Reactions Rules Kinetics Pane

The reaction properties panel is used to display and edit kinetics and annotations for a reaction rule.

The top of the table shows the editable Reaction Name. Below is a table of the kinetic terms used to define the reaction rate. Items in brown cannot be edited.

Note: reaction rule rate may be different from reaction rate.

• Kinetic type: currently, reaction rules can have only mass action kinetics law. For every reaction generated by a rule, the rate law is microscopic forward rate times concentrations of reactant species minus microscopic reverse rate times concentrations of product species.
• Microscopic rate is a rate derived from the first principles. It assumes the probability of different particles of ideal gas to collide. However, the rule generates multiple reactions, in some particles are not any more different, and the rate is automatically adjusted by BioNetGen network generation engine. For example, if rule rate for a+b -> is k, and rule generates a reaction c+c->, then rate for this reaction will be 0.5k
• Forward rate and reverse rate may be any expressions, but they can not depend on concentrations of other species.
• Reversible box must be checked to enable specification of the reverse rate.

Edit the reaction name using the text field. A name already given to another reaction will be rejected.

Edit Expressions and their units in the Expression column.

• Incompatible units will be silently rejected.
• If references to new terms are added, new rows will automatically be added for these terms. An expression for each new term must be added in the expression column
• Terms can be set to global or local using a checkbox, except for the reaction rate, which is always local. Species concentrations and universal constants are always global.