GenoScope is a modular agent-based model designed to simulate how cells respond to environmental stressors or other treatment conditions across species. Genes, treatment conditions, and cell physiology outcomes are represented as interacting agents that influence each other’s behavior over time. Rather than imposing fixed interaction rules, GenoScope initializes with randomized regulatory logic and calibrates rule sets based on empirical data. Calibration is grounded in a common-garden experiment involving 16 mammalian species—including humans, dolphins, bats, and camels—exposed to varying levels of temperature, glucose, and oxygen. This comparative approach enables the identification of mechanisms by which animal cells achieve robustness under extreme environmental conditions.

This agent-based model was built as part of a replication effort of Jeness et al.’s work (linked below). The model simulates an MSM sexual activity network for the purpose of modeling the effects of respectively PrEP and ART on HIV prevention. The purpose of the model is to explore the differences between differerent interpretations of the NIH Indication Guidelines for PrEP.

A System Dynamics Model to anticipate insurgent movements and policy design to handle them .

This model uses ’satisficing’ as a model for farmers’ decision making to learn about influences of alternative decision-making models on simulation results and to exemplify a way to transform a rather theoretical concept into a feasible decision-making model for agent-based farming models.

This is a complex “Data Integration Model”, following a “KIDS” rather than a “KISS” methodology - guided by the available evidence. It looks at the complex mix of social processes that may determine why people vote or not.

STiMUS-HAI (Stigmergic–Mutualistic IMOI Model, Human-AI extension) is an agent-based model of teamwork in socio-technical systems where human and AI contributors collaborate through shared digital artefacts — wiki pages, code files, issue tickets, project cards, Scratch projects — represented as patches in a NetLogo world. It extends the human-only base model STiMUS v2.2, which established that two coordination mechanisms — stigmergy (indirect coordination through traces left in the environment) and mutualism (mutual benefit between contributors and the artefacts they tend) — can be decoupled: stigmergy decides where a contributor works, mutualism decides with what effort. STiMUS-HAI preserves this decoupling unchanged and adds two further theoretical questions: whether mixing AI agents into a human team distorts human coordination in ways that aggregate indicators hide, and whether AI’s cost to team outcomes depends on the type of work AI performs, not only on how much of it is present.

Two breeds of turtle — humans and ai-agents — follow identical target-selection, pheromone, and mutualism rules, so that any behavioural difference is attributable to team composition rather than a built-in advantage. The one designed asymmetry: AI agents never accumulate shared-mental-model and their motivation is fixed rather than adaptive. On top of this v3.0 baseline, v3.1 adds a task-type dimension to artefacts (“prediction” versus “judgment”, set via a judgment-share slider) that scales down AI edit-power specifically on judgment-requiring artefacts, and an ai-trust mechanic: humans build or lose trust in AI contributions based on the population-relative percentile rank of observed AI work quality (bottom-quartile work counts as an observed “error”), and that trust gates how much mutualistic benefit a human derives from continuing an AI’s work. Trust erodes quickly on a single error and recovers only after a streak of confirmed successes — an intentional asymmetry.

Simulates impacts of ants killing colony mates when in conflict with another nest. The murder rate is adjustable, and the environmental change is variable. The colonies employ social learning so knowledge diffusion proceeds if interactions occur.

This agent-based model explores the existence of positive feedback loops related to illegal, unregulated, unreported (IUU) fishing; the use of forced labor; and the depletion of fish populations due to commercial fishing.

This model aims to mimic human movement on a realistic topographical surface. The agent does not have a perfect knowledge of the whole surface, but rather evaluates the best path locally, at each step, thus mimicking imperfect human behavior.

This model illustrates how to apply a simple cluster-analysis on points distributed around 5 centers. The result can be displayed in shades of a color or a spectacular colored pattern.