Organizing a large diagram¶
A model of any real pathway quickly outgrows a screen. ProcessDB gives you four tools for this, and they compose: layout arranges, subdiagrams scope, the mask hides clutter, and colour groups by eye.
Layout¶
The diagram toolbar has three arrangement controls:
| Button | What it does |
|---|---|
| Fit to window | Zooms so everything is visible. A freshly opened diagram keeps fitting itself as the window and the panels around it change size, until you pan or zoom; pressing this hands it back to that automatic fitting |
| Layout | Arranges the whole diagram from scratch, orthogonally |
| Incremental layout | Improves the arrangement while keeping nodes roughly where you put them — often it only reroutes edges |
Use Layout after a large import or a burst of drawing, and Incremental layout after adding a few processes to a diagram you have already tuned by hand. Node positions are part of the model and are saved when you commit, so an arrangement you like will be there next time — and for your colleagues.
Subdiagrams¶
A subdiagram is a named subset of a model's processes: glycolysis within a metabolic model, one signalling branch within a network. Subdiagrams overlap freely — a process can belong to several — and they do not change the model's mathematics at all. They exist so you can look at one part of a network at a time.
To create one, select the processes you want, right-click, and choose Add Process(es) to Subdiagram. The dialog lets you add them to an existing subdiagram or create a new one.
Subdiagrams appear in the Outline. Right-click a subdiagram there to Duplicate it (a quick way to make a variant), Delete it (which deletes only the grouping, never the processes), or open its Properties.
To take a process out again, select the subdiagram and the process, then choose Remove Process(es) from Subdiagram.
The state mask¶
Some states are everywhere and tell you nothing: ATP, ADP, water, protons. Drawn honestly, they connect to half the network and turn the diagram into a hairball.
The state mask solves this per subdiagram:
- Select the offending states, right-click, and choose Mask State(s).
- Turn on the State Mask toggle in the diagram toolbar.
Masked states vanish; the processes that use them stay, and stay correct. Turning the toggle off shows everything again. Unmask State(s) takes a state back off the list permanently, after which it is always drawn as long as it takes part in a visible process.
Masking is purely visual. A masked cofactor is still a reactant, still gets a differential equation, and still appears in the rate laws.
Colour¶
States and processes each have a Color in their Properties dialog. Use it to group by pathway, by evidence quality, by whatever distinction you are carrying in your head — the diagram is a thinking tool as much as a record.
Reading a diagram someone else drew¶
Two things make an unfamiliar model quick to understand:
- The Outline. Selecting a state or process there centres the diagram on it, so walking the list shows where each item lives.
- The Notes panel. Shown beside the diagram, it puts the model's note and every state and process note next to the picture; a well-annotated model reads like a paper. See Notes, history, and sharing.