Cross-references attached to a model metabolite, reaction or gene, for example kegg.compound: C00031 or chebi: CHEBI:17634. They connect a model-specific ID to shared databases. See Metabolite analysis.
Bounds
The lower and upper limits of a reaction's flux, \(lb \le v \le ub\). An irreversible reaction has \(lb = 0\); a blocked one has \(lb = ub = 0\). Many models use ±1000 as "unbounded". See Medium, bounds and objective.
COBRA, COBRApy
COnstraint-Based Reconstruction and Analysis, the family of methods for genome-scale models; COBRApy is its Python implementation, which runs every simulation in GEMs MAP.
Compartment
A cellular location in a model (cytosol, mitochondrion, periplasm, extracellular space…). The same chemical in two compartments is two different model metabolites (pyr_c, pyr_p). Templates use conceptual compartments (cytosol, mitochondria…) with fallbacks.
Constraint-based modelling
Describing what a metabolic network can do with constraints (mass balance, bounds) instead of kinetic equations, and analysing that space by optimisation. See Constraint-based analysis.
Currency metabolite (cofactor)
A metabolite that takes part in very many reactions, such as ATP, ADP, NAD(P)(H), H₂O, H⁺, phosphate, CoA, CO₂, O₂ or NH₄⁺. GEMs MAP hides them in maps, path-finding and the local network by default.
Entity (template entity)
In a template, the chemical a node stands for, identified by names, formula and database identifiers, independently of any model. See Identity and matching.
Exchange, demand and sink reactions
Boundary reactions with metabolites on one side only. An exchange connects an extracellular metabolite to the environment (uptake or secretion); a demand irreversibly removes a metabolite; a sink supplies or removes one artificially. GEMs MAP follows COBRApy's definitions.
FBA (flux balance analysis)
Linear programming that maximises or minimises an objective subject to \(S v = 0\) and the bounds. Returns one optimal flux vector, usually one of many.
Flux
The rate of a reaction, in mmol gDW⁻¹ h⁻¹ (millimoles per gram dry weight per hour) in genome-scale models. The sign gives the direction relative to the written equation.
FVA (flux variability analysis)
For each reaction independently, the minimum and maximum flux compatible with the constraints at (a fraction of) the optimal objective. Intervals are not a joint flux distribution.
GEM (genome-scale metabolic model)
A model of an organism's metabolism with its reactions, metabolites, genes and gene–reaction rules, usually reconstructed from the genome and literature, for example E. coli iML1515.
Gene–reaction rule (GPR)
A Boolean rule linking genes to a reaction, for example b3916 or b1723 (isozymes) or b0726 and b0727 (subunits of a complex).
Identifier mapping
Finding, for each node of a template, the model metabolite or reaction that represents the same biochemical entity. GEMs MAP does this with a scored, evidence-based matcher and a review dialog.
Loopless FBA
An optimal flux distribution without thermodynamically infeasible internal cycles (COBRApy loopless_solution, CycleFreeFlux).
Mapping profile
Your confirmed template mappings for one model (entity @ compartment → model metabolite), reused by every template on that model and never on another.
Medium
The uptake limits of a model's exchange reactions (COBRApy model.medium): which compounds the cell can take up, and how fast.
Metabolite
A chemical species in a compartment of a model, with an ID, name, formula and charge.
Model state
In GEMs MAP, a named set of bound changes and an optional objective on top of the imported model, such as Base model or Anaerobic.
Objective
The linear function an optimisation maximises or minimises, typically a biomass reaction representing growth.
pFBA (parsimonious FBA)
FBA followed by minimisation of the total absolute flux at (a fraction of) the optimum.
Reaction
A transformation of metabolites with a stoichiometry, bounds, and optionally a gene–reaction rule, subsystem and EC numbers.
Slot
An unbound node on a map: a placeholder to be bound to a model metabolite later.
Stoichiometric matrix (S)
A matrix with one row per metabolite and one column per reaction, holding the coefficients of each metabolite in each reaction (negative for substrates, positive for products).
Subsystem
A pathway label attached to reactions in many models (for example Citric Acid Cycle).
Template
A reusable pathway layout that stores biological identity and topology, not model IDs. See Templates.
Turnover (metabolite)
In GEMs MAP, \(\tfrac{1}{2}\sum_j |S_{ij} v_j|\): the total production (= consumption) rate of a metabolite in one flux solution. A derived proxy, not a concentration.