Systems Biology Cheat Sheet

The core ideas of Systems Biology distilled into a single, scannable reference — perfect for review or quick lookup.

PiqCue — piqcue.com/systems-biology/cheatsheet

Quick Reference

Emergent Properties

Properties of a biological system that arise from the interactions among its components but cannot be predicted from studying any single component alone. These system-level behaviors are a hallmark of complex biological organization.

Network Motifs

Recurring patterns of interconnections found in biological networks at frequencies significantly higher than in random networks. These motifs serve as basic building blocks of complex regulatory circuits.

Feedback Loops

Regulatory circuits in which the output of a process influences its own input. Negative feedback stabilizes systems by counteracting changes, while positive feedback amplifies signals and can create bistable switches.

Genome-Scale Metabolic Models

Comprehensive computational models that represent all known metabolic reactions in an organism, enabling predictions about metabolic fluxes, growth rates, and responses to genetic or environmental perturbations.

Multi-Omics Integration

The combined analysis of data from multiple high-throughput platforms (genomics, transcriptomics, proteomics, metabolomics, epigenomics) to build a comprehensive picture of biological system behavior.

Robustness

The ability of a biological system to maintain its function despite internal and external perturbations. Robustness is an inherent design principle of biological networks, achieved through redundancy, modularity, and feedback control.

Flux Balance Analysis (FBA)

A mathematical method that uses linear programming to analyze the flow of metabolites through a genome-scale metabolic network at steady state, predicting optimal metabolic behavior under given constraints.

Stochastic Gene Expression

The inherent randomness in gene expression arising from the probabilistic nature of biochemical reactions, especially when key molecules are present in low copy numbers. This noise can drive cell-to-cell variability even in genetically identical populations.

Boolean Network Models

Simplified computational models of gene regulatory networks in which each gene is represented as either ON (1) or OFF (0), and its state is updated based on logical rules applied to its regulators.

Synthetic Biology

An engineering discipline that applies systems biology principles to design and construct new biological parts, devices, and systems, or to redesign existing natural systems for useful purposes.

Key Terms at a Glance

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

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

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

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

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

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

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

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

High-Throughput Technology:Experimental methods that generate large volumes of data simultaneously, such as DNA sequencing, microarrays, and mass spectrometry.

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

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

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

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

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

Ordinary Differential Equation (ODE):A mathematical equation describing how a quantity changes over time as a function of its current state and parameters.

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