Glossary¶

Action Items — a panel along the bottom of the window with one row for every rate law, initial condition, and boundary formula the current Model Realization needs. Blank rows are highlighted and sorted first, and the panel opens itself when there are any.

Adjustable (Adj) — a parameter marked for estimation by the optimizer.

Bolus — a protocol adding a discrete amount of a species at a given time.

Boundary state — a state whose value is imposed by a formula rather than computed from a differential equation. Marked On boundary in the state's Properties inside a Model Realization.

Browser — the panel of tabs onto everything in the database: Models, Molecules and Complexes, Processes, Places, and Experiments.

Commit — writing your local changes to the ProcessDB database. File → Commit, or the toolbar Save button.

Complex — a molecule assembled from other molecules with a count of each part.

Cursor graph — a graph-window mode showing a selected state or process together with its network context: influxes, outfluxes, precursors, and postcursors for a state; reactants, modifiers, and products for a process.

Data set — one time course belonging to a measurement: a replicate, an animal, a condition. Carries a weight.

Display Names — a toggle that swaps S…/P… symbols for state and process names in equations and tables.

Experiment — the record of one bench experiment: its protocols, its tagged molecules, and its measurements. Independent of any model.

Forcing function — a protocol replacing a species' differential equation with a formula over an interval.

Infusion — a protocol adding material at a steady rate over an interval.

Journal — the local record of uncommitted work that lets ProcessDB offer recovery after a crash.

Kinetic mechanism — how an activator or inhibitor enters a modular rate law: non-competitive, partial, or competitive for an inhibitor; essential, non-essential, or specific for an activator. Chosen when the rate law is built, and part of that law rather than of the diagram.

Layout — one of three ready-made panel arrangements under View → Layout: Build, Simulate, and Write.

Measurement — one observable quantity in an experiment, associated with a model variable so simulation and data can be compared.

Model — a mechanism drawn as a diagram: states, processes, and the roles that connect them. Structural only; no rate constants, no concentrations.

Model bundle — the folder and zip written by File → Export Model Bundle…: the diagram, the open graphs, the equations, the parameters, and the data, with an HTML report, for a paper or report.

Model of Experiment (MOE) — one Model Realization simulated under a chosen set of experiments. Owns the generated equations, parameter sets, MOE functions, traced states and processes, and the simulation time span.

Model Realization (MR) — a quantitative version of a model: a rate law per process, an initial condition per state, boundary formulas, and MR functions. One model can have many.

Modifier — a state that affects a process's rate without being consumed: enzyme, catalyst, transporter, channel, mediator, activator, inhibitor, regulator.

Modular rate law — one of a family of thermodynamically consistent reversible rate laws (Liebermeister, Uhlendorf & Klipp 2010), distinguished by their saturation denominator: CM, DM, SM, PM, FM.

MOE function — a named algebraic definition belonging to one MOE and one experiment.

MR function — a named algebraic definition belonging to a Model Realization, written into every MOE built on it.

Notes panel — the panel that collects the model's note and every state and process note into one running document, edited in place.

Objective function value (OFV) — the weighted sum of squared differences between simulation and data that the optimizer minimises.

Outline — the panel listing the Processes, States, and Subdiagrams of whatever the current tab is showing; clicking one centres the diagram on it.

Panel — any part of the main window other than the Workspace: the Browser, the Outline, Action Items, Notes, and Search Results. A panel is hidden, docked on an edge, or popped out into its own window.

Panel bar — the row of buttons along the bottom of the window, one per panel, grouped by the edge each panel opens on.

Parameter Explorer — the window that compiles a MOE's equations, runs the solver, plots the results, and hosts the optimizer.

Parameter set — a named collection of parameter values for a MOE. Set 0 is the MOE-wide set; further sets hold alternatives. A set stores only the values you changed and inherits the rest.

Place — a compartment. Shared across models.

Potency — a sensitivity ranking: how much each parameter, multiplied by ten, moves the plotted curves. Produced by Find Potent Parameters.

Process — a step that changes states: a reaction, transport, synthesis, degradation. Has reactants, products, and modifiers.

Protocol — a recorded perturbation in an experiment, applied to a state or to a process.

Rate law — the formula for one process's flux in a Model Realization. A process may have several; exactly one is active.

Reference set — a second parameter set loaded alongside the working one, whose values appear in a Ref Value column and whose curves can be plotted for comparison.

Residual — the difference between a simulated value and a measured one at one point.

Role — what a state does in a process: Reactant, Product, Enzyme, Catalyst, Transporter, Channel, Mediator, Activator, Inhibitor, Regulator, Modifier. How an activator or inhibitor acts is its kinetic mechanism, which belongs to the rate law.

Search Results — the panel beneath the search box that lists what the box matches, across models, molecules and complexes, processes, places, and experiments.

State — a molecule in a place. The variable that gets a differential equation.

State mask — a per-subdiagram list of states hidden when the State Mask toggle is on. Purely visual.

Stoichiometry — how many molecules of a reactant a process consumes, or of a product it makes. Editable in the Properties dialogs of the process, the state, and the arrow between them.

Subdiagram — a named subset of a model's processes, used for viewing part of a large network. Has no effect on the mathematics.

Tagged molecule — a labelled version of a molecule, used in tracer experiments. Also called a tracer molecule.

Traced state / traced process — the parts of the network a given label can reach, and does reach given your routing choices, in a MOE's Tracers tab.

Workspace — the tabs in the middle of the main window, one per open model, realization, MOE, or experiment. The one part of the window that is never hidden, moved, or split.