Step 2: Reaction Input


There are several ways to define the set of reactions for the model. The fastest one is probably to type them into the reaction overview table. You find this reaction overview in the tree on the left under Model->Biochemical->Reactions.

(Click here to go to the reaction overview.)

figure: empty reaction overview

To create a new reaction just click on the empty cell in the Equation column and start typing. When you are finished with typing the reaction equation, hit the return key. Now you are in the next row and can type the next reaction. Once you have created all reaction, you click the "commit" button at the bottom of the screen, this will create all the reactions as well as the necessary metabolites and compartments. All reactions are created with an irreversible mass-action kinetic with a kinetic constant of 0.1, all metabolites have an initial concentration of 0.1 standard concentration units (the ones specified in the Model Settings dialog.) and the single compartment has a volume of 1 standard volume units.

figure: empty reaction overview