Computational Model Library

Peer reviewed HyperMu’NmGA - Effect of Hypermutation Cycles in a NetLogo Minimal Genetic Algorithm

Cosimo Leuci | Published Tue Oct 27 21:15:40 2020 | Last modified Sun Jul 31 09:08:14 2022

A minimal genetic algorithm was previously developed in order to solve 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 seems relevant in some types of tumorigenesis and in a more general way, in cells and tissues submitted to chronic sublethal environmental or genomic stress.
For 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 to 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 Levers of HIV Model

Can Gurkan Wouter Vermeer Arthur Hjorth Uri Wilensky C. Hendricks Brown | Published Tue Mar 8 16:19:04 2022 | Last modified Mon Sep 19 15:20:59 2022

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.

Peer reviewed INOvPOP

Aniruddha Belsare | Published Wed Jun 1 13:18:26 2022

INOvPOP is designed to simulate population dynamics (abundance, sex-age composition and distribution in the landscape) of white-tailed deer (Odocoileus virginianus) for selected Indiana counties.

Peer reviewed MOOvPOPsurveillance

Aniruddha Belsare Matthew Gompper Joshua J Millspaugh | Published Tue Apr 4 17:03:40 2017 | Last modified Tue May 12 16:37:24 2020

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.

Peer reviewed Evolution of Sex

Kristin Crouse | Published Sun Jun 5 08:24:01 2016 | Last modified Mon Feb 15 15:40:39 2021

Evolution of Sex is a NetLogo model that illustrates the advantages and disadvantages of sexual and asexual reproductive strategies. It seeks to demonstrate the answer to the question “Why do we have sex?”

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.

Peer reviewed MOOvPOP

Aniruddha Belsare Matthew Gompper Joshua J Millspaugh | Published Mon Apr 10 20:03:42 2017 | Last modified Tue May 12 06:14:14 2020

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.

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.

This model extends the original Artifical Anasazi (AA) model to include individual agents, who vary in age and sex, and are aggregated into households. This allows more realistic simulations of population dynamics within the Long House Valley of Arizona from AD 800 to 1350 than are possible in the original model. The parts of this model that are directly derived from the AA model are based on Janssen’s 1999 Netlogo implementation of the model; the code for all extensions and adaptations in the model described here (the Artificial Long House Valley (ALHV) model) have been written by the authors. The AA model included only ideal and homogeneous “individuals” who do not participate in the population processes (e.g., birth and death)–these processes were assumed to act on entire households only. The ALHV model incorporates actual individual agents and all demographic processes affect these individuals. Individuals are aggregated into households that participate in annual agricultural and demographic cycles. Thus, the ALHV model is a combination of individual processes (birth and death) and household-level processes (e.g., finding suitable agriculture plots).

As is the case for the AA model, the ALHV model makes use of detailed archaeological and paleoenvironmental data from the Long House Valley and the adjacent areas in Arizona. It also uses the same methods as the original model (from Janssen’s Netlogo implementation) to estimate annual maize productivity of various agricultural zones within the valley. These estimates are used to determine suitable locations for households and farms during each year of the simulation.

NetLogo HIV spread model

Wouter Vermeer | Published Fri Oct 25 16:51:17 2019

This model describes the tranmission of HIV by means of unprotected anal intercourse in a population of men-who-have-sex-with-men.
The model is parameterized based on field data from a cohort study conducted in Atlanta Georgia.

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