Notes, history, and sharing¶
Notes and the Notes panel¶
Every model, state, and process has a Notes field in its Properties dialog. This is where the reasoning goes: why a process is drawn the way it is, which paper supports a regulatory edge, what is still uncertain.
The Notes panel collects all of those notes into one running document: the model's own note first, then a section for every process and every state, each headed by its name and its symbol — Hexokinase [P42]. Show it from the panel bar or the View menu, or choose View → Layout → Write, which puts Notes beside the diagram and everything else out of the way. See Arranging the panels.
Notes are edited directly in the panel — a section without a note offers Click to add a note — and a note typed in a Properties dialog appears in the panel at once, and the other way round. Notes are saved with the model by the ordinary Commit.
Double-clicking a heading jumps the diagram to the process or state it names; Ctrl/⌘-click does the same, and a right-click offers it as a menu item. Reading a note about Hexokinase [P42] and wanting to look at P42 is the whole reason the heading prints the symbol.
The panel follows the model behind whatever tab is in front, so the notes are just as available while you work on a Model Realization or a MOE. It needs the model's diagram to be loaded: opened on its own, a MOE does not load it, and the panel says so — open the model or its realization.
Notes are also searched by the search box, so a molecule mentioned only in a note is still findable.
History¶
Press History in the diagram toolbar to open the Model History window, which lists each committed version with its Date and a Comment, newest first.
- Select a version and the diagram highlights the difference between it and the model as it stands now: added items ringed in green, removed items in red, with removed nodes shown as ghosts in place. The window summarises the same difference as counts of states and processes added, removed, and unchanged. Click the selected row again to clear it.
- Type in the Comment column to label a version — "before adding the feedback loop", "as published". Comments are saved with your next commit, like any other edit.
- Restore rebuilds the current model to match the selected version: its processes, its participants and their roles and stoichiometry, and the states, molecules, and places they refer to.
Restore changes your working copy only. Nothing reaches the database until you commit, and the whole restore is a single Undo step if you change your mind. Note that history covers the model's topology: diagram layout, Model Realizations, MOEs, and equations are not rolled back with it.
Sharing a link¶
Press the share button in the diagram toolbar and ProcessDB copies a link to your clipboard, and confirms it:
Paste it into an email, a document, a wiki page, or a note-taking tool. Anyone with ProcessDB installed can click it and land on that model. If you have a subdiagram selected when you press the button, the link carries it, so your colleague opens on the same part of the network you were looking at.
The link is a pointer, not a copy — the recipient sees the model as it is in the database, which means they see it only once you have committed, and only if they have access to it.
Exporting¶
For audiences outside ProcessDB, the File menu offers:
- Export as Image — the diagram as a picture, for slides and manuscripts;
- Export SBML — the model in the community exchange format, including modifier roles;
- Export JSON (for LLMs) — the diagram as a file you can attach to a ChatGPT-style conversation when you want to reason about it outside ProcessDB;
- Export Model Bundle… — the diagram, the open graphs, the equations, the parameters, and the data, as files for a paper or report, with an HTML report tying them together.