Milestones in the modeling process
You and your collaborators have agreed on a model diagram to test
Congratulations! We think joint development of a biological system diagram is one of the most valuable steps you can take to advance a biomedical research project. Indeed, this is why the ProcessDB development team has worked so hard to support collaborative diagram construction and revision - even for collaborators who work far away from one another.
Everyone agrees on the units of time, the units of quantity, and the basis of the model
Units of Time
This is usually not a difficult step, but if you are on the modeling team we recommend you choose units of time that your experimental collaborators use every day in their project discussions and in their data sets.
Units of Quantity
Controversy: Many investigators trained in the physical sciences insist that state variables must have units of concentration. We think concentration units are fine, but they are not not required and are not always the most convenient. For example, the tracer kinetics modeling community almost always uses mass units or mass units normalized to body weight (umol/kgBW).
Basis of the Model
What is the "basis" of a model? This is a fairly intuitive concept, but it is often left implicit. Some modelers think of it as normalization. The basis of a molecular cell biology model might be one cell or it might be a million cells. The basis of a model of whole-animal metabolism might be a kg of body weight. The basis you choose is a matter of convenience and personal preference; it scales all your model's states and fluxes so that they can be compared to results in other laboratories. The ProcessDB team likes to use one cell as the basis for models in molecular cell biology. This means that model state variables will have units of molecules per cell or attomoles/cell. You could just as well choose a million cells as your basis, and then your state variables might have units of pmol/million cells. If we are building models of human metabolism we usually choose umol/kgBW as our units for state variables, but the choice is always yours to make! We are simply recommending that you make that choice explicit.
Your model diagram has been converted to differential equations
One of our design goals for ProcessDB was to translate your biological diagram to equations and produce graphs of your desired variables as quickly as possible. To this end, we offer a single-click option to run a simple steady-state solution plus a simple perturbation of a variable of your choice.
To start the automated process, right-click your model in the Models tab of the database pane, and select "Run Initial Simulation."
Translation from diagram to differential equations is a complex process and there can be unique aspects of your particular model that we did not anticipate when designing our automated process. Take this as a measure of your originality. :) If the initial attempt is unsuccessful, a screen of messages will be displayed. If you are an experienced modeler or are working with one, these messages should be sufficient to determine what additional information is needed in order to get the initial simulation to run. If you are new to modeling or if the messages appear written in a language you do not understand, copy the messages or take a screenshot and go to Fixing Initial Simulations.