Protocols¶
A protocol records a perturbation. State protocols act on a species; process protocols act on a flux. Each one becomes extra equations in the Model of Experiment, applied only to the copy of the model that represents that experiment.
State protocols¶
On the State Protocols tab, press Add to create one. You choose the state it applies to and its type; the panel on the right then asks for what that type needs.
| Type | Describes | You supply |
|---|---|---|
| Bolus | A discrete addition at one or more time points | A table of At Time / Amount |
| Infusion | Material added at a steady rate over an interval | A table of Start Time / End Time / Rate |
| Formula | The species follows an expression you write | The formula (right-hand side), a start and end time, and values for any parameters it names |
| Graph | The species follows a measured time course | A table of Time / Value points |
| Forcing Function | The species is driven by a formula, replacing its differential equation over an interval | The formula, a start time, and an end time |
| Events | Something discrete happens at given times | A table of At Time / Event |
A few distinctions worth having straight:
- Bolus vs. Formula. A bolus adds material to whatever is already there. A formula or graph protocol sets the value, overriding the model's own computation for the interval you specify.
- Formula vs. Forcing Function. Both impose an expression, but a forcing function replaces the state's differential equation outright for its interval, so the model's own fluxes no longer change that state while it is active.
- Graph vs. a measurement. A graph protocol is an input: data you are feeding to the model because you know what that species did. A measurement is an output: data the model is being asked to reproduce. The same data in both roles stops being evidence — the model would be scored on its ability to repeat what it was handed.
- Several protocols on one state. This is allowed, and their time windows are chained in order.
Outside the interval a protocol defines, the state reverts to its ordinary behaviour under the model's equations.
Process protocols¶
On the Process Protocols tab, protocols act on a flux rather than a species, and only two types apply:
| Type | Describes |
|---|---|
| Formula | The flux follows an expression you write, over an interval |
| Graph | The flux follows a measured time course |
Both replace the process's rate law for the duration of the experiment. That is the point: when you have measured a flux directly — from a tracer study, from oxygen consumption, from any direct assay — you can impose it and let the rest of the model respond, rather than asking the model to predict it.
Protocol parameters¶
Formula protocols can name parameters. They appear in the Protocol formula parameter / Value table under the formula, and their values are carried into the generated equations and into the MOE's parameter set. They can be fitted like any other parameter.
Where protocols show up in the equations¶
In the equation listing each protocol contributes lines inside its experiment's block: pulse terms for boluses, driver equations for infusions, an interpolated data table for graph protocols, replacement equations for forcing functions. Reading that block is the definitive check that a protocol has been entered the way you meant.