Drawing the diagram¶

The diagram is where the biology is stated. Everything downstream — equations, simulations, fits — follows from what is drawn here.

Navigating¶

Gesture	Effect
Drag on empty canvas	Pan
Scroll	Zoom
Click	Select a state, process, place, or subdiagram
`Ctrl`/`⌘` + click	Add to or remove from the selection
`Ctrl`/`⌘` + `Alt` + drag	Lasso-select a region
Drag a node	Move it
`Shift` while dragging a node	Allow it to change place

The Gesture Suggestions bar at the bottom of the diagram names what your current keys and mouse buttons will do, and updates live as you press them. It is on by default, and the toolbar toggle turns it off. Help, at the right end of the same toolbar, opens this page.

Creating processes¶

All process drawing is done by holding Alt and dragging from one node to another. A green dot marks a valid target as you move over it. What you get depends on what you drag between:

Drag from	To	Result
State	State	A new process: source is reactant, target is product. Its Properties dialog opens so you can name it.
Place	A state in that place	A synthesis: a process with no reactants that produces the state
State	Its own place	A degradation: a process that consumes the state and produces nothing
Process	State	Adds that state as a product of the process
State	Process	Opens Add Reactant or Modifier — see below

Tip

Releasing Alt once the drag has started makes the rest of the gesture easier; the mode is already engaged.

Roles¶

When you draw from a state to an existing process, the Add Reactant or Modifier dialog asks two things.

1. Role — what does this state do in the process?

Role	Meaning
Reactant	Consumed by the process
Enzyme	Catalyses it; its level multiplies the rate
Catalyst, Transporter, Channel, Mediator	Other catalytic roles, distinguished for clarity and for SBML export
Activator	Increases the rate without being consumed
Inhibitor	Decreases the rate without being consumed
Regulator, Modifier	Affects the rate in a way you have not yet committed to

Products are drawn from the process side, so Product is not on this list.

2. Stoichiometry — how many?

The Stoichiometry field is enabled for a reactant only, and starts at 1. Leaving it blank means "unspecified", which the equation generator reads as 1; only a positive number is stored. Modifiers have no stoichiometric coefficient, so the field is disabled for them. A product drawn from the process side gets a coefficient of 1 without being asked.

Press Add. A coefficient can be changed later in three places, each an editable table cell: the States tab of the process's Properties dialog, the Processes tab of the state's Properties dialog, and the Properties of the arrow itself.

How a regulator acts is a property of the rate law

A role says that an activator or inhibitor regulates a process. How it enters the equation — competitively or non-competitively, as an essential or a non-essential activator — is decided when a rate law is built for the process, and lives in that law's formula. See How regulators enter a modular law.

Editing what you drew¶

Right-clicking in the diagram opens one menu for the whole selection, headed by the name of what you clicked — or "N selected items". What it offers depends on what is selected:

With a state selected: Mask State(s) and Unmask State(s), which add and remove states from the state mask.

With a process selected: the Process Direction submenu — Left to Right, Right to Left, Top to Bottom, Bottom to Top, or Automatic — and Add Process(es) to Subdiagram / Remove Process(es) from Subdiagram. Inside a Model Realization it also offers Edit Rate Law….

With a subdiagram selected: its own items, and Properties.

Always, at the bottom: Properties. For a process that means its name, its place, its colour, its active rate law (with an Edit Rate Law button when you are inside a realization), its notes, and two tabs: Models, the models that use the process, and States, every participant with its Role and Stoichiometry — the coefficient is edited right there in the table. For a state, see A state's properties. Selecting an arrow and opening Properties shows that one participation: its role and, for a reactant or product, its coefficient.

Elsewhere — in the Outline and the browsers — the same objects offer the same items, plus Show in Diagram, which selects and centres the object in the model diagram.

Undo¶

The toolbar's Undo and Redo step through your edits. They are separate from Go → Back and Go → Forward, which retrace where you were looking rather than what you changed.