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FBA

Objective reaction


⚠️ Warning:

The objective reaction is not used for the seed searching, with some exceptions. It is mainly needed to calculate and ensure the flux.

Objective given by user

The objective reaction can be given by the user by using the option --objective or -o and the name of the reaction prefixed with "R_". The tool will first check if the reaction exists in the source file, then apply this reaction as objective reaction for the flux calculation. If the

📃 Examples:

OK ERROR

💻 Command:

seed2lp fba [source_file_path] [output_directory_path] -o R_R2

📝 Notes: "R_R2" is an existing reaction and will replace the objective reaction written into the source file.

📃 Output example:

Objective set:
    Objective reaction from command line

Objective : R_R2

💻 Commands:

 seed2lp fba [source_file_path] [output_directory_path] -o R2

 seed2lp fba [source_file_path] [output_directory_path] -o oops

📃 Output example:

ERROR:
R2 does not exist in network file networks/toys/sbml/toy_accumulation.sbml

ERROR:
oops does not exist in network file networks/toys/sbml/toy_accumulation.sbml

Objective found into source file

When no argument is used for the objective reaction, the tool will find from the objective list of source file the objective. The description of this automatic objective search is described in 📜Network analyse

Seed searching

After analysing and converting the network a seed resoltuion is performed. Please read the 📜network analyse document to understand the technical terms

Description

The FBA mode aims to search randomly sets of seeds by ensuring flux on the objective reaction (found or given). Thus all metabolites can potentially be seeds, except:

  • Transported⭐ metabolites are not defined as possible seeds to reduce combinatorics and avoid very similar solutions.
  • Metabolites that are never consumed as written in the source file. Indeed, the flux rules creates an import/export reaction for seeds, and the programm can by-pass the accumulation🔆 by adding these type of metabolites as seeds and using the export reaction.

💬 Comments:

⭐ A transported metabolite is a metabolite that is transferred from one compartment to another. The formula is therefore generally something like: $\quad$ $\quad$ M_A_e ⟷ M_A_c ⟷ M_A_m

Because it the same metabolites on different compartment, the program tags M_A_c and M_A_m as transported metabolite, therefore only M_A_e is selected as seed.

This restriction allows to avoid similar set of seeds such as {M_A_e, M_B} or {M_A_c, M_B} or {M_A_m, M_B}

🔆 Some source files can create reaction without using the product of this reaction in another reaction, even export reactions. This is an accumulation already existing in the source file.

⚠️ Warning:

However, as the main solution may result in an accumulation, one or more seeds can be added to the set in order to use the export reaction generated during the calculations and therefor avoid accumulation.

If the program does that, these specific seeds are written in red into the terminal and written into the output file.

📃 Output example:

Application with options

We will discuss here some options, it is possible to consult all options.

Target as seeds: $\quad$ --targets-as-seeds $\quad$-tas

In FBA mode, the main purpose is to ensure flux into objective reaction. To do that, we need to be able to produce the reactants of the objective reaction. But one solution of the set of seed could be all reactants of the objective reaction. This is not the purpose of the program.

By default, the program does not allow the reactant of the objective reaction as seed. But that can be allowed by using this target as seeds option. This can be usefull if there is no solutions without this permission.

This option is at False by default, and if used becomes True.

💻 Command:

seed2lp fba [source_file_path] [output_directory_path] -tas

⚠️ Warning:

With this option, one / multiple / all reactants of the objective reaction can be present into the set of seeds.

Forbidden seeds: $\quad$ --forbidden-seeds-file $\quad$ -fsf

It is possible to give a list of metabolites (as file) that are not allowed to be seeds. This option could be interesting to use with the *target as seeds option, to avoid some targetted metabolites to be seeds, but not all of them.

💻 Command:

seed2lp fba [source_file_path] [output_directory_path] -fsf

seed2lp fba [source_file_path] [output_directory_path] -tas -fsf

📝 Notes: The order of the options does not matter

⚠️ Warning:

This option implies upstream knowledge of metabolites that are not desired as seeds. It may be necessary to first run the command without this option, locate the metabolites not desired as seeds and then run with this option again using the file containing this list of metabolites.



📃 Full example