The ProcessDB window¶

The main window is a Workspace of tabs in the middle, panels on its edges, a toolbar across the top, and a panel bar along the bottom.

Click the picture to see it full size.

The numbers in that picture are used throughout this page:

1. Reload, Save, Undo, and Redo.
2. The search box.
3. The Workspace — one tab per thing you have open.
4. The Browser panel.
5. The Browser's own tabs — Models, Molecules and Complexes, Processes, Places, and Experiments.
6. A model expanded to show its Model Realization, expanded in turn to show its Model of Experiment.
7. Filter by, the access filter.
8. The Outline panel — the contents of the active tab.
9. The Notes panel.
10. The panel bar.

The toolbar¶

Four buttons at the left (1), and the search box at the right (2).

Searching¶

Type in the search box (2) and the Search Results panel opens beneath it, on the right edge, listing every model, molecule, complex, process, place, and experiment whose name, ID, or notes match — grouped in that order, with the ID at the right of each row. Double-click a result to open it: a model or an experiment opens as a tab, and a molecule, process, or place opens its Properties dialog. The first hundred matches are shown, with a Show more… row for the rest. Clear the box and the panel leaves on its own.

A single character matches the start of a name — so the first letter you type narrows the list rather than flooding it — and from two characters on, any part of it.

The Workspace¶

Everything you open — a model diagram, a Model Realization, a Model of Experiment, an experiment — opens as a tab in the Workspace (3). The picture has three open: a model's diagram, the Model Realization beneath it, and that realization's Model of Experiment. The Workspace is the one part of the window that is always there: panels can be hidden, moved, and popped out, but the tabs cannot, so the thing you are working on is never lost.

Tabs have a close button, and right-clicking a tab gives the same menu as right-clicking the object in the Browser.

• Ctrl+W (⌘W on macOS) closes the current tab.
• Ctrl+Shift+W (⇧⌘W) closes them all.

The panels¶

Five panels live around the Workspace. Each is shown or hidden from the panel bar (10) or the View menu, and each can be resized, moved to another edge, or popped out into its own window — see Arranging the panels. What they are for:

Browser¶

The Browser (4) is a set of tabs (5) onto everything in the database:

• Models — a tree of models. Expand a model to see its Model Realizations, and expand a realization to see its Models of Experiments (6). Double-click any of them to open it in a tab. Right-click for Properties, Create Model Realization, Create MOE, Regenerate Equations for All MOEs, and Regenerate Equations.
• Molecules and Complexes — every molecule and complex in the database.
• Processes — every process, across all models.
• Places — every compartment.
• Experiments — every experiment.

Each Browser tab has its own search box. The Models tab additionally has a sort order — by name, by ID, or by how recently you opened each model, which is the default — and the Filter by access filter (7) described in Getting started.

Objects in the Browser can be dragged into a diagram to add them to a model, and experiments can be dragged onto a MOE to include them. This is usually faster than the equivalent dialogs.

Outline¶

The Outline (8) is a tree of whatever the active tab is showing: the Processes, States, and Subdiagrams of the open model, with a search box above them. Clicking an entry centres the diagram on that object, zooming in if it would otherwise be too small to read; right-clicking offers Show in Diagram, Properties, and the same items the diagram's own menu has. A process or state that carries a note is marked with a small note symbol, and inside a Model Realization a process with an active rate law is marked ƒ.

The Outline has something to show only while a tab is open. With none, it leaves the screen, and its button in the bar says why.

Notes¶

The Notes panel (9) is a running document of every note in the model: the model's own note first, then one section per process and per state, headed by its name and symbol. Notes are edited right there, and a section without one offers Click to add a note. Double-clicking a heading jumps the diagram to that process or state. The panel follows the model behind whatever tab is in front, so it works just as well from a Model Realization or MOE tab. See Notes, history, and sharing.

Action Items¶

Action Items opens along the bottom edge when a Model Realization has something that still needs filling in — a rate law, an initial condition, a boundary formula — and lists what. It is the checklist of a realization's quantitative side; see Model Realizations. It is absent from the picture because a model's diagram tab gives it nothing to show.

Search Results¶

Search Results is where the search box (2) answers, as described above.

The panel bar¶

The bar along the bottom (10) has one button per panel, grouped by the edge the panel opens on — left, bottom, right. A pressed button means the panel is on screen; click it to hide the panel or bring it back. Rest the pointer on a button and a rectangle pulses over that panel, which is the quickest way to learn which is which.

Arranging the panels covers resizing, moving, popping out, and the three ready-made layouts.

The menus¶

The menu bar sits at the top of the window on Windows and Linux. On macOS it is in the system menu bar at the top of the screen, which is why it does not appear in the picture above.

File

Edit holds Preferences…, where the application-wide font size lives. Changes apply immediately across every window.

View lists the five panels, with a tick beside each one that is on screen; then Layout, holding the Build, Simulate, and Write layouts and Reset Layout; then Import Dialog. See Arranging the panels.

Go holds Back and Forward. These retrace where you were looking — the jumps you make by double-clicking a symbol in an equation, or by choosing Show in Diagram — and are unrelated to Undo, which retraces what you changed. The shortcuts are ⌘[ and ⌘] on macOS, Alt+← and Alt+→ elsewhere.

Help → Online Documentation opens this site in your browser. Help → About reports your ProcessDB version — worth quoting when you report a problem.

Making things bigger¶

Everything in ProcessDB scales with one font-size setting:

• Ctrl+= / ⌘= — larger
• Ctrl+- / ⌘- — smaller
• Ctrl+0 / ⌘0 — back to the default

The setting persists between sessions, as do the size of the main window and the arrangement of the panels. It is also in Edit → Preferences… with a live preview.

Windows that open on their own¶

Three things open in their own windows rather than as tabs or panels, so they can sit beside the main window rather than replace it:

• the Parameter Explorer, where simulations run;
• graph windows spawned from it;
• the Biology Agent.

Any panel can join them: pop it out from its header, and it becomes a window of its own until you dock it back.