The model’s primary aim was not to be entirely realistic; instead, it was designed to point to new questions, test the usefulness of the tool, and lay the groundwork for new insights. As such, this model is targeted at ecologists, ornithologists, and urban planners who want to test and simulate how different birds face the challenge of a densely urbanized city that aims to enhance its natural connectivity and foster a wide range of biodiversity. We aimed to identify bird movement at the city-wide scale, encompassing representatives from the entire avian community, while examining differences in movement between totally random models and an informed model, defined by expert criteria.

This archive contains the SAFE-ABM computational model developed to evaluate targeted intervention strategies for protecting essential workers during epidemic conditions, accompanying the published article “Essential Workers at Risk: An Agent-Based Model (SAFE-ABM) with Uncertainty Quantification” in the Journal of Artificial Societies and Social Simulation, 29(4), Article 7 (2026). https://doi.org/10.18564/jasss.6276. SAFE-ABM is an agent-based model that simulates disease transmission through structured interactions across households, workplaces, and schools, while incorporating stochastic disease progression and uncertainty in transmission, recovery, and mortality parameters.

The model evaluates five intervention scenarios: Scenario 1, no restrictions; Scenario 2, school-from-home; Scenario 3, essential-workers-only movement; Scenario 4, rotational shifts among essential workers with quarantine of symptomatic active workers; and Scenario 5, rotational shifts among essential workers without quarantine. The archive includes scenario-specific simulation scripts, comparison-analysis scripts, saved derived outputs, README documentation, software requirements, and reproducibility notes.

The included comparison scripts reproduce the main numerical summaries and manuscript outputs, including median epidemic trajectories, predictive-uncertainty plots, cumulative recovery and death summaries, inflection-point summaries, Welch-test comparisons, and mutual-information sensitivity rankings. Saved derived outputs are included so that the main figures and tables can be reproduced without rerunning all large-scale simulations.

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Viking Sailing is a spatially explicit agent-based simulation for conditional exploration of how rasterized coastlines, wind, and
surface-current conditions interact with simplified ship movement, sailing, rowing, navigation, and land-avoidance rules. The
model compares simulated route trajectories and terminal outcomes for hypothetical Viking-era small-ship voyages. It includes an example dataset representing sea surface winds and currents from June 1000 CE. Additional data can are downloaded from Zenodo: https://zenodo.org/records/23213147.

This NetLogo model simulates the movement and foraging behavior of 20 bird species (classified as urban avoiders or utilizers) across a 20×20m grid landscape representing southern Bogotá, Colombia. Agents follow an optimal foraging strategy (90% of the time) or move randomly (10%), gaining energy from land-cover-dependent food sources and dying if energy falls below their basal metabolic rate. The model compares two landscape scenarios — current land cover (2016) and a proposed scenario incorporating the ‘Media Luna del Sur’ ecological corridor from Bogotá’s 2022–2035 Land Use Plan (POT) — to evaluate whether the proposed green infrastructure improves functional connectivity for avian biodiversity across the urban matrix. Outputs include cumulative patch visitation counts, exported as raster files, used to generate connectivity heatmaps.

This NetLogo model simulates the impact of mowing frequency, mower type and the percentage of refuge strips on the abundance of arthropods in managed grasslands. It represents five functional arthropod groups: holometabolous plant-dwelling arthropods (HoP, represented by butterflies); holometabolous ground-dwelling arthropods (HoG, represented by ants); nesting pollinators (NP, represented by bees); hemimetabolous plant-dwelling arthropods (HeP, represented by grasshoppers); and ground-resident arthropods (GR, represented by spiders). Three mowing frequencies are simulated: intensive (four mowings per year), intermediate (two mowings per year) and extensive (one mowing per year). Bar and disc mowers differ in their effects on arthropod mortality and vegetation height. Refuge strip coverage can be set to 0%, 10% or 20%. Arthropod abundance changes over time through movement, reproduction, natural mortality, mower-related mortality and vegetation regrowth.

Considering that two of the three avoider species could not reach the target area in the inittial scenario, five alternative corridor scenarios were created. In all cases, we generated a greater amount of cover area under ‘Urban forest’, including elements such as scattered trees, woody plants, wooded areas, and rows of trees. This covered type was selected since all three species use it as a regular habitat. That is the second sceneario where those ecological parks and other areas inside the capital city were boostered into “urban forest patches” or buffer points, with the idea of improving the survive of the three bird species and their movement. However one of the most restrictive specie was still having movement and survival issues.

The purpose of this model is to analyze different configurations and scenarios of ecological corridors to simulate the movement of three avoider bird species at a local scale: Chondrohierax uncinatus (Accipitridae), a large carnivorous bird; Ampelion rubrocristatus (Cotingidae), a species that seeks areas with substantial land cover for refuge and rest; and Coeligena bonapartei (Trochilidae), a large hummingbird that prefers areas with a rich and diverse food supply. The model focusses on juvenile bird individuals seeking refuge and food, taking into account the mobility parameters of each species and the existing land cover types within the study area.
Specifically, the model aims to:
• Simulate the movement of 45 avoiders birds which are considered umbrella species sensitive to urban changes (which were chosen based on their specific biological and ecological requirements and parameters relevant to urban conservation efforts), 15 avoiders birds per specie to cross a two-dimensional world predominant urban.
• To be able to select which corridor scenario would be the most beneficial, in order to help the mobility of other species affected by urban fragmentation.
• Contribute to urban ecology research and support decision-making processes by relevant stakeholders.

This model simulates a simple aquatic ecosystem containing fish and food. It explores how individual interactions such as movement, feeding, and reproduction shape the population dynamics of fish over time.

This model visualizes gradient descent optimization - the fundamental algorithm used to train neural networks and other machine learning models. Agents represent different optimization algorithms searching for the minimum of a loss landscape (the “error surface” that ML models try to minimize during training).

The model demonstrates how different optimizer types (SGD, Momentum with different parameters) behave on various loss landscapes, from simple bowls to the notoriously difficult Rosenbrock “banana valley” function. This helps build intuition about why certain optimization algorithms work better than others for different problem geometries.

HOW IT WORKS

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This computational model is an agent-based model (ABM) developed to investigate how repeated failures of emerging niches accumulate and influence the trajectory of socio-technical transitions. Built in AnyLogic 8.7.11, the model simulates the dynamic interactions between a dominant regime and sequential niche entrants within a two-dimensional practice space. It models alignment, movement, and competition based on technological maturity and market penetration. The model utilizes a reinforcing feedback structure linking consumer support, output, resource accumulation, and capacity development (Physical and Institutional Capacity). A complete model specification following the ODD+D (Overview, Design concepts, Details, and Decision) protocol is included in the documentation.