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 four tabs (Models, Processes, Places, and Molecules and Complexes) 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 four tabs is information stored in the ProcessDB database on the Integrative Bioinformatics server. This server is on a T1 line at a large internet service provider that has established and maintained a 99.999% up-time record for over 5 years. Other users do not have access to your models and processes unless you have made these models public.
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.