Models of Experiments¶
A Model of Experiment (MOE) is one Model Realization simulated under a chosen set of experiments. It is the object that actually runs.
Everything that is specific to this comparison of model and data lives on the MOE: the generated equations, the parameter sets, the traced states, the simulation time span, and the graph layout you last used.
Creating a MOE¶
Right-click a Model Realization — in the Models browser or in its own tab — and choose Create MOE. Name it after the question you are asking, since a realization usually collects several.
The MOE tab¶
▶ Simulate, top left, is the point of the whole tab: it opens the Parameter Explorer with these equations, this parameter set, and this experimental data. The button is disabled for a moment after opening while the equations and parameter values load.
Experiments in MOE lists the experiments included. Add one with +, or drag it in from the Experiments browser; − removes the selected one. Double-click an experiment to open it.
The summary beside it shows the MOE's name and ID, its Model Realization, the model it ultimately comes from (with Open Model to jump there), and the Start / End Time.
When a MOE is ready to be written up, File → Export Model Bundle… works from this tab: it collects the diagram, the open graph windows, the equations, the parameter sets, the last simulation, and the data into files for a paper or report. See The model bundle.
Start and end time¶
ProcessDB calculates a sensible simulation window from the experiments: the earliest and latest time anything refers to — data points, protocol windows, bolus times, infusion intervals, bleach and activation pulses — extended backwards to allow any pre-experiment steady state to settle. That calculated window is shown marked (auto).
Press Edit to override it. Your values are what the solver receives; the calculated ones remain visible in the equation listing as a comment, so you can always see what ProcessDB would have chosen.
Widen the window when you want to see where the model goes after the data stops. Narrow it when a long pre-equilibration is making the interesting part of the plot unreadable.
The tabs at the bottom¶
| Tab | Contents |
|---|---|
| Equations | The complete generated mathematical model — see The equation listing |
| MOE Functions | Algebraic definitions specific to this MOE and experiment |
| MR Functions | The realization's shared definitions, editable here |
| Parameter Sets | Named collections of parameter values — see Parameter sets |
| Tracers | Which states and processes carry each label — see Tracers |
Keeping the equations current¶
A MOE's equations are derived. Editing the model, changing a rate law, adding an experiment, or changing a protocol all make them out of date.
ProcessDB never regenerates them behind your back — the listing you are looking at is always the one that produced the results you are looking at. Instead, a banner appears above the listing saying what changed:
- "generated before your latest changes — rate laws, initial conditions" — press Regenerate.
- "loaded from the database … has not been checked" — the equations came from storage with no record of what produced them. Press Check and ProcessDB generates a listing and compares; if they differ, the same dialog offers to replace them.
You can also regenerate from the right-click menus: Regenerate Equations on a MOE, or Regenerate Equations for All MOEs on a realization.
An incomplete realization blocks generation
If rate laws or initial conditions are still missing, ProcessDB says so rather than generating equations with undefined symbols, and offers to fill the gaps with defaults first. Fix the blanks in the Action Items panel.
What a MOE is not¶
A MOE holds no biology of its own. If you want to change the mechanism, edit the model; to change the kinetics, edit the realization; to change what was done at the bench, edit the experiment. The MOE only decides which realization meets which experiments — and holds the numbers that result.