Reactions Table

A table of reactions can be used to create and edit reactions, membrane fluxes and reaction rules.

The Reactions table has several columns:

Below the table are buttons to create or delete reactions or rules, to duplicate reaction rules, define Pathway Links and to search the reaction table.

The bottom pane of the window displays a Reaction Properties Pane, Membrane Flux property pane, or Reaction Rules Properties pane, depending on the current selection.

New Reaction calls a popup menu to add a new reaction or flux. Select the structure where the reaction occurs from the Structure drop-down menu, define a name for the reaction and type the reaction using the format "a+b->c" where a and b, etc. are reactants and c, etc are products. Numbers before a species name are used to indicate stoichiometry. If a, b, etc have not been defined, they are automatically created as species within the structure where the reaction occurs.

New Rule opens the reaction rule editor in the properties pane below. New rules must be created and edited within the Editor.

Edit kinetic laws by selecting a row in the table and editing the Reaction Properties pane, Flux Properties pane or Rule Editor as appropriate.

Delete a reaction, flux or rule by selecting a row or rows.

Duplicate will create an exact copy of highlighted rule with a new name "oldname_0".

Use the Pathway Links button to identify reactions within Pathway Commons Database. Pathway Links are not available for reaction rules at this time.

Search the list of reactions and reaction rules using the Search Box to enter reaction name, structure, or any part of a BNGL string.