The reactions diagram shows a bipartite graph consisting of of species (green balls for species that do not have molecular details, or blue balls for species with molecular details) and reaction (yellow squares) nodes, each within the appropriate compartments, and connected by lines connecting species that participate in the reaction. In rule-based models, species patterns representing reactants and products defined within rules are depicted with ovals around balls (molecules) of various colors.
Structures are depicted as connected rectangles within the workspace. Species are green or blue balls and reactions are yellow squares placed into the structures. Lines each connect one species with one reaction: solid lines with arrows denote reactants and products; dashed lines denote catalysts. Stoichiometric coefficients, if different from one, are displayed next to the appropriate lines. When reactions are defined by rules, the reactants and product species patterns are depicted as ovals with one or more balls of various colors.
A toolbar above the graph provides buttons for editing, adjusting zoom, and changing the layout of the elements.
A toolbar at the bottom of graph provides a means to search a text field, delete items, or. when using the Pathways Commons database, to select species and use the Pathway Links button.
The tool bar above the graph provides tools for creating and editing species, reactions, and fluxes; selecting the tool alters the
function of the mouse as described below.
'Selection tool' enables selection mode. Species (graph nodes) and connecting lines (edges) can be selected by mouse click, or drag the mouse to select multiple components. Add elements to the selection using the shift key with the left mouse button, toggle the selection using the control key.
'Structure tool' inserts a new structure by clicking between existing structures or appending new structures to the ends.
dashed vertical lines appear on the reaction diagram to indicate where structures can be added (indicator under mouse turns green to allow adding new structure).
Move a structure using the 'Selection tool'. Click and drag on a structure name to enable drag to move; releasing the mouse over any set of vertical dashed lines moves the structure and contents to the new location.
'Species tool' enables adding new species enables adding new species by clicking within a structure. Names automatically generated for species can be edited in the species property pane. New species are created without molecular details and appear green; species change to blue if the molecular composition of the species is specified using the species properties pane.
'Reaction tool' enables one to create reactants/products of a reaction or membrane flux.
For non-flux reactions, drag the mouse to assign reactant or product roles by connecting species or reactions. The direction of
the drag determines whether a reactant or product role is assigned (e.g. dragging from species to reaction
creates a reactant role, dragging from reaction to species creates a product role). No relationship is created
if VCell constraints would be violated, e.g. two reactants cannot be in different volume compartments.
Create a reaction by dragging from species to species (or open space). Create an intermediary
species by dragging from reaction to reaction (or open space).
'Membrane flux tool' creates a membrane flux by clicking in a membrane structure. Add flux participants by selecting
the 'reaction tool' and dragging, first from an existing species to the newly created flux component then click and drag again from the flux component
to another existing species.
'Catalyst tool' creates a catalyst annotation by dragging from a species to a reaction or vice versa. The 'catalyst tool' creates a visual cue (dotted line) between a reaction and a species but does not change the model physiology.
(Note: for convenience, connecting a species with empty space creates a new reaction and connecting a reaction to empty space creates a new species.)
buttons vary the display magnification of the reaction diagram.
The layout buttons automatically arrange the components (graph elements) by different algorithms. These include (from left to right) random, within an ellipse within each structure, so that most lines point downward, to make lines shorter and more similar to each other in lengths, and to place nodes more evenly across each structure. For rule-based models, there are additional buttons to either have all participants in a reaction depicted separately (and therefore reactants/products may be duplicated in the view) or have the same reactant/product depiction connected to multiple reactions.
The mouse popup menu provides several functions depending on the current selection (structures,reactions,species):
The search text field allows the user to select multiple components that have a similar name.
The delete button deletes selected elements. Delete will fail if a species is connected to a reaction or flux; you must first delete the reaction or disconnect the species from the reaction.
The Pathway Links button allows the user to follow links from model elements (species, reactions or fluxes) to pathway elements, or to edit pathway links.
Depending on the type of object selected, the bottom pane of the window displays a reaction, membrane structure, species, stoichiometry or volume structure properties pane.