Step by step model
Getting Started with a Sample Model to demonstrate that ProcessDB is installed and functioning properly
Log on to ProcessDB. Enter your login name and password. Click Launch. You will then be connected and the Database pane will be populated with a list of currently available models. In the Display pulldown list (below the models), select "Public". This will show you all public models in the ProcessDB database.
Scroll down to the model named "catalytic subunit cAPK", which has a model ID of 375. This is a simple model of the cAMP-dependent protein kinase system that we have used to teach workshops on ProcessDB. Double click the model to load the model diagram. You should see a diagram similar to the one shown here:
Briefly notice the Model Tree Structure pane in the lower left. This hierarchy makes it easy to drill down to model details even in the most complex models.
In ProcessDB a Model Realization (MR) is a quantitative model corresponding to a particular model diagram. If necessary, expand the directory tree for the "catalytic subunit cAPK" model by clicking the + to the left of the model icon. Then open this model realization in the diagram screen by double-clicking anywhere on the line the contains the blue MR icon and the words "catalytic subunit cAPK ID=241". You should see the same model you saw in the previous step, but with a blue background (indicating this is an MR) as shown here:
Notice the tree structure in the "MR Pane" that now appears between the Database Pane and the MR diagram. There is an enormous amount of functionality in the context menus associated with this tree structure and in the context menus associated with the MR diagram itself. Later you can come back and explore these, but for this installation verification test, move your cursor to the MR pane and select "simple FRAP for workshop ID=309" to open the corresponding Model of Experiment screen. In ProcessDB a Model of Experiments (MOE) is a model realization (quantitative model) combined with one or more experiments. In this case the quantitative cAPK model has been combined with a simple experimental protocol involving Fluorescence Recovery After Photobleaching (FRAP).
Again, you can return later to explore the features of this screen, but to continue the installation verification, just right-click on the MOE and select Solve. You will be prompted to select a parameter set; select parameter set zero and click OK. This will launch the parameter explorer with an initial solution.
If you want to test your model by running it in Berkeley Madonna, right click on the MOE and select "Export to Solver". Enter a file name for the exported Madonna file that encodes the model of experiments (MOE309).
Click the Launch Solver button. This converts the quantitative model and its associated experimental protocols to a native Berkeley Madonna file, downloads the file to your computer, and launches it in your locally installed copy of Berkeley Madonna.
