Models¶

A model is a mechanism drawn as a diagram: states, the processes that connect them, and the compartments they sit in. It holds no rate constants and no concentrations — those belong to a Model Realization. This separation is what lets one diagram support several competing quantitative treatments.

Finding a model¶

The Models browser lists models as a tree; expanding a model shows its Model Realizations, and expanding a realization shows its Models of Experiments. You can:

• Search by name, ID, or notes with the box at the top — or by the name of a colleague the model is shared with;
• Sort by name, by ID, or by most recently opened;
• Filter by access level — All Models, Recent Models (the starting filter), My Models, Shared Models, Public Models.

Double-click a model to open it in a tab; the diagram loads in the background and appears in a moment.

The search box in the main toolbar is broader: it searches models, molecules, processes, places, and experiments at once, including their notes, and answers in the Search Results panel beneath it. Use it when you know a molecule appears somewhere but not which model. See Searching.

Creating a model¶

Press New Model in the Models browser. A model named "New Model" is created and opened. Right-click it and choose Properties to give it a real name and description; the Properties dialog also shows how many processes and states it contains, and holds the model's notes.

New models are yours; sharing them with colleagues or making them public is managed by your ProcessDB administrator.

Working with an open model¶

An open model shows its diagram in the Workspace and its contents as a tree in the Outline panel. The two are linked: clicking a state or process in the Outline centres the diagram on it, zooming in if it would otherwise be too small to read, which is the fastest way to find something in a large network.

The model's notes — its own, and one section for every process and state — live in the Notes panel, which sits beside the diagram when you show it. See Notes, history, and sharing for what the notes are good for, and Arranging the panels for the Write layout, which puts Notes beside the diagram and everything else out of the way.

Copying material between models¶

Drag from the browsers straight into a diagram:

Because molecules, places, and processes are shared across the database, this is re-use rather than copying: the same process appearing in two models really is the same process, and editing it in one place changes both. That is the point — it is how ProcessDB keeps a growing body of models consistent — but it is worth knowing before you edit a process you dragged in from elsewhere.

Deleting¶

Select states or processes in the diagram and press the Delete button in the diagram toolbar. Deleting a process removes it from this model; the molecules and places it referred to remain in the database for other models to use.

Deletions, like every other edit, take effect in the database only when you commit.

Next¶

• Molecules, places, and states
• Drawing the diagram
• Organizing a large diagram