ProcessDB takes you through a 6-step process for constructing and evaluating a biological hypothesis or theory. First, we need to introduce a few ProcessDB concepts. When ProcessDB is launched you see the screen below:
Below the menu bar and the toolbar, there are three panes. Before you have built your model, two of the panes are blank and ready for you to start your project. The upper left pane, however, already contains information. This upper left pane is the Database Pane. It has five tabs (Models, Processes, Places, Molecules and Complexes, and Experiments) each with an associated toolbar. The information you see here consists of all public information in ProcessDB plus any information entered from your lab. What you see on these five tabs is information stored in the ProcessDB database on the Integrative Bioinformatics server. Other users do not have access to your models and processes unless you have made these models public.
The Display pulldown list just below the database pane controls what models appear in the database pane. The choices are:
- My Models
When you select My Models from the pulldown list, only models that you have created appear in the database pane. When you select Shared from the pulldown list, models that others have created and shared with you appear in the database pane. When you select Public, you will see all public models in the ProcessDB database.
To construct a new model first click the New Model icon () on the toolbar of the Models tab. Enter a meaningful name for your model in the “Choose model name” dialog that appears. Click OK and two things happen: 1) your blank model diagram is opened in the diagram pane and the toolbar for the diagram pane is activated, and 2) an empty tree structure for your new model is started in the tree structure pane at the lower left of the screen.
At this point you are ready to perform Step 1. Some users want to know the function of every tool and menu item before they begin work; others want to learn these as they do their work. If you prefer to learn by going through the tools, please go to the ProcessDB Reference Manual. If you prefer to have a specific context or example then proceed directly to Step 1. ProcessDB can do nearly everything you can do with other modeling software tools, and ProcessDB has dozens of new features designed to create a unique environment supporting collaborative formulation and testing of mechanistic models ranging from a few variables to hundreds of variables. This summary of ProcessDB features and philosophy may be of interest to scientists familiar with other modeling software.