Interactive Model Simulations

Disclaimer

This server is set up for communicating models between partners of ongoing projects. The simulations are primarily intended for testing and discussion. Occasional use by guests is allowed as long as server load remains within reasonable limits.

This service will be available for limited time. In case of questions, please consult our official website at http://tu-dresden.de/hydrobiologie

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Models

Teaching Demos	Logistic growth: a discrete solution creates period doubling chaos, while the continuous solution reaches a stable equilibrium. Resource limited Lotka-Volterra: change parameters of a three-compartment predator-prey model with resource S, producer P and consumer K. SEIR model: a simple demo of the main principle of models used in the COVID-19 crisis webLAB Wastewater treatment plant model: a web-based teaching implementation of the ASM3 model with 3 reactors (in English and German). Lake Profile Plotter: plot lake profile data Trend test app: simple trend test for teaching purposes
Research Projects	One box lake model with 3 phytoplankton groups: Simulation of the pelagic food-web of a shallow lake. A simplified interface allows interactive exploration. Phosphorus release at the sediment-water interface: Interactive exploration of pre-calculated simulations of an 1D sediment model (in German). Ecoffinder: estimate cutoff values from antibiotic resistance data (package antibioticR)
Snippets	Two-compartment model: Demonstrates the influence of start parameters when fitting a model to given data.
Conferences	Pre-conference tutorial about simulation of differential equation models with R from the useR!2017 conference in Brussels, given by Thomas Petzoldt and Karline Soetaert Growthrate apps: Supplementary material for useR!2017 and DGL 2017

Technology

• The models are implemented in R and Gnu Fortran using the R package rodeo for code generation, package deSolve for numerical integration of the differential equations and package shiny and the Shiny Server for the web interface.

• All main components, the models and parts of the data are free and open source software, available from RStudio, github/dkneis, github/tpetzoldt, R-Forge and CRAN.

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