Step 2

Quantify Your Hypothesis

To begin step 2, right-click the model you want to quantify on the Models tab in the database pane. Select “Create Model Realization”. A model realization (sometimes called a quantitative model) is a version of your diagram that can be solved computationally. A given model may have many model realizations. This is because you might have several ideas about how best to write the rate law for a given process and you might want different model realizations with different initial values for your states. You also might want to impose different sets of constraints in different model realizations.

We often use MR as an abbreviation for Model Realization.

We’ll illustrate the process of creating and completing an MR using the cAMP model developed in Step 1. scroll or use the search box to find “new model for Help System” on the Models tab of the database pane. Right click and select Create Model Realization.

ProcessDB will then automatically create an MR for this model. This can take a few seconds for large models because default rate laws are being written for every process in the model based on the mass action principle from chemical kinetics.

When your MR has been created it is automatically added as a branch in the model tree structure in the database pane as shown below. Notice that just like other parts of ProcessDB a new MR will have a negative ID until it is explicitly saved (or committed, if you want to use database lingo) to the database. Click the save icon () to save the MR to the server.