Experiments¶
An experiment in ProcessDB is the record of one bench experiment: the perturbations that were applied, any labelled species that were introduced, and the time courses that were measured.
Experiments are stored independently of any model. That is deliberate: the same experiment can be used to test several competing models, and a model can be tested against a whole series of experiments at once. An experiment is evidence; a model is a claim; the Model of Experiment is where they meet.
Creating an experiment¶
Press New Experiment in the Experiments browser. Open it and give it a name, a description, and a date; Rename and Change Date are also on the right-click menu, in the browser and on the tab.
The experiment tab¶
A summary sits across the top — name, description, and date — beside a Target Models list showing the models this experiment is currently being used to test. That list fills in automatically from the MOEs that include the experiment; you can also add a model to it by hand, to keep a model you are about to test in view while you enter the protocols.
The rest of the tab is four sub-tabs. A green dot on a tab means it has content, so you can see at a glance what has been entered:
| Tab | Holds |
|---|---|
| State Protocols | What was done to individual species — additions, infusions, clamps, imposed time courses, discrete events |
| Process Protocols | What was done to a flux — imposed rates or measured flux time courses |
| Tracer Protocols | Labelled molecules and how the label was introduced or destroyed |
| Experimental Measurements and Data | What was measured, and the numbers |
See Protocols, Tracers and tagged molecules, and Measurements and data.
How an experiment reaches a simulation¶
Add the experiment to a Model of Experiment — press + on the MOE's Experiments in MOE list, or drag the experiment there from the browser. When the MOE's equations are generated, ProcessDB writes:
- one copy of the state equations per experiment, with each symbol tagged
by the experiment ID (
S123_7is state 123 in experiment 7); - the protocol equations for that experiment, layered onto those copies;
- the tracer equations for any tagged molecules the experiment uses.
Everything runs in a single simulation. That means one parameter set has to explain every experiment in the MOE at once, which is exactly the constraint that makes a fit meaningful. It also means adding an experiment to a MOE changes its mathematics — ProcessDB will tell you the equations are out of date and offer to regenerate them.
A note on scope¶
An experiment describes conditions and observations, not kinetics. Nothing entered here changes a rate law. When an experiment seems to call for a different rate constant, that is what a second Model Realization is for — or a protocol that imposes the altered quantity directly.