed2lp full. A objective reaction argument can be used or not.
If a target file is provided, an error will be raised.

With objective reaction

If an objective reaction is set, this reaction is used to flux calculation for FBA and Hybrid search mode.

Without objective reaction

If no objective reaction is set, the tool will search on SBML file the objective reaction following these rules:

  • No reaction present on the objective list into the SBML file -> An error is raised
  • Multiple reactions or one reaction present on the objective list into the SBML file
    • None of the reactions have a coefficient to 1 -> An error is raised
    • One reaction has a coefficient to 1 -> the reaction is selected
    • Multiple reactions have a coefficient to 1 -> An error is raised *(for multiple reactions case)

Same objective rules as target mode

Rules

Reasoning

The reasoning do not focus on objective reaction, only on metabolites. In the Full Network mode all metabolites are targeted. The seed searching focus to the target metabolites producibility.

Hybrid

The hybrid focus on the objective reaction and the metabolites. In the Full Network mode all metabolites are targeted. It will ensure flux on objective reaction.

FBA

The hybrid focus only the objective reaction, not on the metabolites. It will ensure flux on objective reaction.
Same rules as target mode

Software diagram

software_diag

Edited by GHASSEMI NEDJAD Chabname
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