Reactions Table

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

The Reactions Tab has several columns:

• Reaction column specifies either editable reaction or flux, or uneditable "Reaction Rule" text.
• Name column has a sortable name that is autogenerated as r_number but can be edited.
• structure where reaction, flux or reaction rule takes place. For rule-based models, this field is uneditable, as the model may contain only one compartment.
• Depiction shows the molecular details of the reactants and products. If species does not have molecular details, it is shown as green shape. For reactions, species with molecular details must be already specified in the Species tab. For reaction rules, reactant and product patterns must be specified below in Reaction Rules Properties pane. Green color for sites of species with moledcular details denote that either binding or state specified, white sites are undefined and can be connected to anything or be in multiple states (if yellow shape is shown). States of sites are omitted for clarity.
• Kinetics can be selected here and specified in properties pane below. For reaction rules, the only is allowable kinetics is mass Action and is currently uneditable.
• BioNetGen Definition provides BNGL string with rule encoding. It is uneditable but searchable.
• Link does not work for reaction rules at this time.

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

New Reaction adds a new reaction or flux. If there are multiple compartments, in the popup box select the structure where the reaction occurs, 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 adds a new reaction rule. The only way to specify and edit the new rule is via properties pane below.

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. This is very useful feature when a new rule is a slight modification of the previous one.

Use the Pathway Links button to match reactions within Pathway Commons Database.

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