Genome Analysis Software Info Site

Before this operation, execute "Set Pathway Draw Data". Execute it only once after IMC is started.

Panes used in the Local Pathway Builder
P13: 3rd column at the top: LMS: Local Pathway Builder tab pane
This is the metabolic pathway drawing area. Metabolic pathways are drawn here.
This tab pane is detachable and resizable.
P21: 1st column at the middle: GSM: GenomeScaleModel tab pane
P32: 2nd column at the bottom: EM: Extendable Metabolites tab pane
This tab pane displays a list of metabolites that can be reached in one reaction from the currently drawn metabolic pathway.
P33: 3rd column at the bottom: Rxn: Rxns List tab pane
This tab pane displays the Reaction List of the Current GenomeScaleModel.
You can sort by each column.
P33: 3rd row at the bottom: Mets: Species List tab pane
This tab pane displays the Metabolte(Species) List of the Current GenomeScaleModel.
P34: 4th row at the bottom: ER: Extendable Rxns tab pane

How to use
From the menu, click METABOLIC STREAM > Load GenomeScaleModel.
The Load SBML file selection dialog appears, so select the genome scale model (SBML format).
Note: The currently available genome scale model is the BiGG model.
When loading is complete, the information is displayed in a list in the Rxns List tab pane in the 3rd row at the bottom of P33.
Drawing a single reaction
Select the reaction you want to draw first from the P33: Rxns List tab pane and click it.
The reaction is drawn in the P13: Local Pathway Builder tab pane.
Add a reaction following a metabolite of the currently drawn reaction.
Clicking a metabolite displayed in the P32: Extendable Mets List tab pane will display the reaction mediated by that metabolite in the P34: Extendable Rxns List tab pane.
Clicking a reaction in the P34: Extendable Rxns List will add that reaction to P13: Local Pathway Builder.