CoMSES Net maintains cyberinfrastructure to foster FAIR data principles for access to and (re)use of computational models. Model authors can publish their model code in the Computational Model Library with documentation, metadata, and data dependencies and support these FAIR data principles as well as best practices for software citation. Model authors can also request that their model code be peer reviewed to receive a DOI. All users of models published in the library must cite model authors when they use and benefit from their code.
CoMSES Net also maintains a curated database of over 7500 publications of agent-based and individual based models with additional metadata on availability of code and bibliometric information on the landscape of ABM/IBM publications that we welcome you to explore.
The Holmestrand model is an epidemiological agent-based model. Its aim is to test hypotheses related to how the social and physical environment of a residential school for children with disabilities might influence the spread of an infectious disease epidemic among students and staff. Annual reports for the Holmestrand School for the Deaf (Norway) are the primary sources of inspiration for the modeled school, with additional insights drawn from other archival records for schools for children with disabilities in early 20th century Norway and data sources for the 1918 influenza pandemic. The model environment consists of a simplified boarding school that includes residential spaces for students and staff, classrooms, a dining room, common room, and an outdoor area. Students and staff engage in activities reflecting hourly schedules suggested by school reports. By default, a random staff member is selected as the first case and is infected with disease. Subsequent transmission is determined by agent movement and interactions between susceptible and infectious pairs.
Chicago’s demographic, neighborhood, sex risk behaviors, sexual network data, and HIV prevention and treatment cascade information from 2015 were integrated as input to a new agent-based model (ABM) called the Levers-of-HIV-Model (LHM). This LHM, written in NetLogo, forms patterns of sexual relations among Men who have Sex with Men (MSM) based on static traits (race/ethnicity, and age) and dynamic states (sexual relations and practices) that are found in Chicago. LHM’s five modules simulate and count new infections at the two marker years of 2023 and 2030 for a wide range of distinct scenarios or levers, in which the levels of PrEP and ART linkage to care, retention, and adherence or viral load are increased over time from the 2015 baseline levels.
This paper tries to shed some light on the mutual influence of citizen behaviour and the spread of a virus in an epidemic. While the spread of a virus from infectious to susceptible persons and the outbreak of an infection leading to more or less severe illness and, finally, to recovery and immunity or death has been modelled with different kinds of models in the past, the influence of certain behaviours to keep the epidemic low and to follow recommendations of others to apply these behaviours has rarely been modelled. The model introduced here uses a theory of the effect of norm invocations among persons to find out the effect of spreading norms interacts with the progress of an epidemic. Results show that norm invocations matter. The model replicates the histories of the COVID-19 epidemic in various region, including “second waves”, and shows that the calculation of the reproduction numbers from current reported infections usually overestimates the “real” but in practice unobservable reproduction number.
NetLogo model that allows scenarios concerning general social distancing, shielding of high-risk individuals, and informing contacts when symptomatic. Documentation includes a user manual with some simple scenarios, and technical information including descriptions of key procedures and parameter values.
The Episim framework builds upon the established transportation simulation MATSim and is capable of tracking agents’ movements within a network and thus computing infection chains. Several characteristics of the virus and the environment can be parametred, whilst the infection dynamics is computed based upon a compartment model. The spread of the virus can be mitigated by restricting the agents’ activity in certain places.
This repository includes an epidemic agent-based model that simulates the spread of Covid-19 epidemic. Normal.nlogo is the main file, while Exploring-zoning.nlogo and Exploring-Testing-With-Tracking.nlogo are modefied models to test the two strategies and run experiments.
In the face of the COVID-19 pandemic, public health authorities around the world have experimented, in a short period of time, with various combinations of interventions at different scales. However, as the pandemic continues to progress, there is a growing need for tools and methodologies to quickly analyze the impact of these interventions and answer concrete questions regarding their effectiveness, range and temporality.
COMOKIT, the COVID-19 modeling kit, is such a tool. It is a computer model that allows intervention strategies to be explored in silico before their possible implementation phase. It can take into account important dimensions of policy actions, such as the heterogeneity of individual responses or the spatial aspect of containment strategies.
In COMOKIT, built using the agent-based modeling and simulation platform GAMA, the profiles, activities and interactions of people, person-to-person and environmental transmissions, individual clinical statuses, public health policies and interventions are explicitly represented and they all serve as a basis for describing the dynamics of the epidemic in a detailed and realistic representation of space.
Model of the Corona pandemic outbreak
The COVID-19 ABM aims to predict the qualitative behaviour of the CoViD-19 epidemic dynamics for the greater region of Salzburg City. Specifically, by means of scenario testing, it aims to help assessing how containment interventions can allow a stepwise relaxation of the lockdown without risking a new outbreak.
The Mission San Diego model is an epidemiological model designed to test hypotheses related to the spread of the 1805-1806 measles epidemic among indigenous residents of Mission San Diego during the early mission period in Alta California. The model community is based on the population of the Mission San Diego community, as listed in the parish documents (baptismal, marriage, and death records). Model agents are placed on a map-like grid that consists of houses, the mission church, a women’s dormitory (monjeria) adjacent to the church, a communal kitchen, priest’s quarters, and agricultural fields. They engage in daily activities that reflect known ethnographic patterns of behavior at the mission. A pathogen is introduced into the community and then it spreads throughout the population as a consequence of individual agent movements and interactions.