Get Some Paths module

Description

This module returns several random paths between the sources defined in the program configuration ("Sources and bounds configuration" module) and an objective compound going through an user defined reaction. It starts collecting the shortest path, then removes one random reaction from the shortest path and collects again the shortest path. The algorithm repeats the same steps as many times as the number of iterations is allowing it to continue. takes into account the stoichiometry and bound of the reactions.

It creates a new SBML file that can be visualized selecting it in the left side of the screen and using the right button of the mouse to select the options "Visualize".

The initial or unprocessed SBML models don't have contain any graph so they can't be visualized.

When the new model is saved inside a project, its comments/information and its graph will be saved with it in separated files. The SBML file can be also saved as a single SBML file to be used in other software by selecting the option "Save model in a file" which appears when the model is selected and the the right button of the mouse is pressed.

Method parameters

Compound ID
ID of the compound objective for the algorithm.
Number of iterations
Minimum number of steps in which the algorithm will search for the path. It should be between 10 and 100 depending on the size of the model.
Excluded compounds
Cofactors, H20, O2, CO2. Example for yeast 7.6 model: s_0434, s_1203,s_1207,s_1198,s_0394,s_0794,s_0803,s_1322,s_1212,s_0529,s_0687,s_0689,s_0451,s_1801,s_0456,s_0719,s_0924,s_0849,s_1405,s_1396