Systems Biology Glossary

A dynamical property of a system that has two stable steady states, allowing switch-like behavior between distinct cellular states.

A mathematical model of a regulatory network where each node has a binary state (ON/OFF) updated by logical rules.

A modeling framework that uses physicochemical constraints (stoichiometry, thermodynamics, capacity) to predict feasible metabolic behaviors without requiring kinetic parameters.

A system-level characteristic that arises from component interactions and is not present in any individual component.

A regulatory circuit in which the output of a process influences its own input, either amplifying (positive) or dampening (negative) the signal.

A linear programming method for predicting steady-state metabolic flux distributions through a genome-scale metabolic network at steady state.

A network of interactions among genes and gene products (transcription factors, RNA, proteins) that governs gene expression levels.

The study of the complete set of DNA (genome) of an organism, including gene sequences, organization, and variation.

Experimental methods that generate large volumes of data simultaneously, such as DNA sequencing, microarrays, and mass spectrometry.

The maintenance of a stable internal environment in a biological system through regulatory mechanisms, typically involving negative feedback.

The full set of molecular interactions within a cell, encompassing protein-protein, protein-DNA, and metabolic interactions.

The comprehensive study of small-molecule metabolites in a biological sample, providing a snapshot of metabolic activity.

The degree to which a biological network is organized into relatively independent functional units (modules).

A recurring pattern of connections in a biological network that appears significantly more often than expected by chance.

A mathematical equation describing how a quantity changes over time as a function of its current state and parameters.

The process of fitting model parameters to experimental data so that model predictions match observed behavior.

A deliberate or natural change to a system component (gene knockout, drug treatment, environmental shift) used to study system response.

The large-scale study of proteins, including their expression levels, modifications, interactions, and functions.

The ability of a system to maintain its function despite perturbations to its components or environment.

The process by which a cell converts an external signal into an intracellular response through a cascade of molecular events.

A condition where the concentrations of all species in a system remain constant over time because production and consumption rates are balanced.

Inherent randomness in biological processes, especially significant when molecules are present in low copy numbers.

A matrix encoding the stoichiometric coefficients of all metabolites in all reactions of a metabolic network.

The design and construction of new biological systems or the re-engineering of existing ones using engineering principles.

The study of the complete set of RNA transcripts produced by the genome under specific conditions.