Models
Simulation models are a central tool of research at our chair. We apply individual- and agent-based models (IBM / ABM), cellular automaton as well as systems of differential equations. Methods of applied and spatial statistics (statistical models) complete our toolbox. In the following, a brief description of some simulation models is given.
PINUS-Syria (IBM) | PeatFire | PlasSim | IPS-SPREADS | DEB-IBM Krill Model | Bettina | PlasmidActionIBM | ASPIK | mesoFON
NetLogo interface of the Pinus Brutia IBM
The model simulates the growth and mortality of Pinus brutia influenced by distance-independent competition under different site conditions. It can be used to optimize rotation age and thinning regime.
Model world showing the simulated fire spread
PeatFire is a simple individual-based model which simulates fire occurrences in a virtual tropical peatland ecosystem. It involves not only fire on the surface (above-ground) but also below-ground fire. The model tries to simulate how fire could spread from the peat surface to underneath and produce dynamic pattern of burnt patches.
Kirana Widyastuti
https://peatfire-abm.github.io/
The type of compensatory evolution determines the capabilities for the transmission of a compensatory mutation (A), which has consequences on plasmid fitness (B).
PlasSim - Plasmid population dynamics Simulator
The model consists of three ordinary differential equations describing the dynamics of plasmid-free bacteria, F, nonadapted plasmid bearers, P, and adapted plasmid bearers, A, respectively.
An interactive web app can be used to run simulations with self-defined parameters and download the results: https://martin20.shinyapps.io/plassim/
Further information: see publication in 'mSystems'.
Model world of IPS-SPREAD showing a forest infestion
Integrates GIS data on tree allocation into IPS (Infestation Pattern Simulation, Kautz et al. 2014) to perform predisposition and risk assessment of bark beetle infestations - still in development
Simulates the Performance of Krill vs. Salps to withstand a warming Southern Ocean
Further information: see publication in 'Nature Ecology & Evolution'
Model structure of 'Bettina'
Mechanistic model for tree growth and plasticity based on hydraulic architecture
Further information: see publication in Ecological Modelling
GUI snapshot listing all customizable model definitions along with a short explanation and magnification of a model world view showing how plasmids reside as linear elements on bacteria (in lightgrey); Plasmid-free cells are darkgrey; Empty space is white
Simulates the intra- and intercellular interaction of one type of non-transmissible and one type of conjugative plasmid considering plasmid incompatibility and a switch between repression and derepression of transfer genes.
Further information and full model code: see publication in 'Plasmid'
Simulates poplar leef beetles in short rotation coppice
Neture
Evolutionary Ecology
UIBM
Biodiversity Model
Mangrove forest model with crown plasticity
mesoFON Braganca
Hypthesis Test
mesoFON Sri Lanka
Clonal Plant Model
mesoFON Europe
From Yield Tables to IBMs
GEM
General Ecosystem Model in Java
WiTh Mechanistic
Mechanistic Windthrow Model
Interaction Network
Food Web Model
Rescue the Ecosystem
Ecosystem Model with decay of SOC
SimMarket
Artificial Stock Market