Computational Model Library

Leptospirosis is a neglected, bacterial zoonosis with worldwide distribution, primarily a disease of poverty. More than 200 pathogenic serovars of Leptospira bacteria exist, and a variety of species may act as reservoirs for these serovars. Human infection is the result of direct or indirect contact with Leptospira bacteria in the urine of infected animal hosts, primarily livestock, dogs, and rodents. There is increasing evidence that dogs and dog-adapted serovar Canicola play an important role in the burden of leptospirosis in humans in marginalized urban communities. What is needed is a more thorough understanding of the transmission dynamics of Leptospira in these marginalized urban communities, specifically the relative importance of dogs and rodents in the transmission of Leptospira to humans. This understanding will be vital for identifying meaningful intervention strategies.
One of the main objectives of MHMSLeptoDy is to elucidate transmission dynamics of host-adapted Leptospira strains in multi-host system. The model can also be used to evaluate alternate interventions aimed at reducing human infection risk in small-scale communities like urban slums.

Myside Bias and Group DIscussion

Edoardo Baccini | Published Mon Nov 14 14:45:47 2022

To investigate the effects of myside bias in group discussions, we created an agent-based model in NetLogo. This model simulates a group discussion in which the agents debate a binary issue. The debated issue has a correct/true alternative and an incorrect/false alternative. Our goal is to evaluate the impact of mybias by determining what effect it has on the ability to track the truth in discussions between agents with a myside bias compared to agents without this bias.

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.

A road freight transport (RFT) operation involves the participation of several types of companies in its execution. The TRANSOPE model simulates the subcontracting process between 3 types of companies: Freight Forwarders (FF), Transport Companies (TC) and self-employed carriers (CA). These companies (agents) form transport outsourcing chains (TOCs) by making decisions based on supplier selection criteria and transaction acceptance criteria. Through their participation in TOCs, companies are able to learn and exchange information, so that knowledge becomes another important factor in new collaborations. The model can replicate multiple subcontracting situations at a local and regional geographic level.
The succession of n operations over d days provides two types of results: 1) Social Complex Networks, and 2) Spatial knowledge accumulation environments. The combination of these results is used to identify the emergence of new logistics clusters. The types of actors involved as well as the variables and parameters used have their justification in a survey of transport experts and in the existing literature on the subject.
As a result of a preferential selection process, the distribution of activity among agents shows to be highly uneven. The cumulative network resulting from the self-organisation of the system suggests a structure similar to scale-free networks (Albert & Barabási, 2001). In this sense, new agents join the network according to the needs of the market. Similarly, the network of preferential relationships persists over time. Here, knowledge transfer plays a key role in the assignment of central connector roles, whose participation in the outsourcing network is even more decisive in situations of scarcity of transport contracts.

This study simulates the evolution of artificial economies in order to understand the tax relevance of administrative boundaries in the quality of life of its citizens. The modeling involves the construction of a computational algorithm, which includes citizens, bounded into families; firms and governments; all of them interacting in markets for goods, labor and real estate. The real estate market allows families to move to dwellings with higher quality or lower price when the families capitalize property values. The goods market allows consumers to search on a flexible number of firms choosing by price and proximity. The labor market entails a matching process between firms (given its location) and candidates, according to their qualification. The government may be configured into one, four or seven distinct sub-national governments, which are all economically conurbated. The role of government is to collect taxes on the value added of firms in its territory and invest the taxes into higher levels of quality of life for residents. The results suggest that the configuration of administrative boundaries is relevant to the levels of quality of life arising from the reversal of taxes. The model with seven regions is more dynamic, but more unequal and heterogeneous across regions. The simulation with only one region is more homogeneously poor. The study seeks to contribute to a theoretical and methodological framework as well as to describe, operationalize and test computer models of public finance analysis, with explicitly spatial and dynamic emphasis. Several alternatives of expansion of the model for future research are described. Moreover, this study adds to the existing literature in the realm of simple microeconomic computational models, specifying structural relationships between local governments and firms, consumers and dwellings mediated by distance.

The western honey bee Apis mellifera is the most important pollinator in the world. The biggest threat to managed honey bees is the ectoparasitic mite Varroa destructor and the viruses DWV (Deformed Wing Virus) and APV (Acute Paralysis Virus) it transmits. Untreated honey bee colonies are expected to die within one to three years. This led to the development of strategies for beekeepers to control the Varroa mite in honey bee colonies and ensure the health and survival of their bee colonies, so called Good Beekeeping Practice. The aim of the extension of BEEHAVE was to represent the Good Beekeeping Practice of Varroa control in Germany. The relevant measures within the Varroa control strategies are drone brood removal as a Varroa trap and the treatment of bee colonies with organic acaricides (formic and oxalic acid) to kill the mites. This extension improves BEEHAVE and builds a bridge between beekeepers in practice and in the modelling world. It vastly contributes to the future use of BEEHAVE in beekeeping education in Germany.

Peer reviewed AgentEx-Meta

Nanda Wijermans Helen Fischer | Published Fri Oct 28 21:26:35 2022

The purpose of the study is to unpack and explore a potentially beneficial role of sharing metacognitive information within a group when making repeated decisions about common pool resource (CPR) use.

We explore the explanatory power of sharing metacognition by varying (a) the individual errors in judgement (myside-bias); (b) the ways of reaching a collective judgement (metacognition-dependent), (c) individual knowledge updating (metacognition- dependent) and d) the decision making context.

The model (AgentEx-Meta) represents an extension to an existing and validated model reflecting behavioural CPR laboratory experiments (Schill, Lindahl & Crépin, 2015; Lindahl, Crépin & Schill, 2016). AgentEx-Meta allows us to systematically vary the extent to which metacognitive information is available to agents, and to explore the boundary conditions of group benefits of metacognitive information.

BEGET Classic

Kristin Crouse | Published Mon Nov 11 07:30:59 2019 | Last modified Mon Nov 25 07:25:33 2019

BEGET Classic includes previous versions used in the classroom and for publication. Please check out the latest version of B3GET here, which has several user-friendly features such as directly importing and exporting genotype and population files.

The classic versions of B3GET include: version one and version three were used in undergraduate labs at the University of Minnesota to demonstrate principles in primate behavioral ecology; version two first demonstrated proof of concept for creating virtual biological organisms using decision-vector algorithms; version four was presented at the 2017 annual meeting at the American Association of Physical Anthropologists; version five was presented in a 2019 publication from the Journal of Human Evolution (Crouse, Miller, and Wilson, 2019).

This model is intended to support oak tree management by representing the dynamics of oaks in multiple life stages and their competitors and consumers. This is implemented using a differential equation-based theoretical model representing three life stages of oaks: seedlings, juveniles, and adults. It includes the population dynamics of seedlings transitioning to juveniles, juveniles to adults, and adults producing new seedlings, as well as survival rates for each of the stages. It also includes a model of competition for light and water within seedlings and between seedlings and annual grasses. Finally, there is a predation term representing herbivores eating seedlings and grasses, using a Holling Type II (satiating) response with interference for predators and a death rate which depends on the resource extraction rate.

This is the agent-based model of information market evolution. It simulates the influences of the transition from material to electronic carriers of information, which is modelled by the falling price of variable production factor. It demonstrates that due to zero marginal production costs, the competition increases, the market becomes unstable, and experience various phases of evolution leading to market monopolization.

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