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.

Context menu - A menu, accessed by right-clicking, that lists what ProcessDB can do in the context of the right-clicked item.

Database pane - A portion of the ProcessDB user interface displayed in the upper left corner of the main ProcessDB screen. It includes 5 tabs that provide search or browse access to the ProcessDB database of 1)Models, 2)Molecules and Complexes, 3)Places, 4) Processes, and 5)Experiments. Molecules and Complexes and Places are public lists. Models, Processes, and Experiments are private and can only be seen by the user who created them, unless that user explicitly shares them with one or more other users. A model can be made public by its owner.

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. A model is a collection of processes. These processes are of three principal kinds: 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 - A portion of the ProcessDB user interface displayed in the lower left of the main ProcessDB screen. This pane displays an expandable, collapsible, searchable, and right-clickable hierarchy of the processes and states in the currently displayed model.

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 an 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.

Simulator - A simulator mimics the behavior of a real system. In ProcessDB we use this term to refer to the application component that mimics the biology as well as the independent variables from the experiment. This includes the solver, which solves the system of ODEs modeling the biology, and the discrete events mimicking independent variables of an experiment. The simulator also sends data to the main application for plotting or optimization and receives commands from the application to start, stop, set the end time, set the tolerances, etc.. See Simulator

Solver - In general terms a "solver" computes or finds the solution to a mathematical problem. In ProcessDB we use this term to refer to solvers of ODE systems using numerical methods. Contrast this with "simulator" above.

State - A state is a molecule or complex in a physiological place. The word state was chosen as an abbreviation of "state variable." Unless otherwise specified by the user, the numerical value of a state will be defined by a differential equation. Thus, a state will typically vary as a function of time. The ProcessDB icon for a state is a red spherical molecule superimposed on the dented pillow place icon.

Traced Process

Traced State

Tracer State - ProcessDB was designed to support the entire field of tracer kinetics.

Tracer Molecule