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.
CINCH1 (Covid-19 INfection Control in Hospitals), is a prototype model of physical distancing for infection control among staff in University College London Hospital during the Covid-19 pandemic, developed at the University of Leeds, School of Geography. It models the movement of collections of agents in simple spaces under conflicting motivations of reaching their destination, maintaining physical distance from each other, and walking together with a companion. The model incorporates aspects of the Capability, Opportunity and Motivation of Behaviour (COM-B) Behaviour Change Framework developed at University College London Centre for Behaviour Change, and is aimed at informing decisions about behavioural interventions in hospital and other workplace settings during this and possible future outbreaks of highly contagious diseases. CINCH1 was developed as part of the SAFER (SARS-CoV-2 Acquisition in Frontline Health Care Workers – Evaluation to Inform Response) project
(https://www.ucl.ac.uk/behaviour-change/research/safer-sars-cov-2-acquisition-frontline-health-care-workers-evaluation-inform-response), funded by the UK Medical Research Council. It is written in Python 3.8, and built upon Mesa version 0.8.7 (copyright 2020 Project Mesa Team).
A minimal genetic algorithm was preliminarily developed to search for the solution of an elementary arithmetic problem. It has been modified to explore the effect of a mutator gene and the consequent entrance into a hypermutation state. The phenomenon is particularly important in some types of tumorigenesis and in a more general way, in cells and tissues submitted to chronic sublethal environmental or genomic stress.
Since a long time, some scholars suppose that organisms speed up their own evolution by varying mutation rate, but evolutionary biologists are not convinced that evolution can select a mechanism promoting more (often harmful) mutations looking forward an environmental challenge.
The model aims to shed light on these controversial points of view and it provides also the features required to check the role of sex and genetic recombination in the mutator genes diffusion.
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.
EMMIT is an end-user developed agent-based simulation of malaria transmission. The simulation’s development is a case study demonstrating an approach for non-technical investigators to easily develop useful simulations of complex public health problems. We focused on malaria transmission, a major global public health problem, and insecticide resistance (IR), a major problem affecting malaria control. Insecticides are used to reduce transmission of malaria caused by the Plasmodium parasite that is spread by the Anopheles mosquito. However, the emergence and spread of IR in a mosquito population can diminish the insecticide’s effectiveness. IR results from mutations that produce behavioral changes or biochemical changes (such as detoxification enhancement, target site alterations) in the mosquito population that provide resistance to the insecticide. Evolutionary selection for the IR traits reduces the effectiveness of an insecticide favoring the resistant mosquito population. It has been suggested that biopesticides, and specifically those that are Late Life Acting (LLA), could address this problem. LLA insecticides exploit Plasmodium’s approximate 10-day extrinsic incubation period in the mosquito vector, a delay that limits malaria transmission to older infected mosquitoes. Since the proposed LLA insecticide delays mosquito death until after the exposed mosquito has a chance to produce several broods of offspring, reducing the selective pressure for resistance, it delays IR development and gives the insecticide longer effectivity. Such insecticides are designed to slow the evolution of IR thus maintaining their effectiveness for malaria control. For the IR problem, EMMIT shows that an LLA insecticide could work as intended, but its operational characteristics are critical, primarily the mean-time-to-death after exposure and the associated standard deviation. We also demonstrate the simulation’s extensibility to other malaria control measures, including larval source control and policies to mitigate the spread of IR. The simulation was developed using NetLogo as a case study of a simple but useful approach to public health research.
The Netlogo model is a conceptualization of the Moria refugee camp, capturing the household demographics of refugees in the camp, a theoretical friendship network based on values, and an abstraction of their daily activities. The model then simulates how Covid-19 could spread through the camp if one refugee is exposed to the virus, utilizing transmission probabilities and the stages of disease progression of Covid-19 from susceptible to exposed to asymptomatic / symptomatic to mild / severe to recovered from literature. The model also incorporates various interventions - PPE, lockdown, isolation of symptomatic refugees - to analyze how they could mitigate the spread of the virus through the camp.
This model was developed to test the usability of evolutionary computing and reinforcement learning by extending a well known agent-based model. Sugarscape (Epstein & Axtell, 1996) has been used to demonstrate migration, trade, wealth inequality, disease processes, sex, culture, and conflict. It is on conflict that this model is focused to demonstrate how machine learning methodologies could be applied.
The code is based on the Sugarscape 2 Constant Growback model, availble in the NetLogo models library. New code was added into the existing model while removing code that was not needed and modifying existing code to support the changes. Support for the original movement rule was retained while evolutionary computing, Q-Learning, and SARSA Learning were added.
MIOvCWD is a spatially-explicit, agent-based model designed to simulate the spread of chronic wasting disease (CWD) in Michigan’s white-tailed deer populations. CWD is an emerging prion disease of North American cervids (white-tailed deer Odocoileus virginianus, mule deer Odocoileus hemionus, and elk Cervus elaphus) that is being actively managed by wildlife agencies in most states and provinces in North America, including Michigan. MIOvCWD incorporates features like deer population structure, social organization and behavior that are particularly useful to simulate CWD dynamics in regional deer populations.
MOOvPOPsurveillance was developed as a tool for wildlife agencies to guide collection and analysis of disease surveillance data that relies on non-probabilistic methods like harvest-based sampling.
MOOvPOP is designed to simulate population dynamics (abundance, sex-age composition and distribution in the landscape) of white-tailed deer (Odocoileus virginianus) for a selected sampling region.