The equation listing¶

The Equations tab of a MOE holds the complete mathematical model: every differential equation, every rate law, every protocol, every parameter value the solver will use. It is generated from the model, the realization, and the experiments, and it is the definitive answer to "what is actually being simulated?".

Reading it is never necessary to use ProcessDB. It is, though, where the answer lives when a simulation does something unexpected.

Reading it¶

The listing is a numbered table of lines. Above it are three controls:

• Display Names replaces the S…/P… symbols with state and process names. Excellent for reading; turn it off when you need the symbols.
• Search narrows the listing to matching lines — the quickest way to find every equation a parameter appears in.
• Double-clicking a symbol in a line jumps to it: a state or process symbol selects and centres it in the diagram; a parameter opens the rate law that defines it.

What the blocks are¶

Roughly in order:

Header. Solver method, step size, the simulation start and end time (with the auto-calculated values noted alongside if you overrode them), and the error tolerances.

Model-level equations. One differential equation per state, assembled from the fluxes of every process the state takes part in, with stoichiometric coefficients applied. Boundary states appear as equations fixing their value rather than its rate of change. Then the rate laws, and the INIT lines giving initial conditions.

One block per experiment. Everything above, repeated with each symbol tagged by the experiment ID — S123_7 is state 123 as it behaves in experiment 7 — so all the experiments in the MOE run as one system. Layered into each block are that experiment's protocols: pulses for boluses, driver equations for infusions, interpolated tables for graph protocols, replacement equations for forcing functions and process protocols.

Tracer equations. For each tagged molecule, a parallel set of equations for the labelled material, plus whatever the tracer protocols require — bleached and retained fractions, an activated pool, a FRAP readout.

Functions. The realization's MR functions, then the MOE's own functions, with their parameters.

Parameter values. Every constant the equations use, with the value the solver starts from.

Symbols¶

Symbols are used rather than names because names change and are not guaranteed unique; the Symbols… button in the Edit Rate Law dialog shows the full table for a model.

Things worth checking in the listing¶

• A parameter you expected to fit is not there. It is probably defined by a rate law that is not the active one. Check the process in the Edit Rate Law dialog.
• A protocol seems to have no effect. Find its experiment's block and look for the protocol's equations. If they are missing, the protocol is on a state the experiment's block does not contain, or its time window falls outside the simulation window.
• A state is constant when it should not be. Look for a boundary equation or a forcing-function replacement in that block.
• A line reads something = 0 with a name you do not recognise. The generator emits a placeholder when a formula refers to a symbol nothing defines — usually a rate law naming a state that has since been deleted. That is a real problem: fix the rate law rather than the placeholder.

Regenerating¶

The listing is derived data and is rebuilt on demand rather than automatically. See Keeping the equations current for the banner, the Regenerate button, and what blocks generation.

Regenerating never changes your model, your realization, or your parameter sets — it only rewrites the listing from what those already say.