Step 1

STEP 1: Formulating Your Hypothesis As A ProcessDB Diagram

Biological diagrams represent molecules and molecular complexes in a variety of physiological places or locations. These diagrams also indicate the processes that transport molecules from one location to another, the biochemical processes that transform molecules, and the binding processes that form homo- or heteromultimers from individual molecules. All of these features are easily captured in ProcessDB diagrams.

Add the physiological places to your diagram. Click the Places tab in the database pane. Click the new place icon and enter the name of the place you want to add to your model. Places are the physiological locations of your molecules and molecular complexes. Examples are cytoplasm, plasma membrane, ER lumen, extracellular space, blood plasma. A place is the answer to the question, “Where is this molecule located in the system I am studying”? You can add all your places immediately or add them as you need them. Notice that molecules and complexes may be present in more than one place.

If the place name you chose is already in the ProcessDB database you can use it to build your own diagram; if it is not already in the database, your name will be added to the place list. In either case your place will be highlighted in the place list and you can now drag it onto the diagram pane. For example, if you type Cytoplasm and then drag the name from the database pane to the diagram pane you will see a yellow rectangle named Cytoplasm added to your diagram.

Hint: It is sometimes useful to define places that you might not ordinarily think of as places. For example, if you want to model a molecular complex whose composition changes with time, it can be very helpful to define that complex as a "place". This allows you to add the various molecular constituents to that complex and have the relative abundances of these constituents change with time. A good example of this is a plasma lipoprotein, like the famous HDL or LDL. These are the vehicles carrying lipids in the blood. They are composed of a phospholipid-cholesterol surface monolayer and a neutral lipid (triglyceride and cholesteryl ester) core. By treating LDL as a ProcessDB place it's easy to account for changes in lipoprotein composition with time.