Glossary of ProcessDB terminology

Complex - A heteromultimer defined as two or more molecules bound together non-covalently. The ProcessDB icon for a complex is three spheres combined.

Database pane

Experiment - An experiment is a time line of perturbations or investigator-initiated changes carried out in a laboratory or clinic using isolated biological molecules, living cells, tissues, organs or organisms. ProcessDB applies these perturbations to a model so that the modeler can compare model solutions directly with experimental data. The ProcessDB icon for an experiment is a small blue notebook with the word "Lab" on the front.

Molecule - A biological or pharmaceutical assembly of covalently bonded atoms identified by a name. You are free to use all the molecules named by other ProcessDB users or you may create your own named molecules. The ProcessDB icon for a molecule is three spherical atoms connected by straight lines. It looks like a ball-and-stick model of a water molecule. If everyone in your workgroup uses the same molecule names, you will be able to compare and combine different models with a single click.

Model - A model or model diagram defines the structure of your biological working hypothesis or theory. It consists of three kinds of processes: 1) biochemical reactions, 2) binding, and 3) transport. The ProcessDB icon for a model is a white cube of connected states.

Model Realization (MR) - A model realization is a quantitative model. The MR has differential equations and process rate laws in addition to the diagram or structure of its underlying model. The ProcessDB icon for a model realization is a blue cube of connected states.

Model Of Experiments (MOE) - A model of experiments is an MR combined with one or more experiments. The ProcessDB icon for a model of experiments is a green cube of connected states.

Model Tree Structure Pane

MR Pane

Parameter Set

Place - A place is a defined physiological location where one or more molecules or complexes can reside. See State. The ProcessDB icon for a place looks like a dented pillow or and orange red blood cell.

Process - A process is a chemical reaction, a binding reaction, or a transport reaction. A model can be seen as a collection of processes. The ProcessDB icon for a process is an "S-shaped" curve with a black triangular arrowhead.

State - A state is a molecule or complex in a physiological place. The ProcessDB icon for a state is a red spherical molecule superimposed on the dented pillow place icon.

Traced Process

Traced State

Tracer Molecule