Molecules, places, and states¶

These three objects are the nouns of ProcessDB. Molecules and places are shared across the whole database; states are the combination of the two and are what the equations are written about.

Molecules¶

A molecule is a chemical identity — a metabolite, a protein, an ion. It has a name and notes, and nothing else: no location, no amount.

Create one with New Molecule in the Molecules and Complexes browser. The browser's search box finds molecules that already exist, and reusing one is what lets ProcessDB recognise that two models are talking about the same substance.

Molecule names are edited only while the molecule is new. Once it has been committed, the name is fixed, since other people's models may already refer to it.

Complexes¶

A complex is a molecule assembled from other molecules with a count of each part: a dimer, a protein with a bound cofactor, a ribonucleoprotein particle. Create one with New Complex, then double-click molecules and complexes in the list to add them as parts; double-clicking the same part again increases its count.

Complexes behave exactly like molecules everywhere else — they occupy places, form states, and participate in processes.

Tagged molecules¶

A tagged molecule (also called a tracer molecule) is a labelled version of a simple molecule: 13C-glucose, a photoactivatable fluorescent protein, a radiolabelled amino acid. Select a simple molecule and press Create Tagged Molecule, or right-click it and choose the same item.

A tagged molecule is what tracer experiments are built around. It never appears as a state in the diagram; instead ProcessDB derives a parallel set of tracer equations that ride along on the chemical model, so labelled and unlabelled material share the same rate laws. See Tracers and tagged molecules.

Places¶

A place is a compartment: a cell compartment, an anatomical pool, a culture medium. Create one with New Place in the Places browser.

A place has a type — a volume by default — and, in a diagram, a size. Places are drawn as large containers and everything inside one is understood to be in that compartment. Moving a state into a different place in the diagram is a real change to the biology, so ProcessDB asks you to hold Shift while dragging to do it; without the modifier the state stays where it belongs.

As with molecules, a place's name can be edited only while it is new.

States¶

A state is a molecule in a place. It is created for you — you never make one from a dialog:

• drop a molecule onto a place in a diagram, or
• draw a process to or from somewhere that implies one.

If the molecule already has a state in that place, ProcessDB reuses it rather than making a duplicate. The state's name is formed automatically as "molecule in place".

States are the variables of the model. Each one gets a differential equation, an initial condition, and — if you mark it as a boundary state — a formula that fixes its value instead. Measurements are associated with states, and it is state trajectories the graphs plot.

A state's properties¶

Right-click a state and choose Properties to see and edit:

• the molecule and the place it combines, with a ➔ button that jumps to the molecule;
• its ProcessDB ID, which is the S… symbol used in the equations, and a Show in Diagram button;
• its colour in the diagram;
• the molecule's Identity References and Parts References — links to the external registries the molecule is identified by. Long links are shown shortened, with their beginning and end kept; Edit shows the whole link, and Add and Remove maintain the list;
• its notes;
• a Processes tab listing every process in the open model that the state takes part in, with its Role and, for a reactant or product, its Stoichiometry — which is edited right there in the table. Double-clicking a row opens that process's Properties.

Opened from within a Model Realization, the same dialog also shows that realization's Initial condition, the On boundary checkbox, and — once that is ticked — the Boundary formula (RHS) in place of the initial condition. Those are properties of the state in that realization, not of the state itself.