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:

• The Reaction column lists either a reaction (or flux) that can be edited in place, or "Reaction Rule" text that cannot be edited.
• Name lists the reaction name; reaction names are generated automatically as "r_number" but can be edited to any text (without spaces).
• Structure lists the structure where the reaction, flux or reaction rule occurs.
• Depiction shows the molecular details of the reactants and products. Species that do not have molecular details are depicted as green balls. For reactions, molecular details of species appear only if they are first specified in the Species tab. For reaction rules, reactant and product molecular details are specified below in the Reaction Rules Properties pane. For species with molecular details, green sites denote that the state of the site is specified in the Reaction Rule (e.g. bound/unbound, phosphorylated/unphosphorylate), white sites are undefined in the Reaction Rule. Yellow sites indicate that multiple states are specified. Names of states of sites are omitted in the table for clarity.
• Kinetics list the kinetic type for the reaction; select the reaction and edit in the properties pane below. For reaction rules, only Mass Action kinetics are allowed.
• BioNetGen Definition provides the BioNetGen Language (BNGL) string that encodes the rule. It cannot be edited but can be searched.

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.