BacSimResources*
Homepage*
Jan-Ulrich Kreft's homepage* Local directory:
BacSimVersionNo version info.
Distribution methodFree. Open source.
DocumentationI am not able to find. But since the source is provided, at least we can read the source.
What is it?BacSim
* is an extension of Gecko.
* written by Jan-Ulrich Kreft (University of bonn, Germany)
* I am not able to find any document files. The comments in the source file seems not complete
Gecko
* is an ecological flight simulator written by Ginger Booth (a programmer with the Center for Computational Ecology, Yale Institute for Biospheric Studies) .
* started as a prototype based on John Holland's Echo models. It then became one of the first programs to be based on the Swarm toolkit for multi-agent based simulations written in Objective-C, originally developed at the Santa Fe Institute.
* Now is pure java, using Ginger's own CourseWare, a Java Toolkit for online simulators for the teaching of ecology.
Jan-Ulrich Kreft
* Wissenschaftlicher Assistent (~ Assistant Professor)
* His CV
jan_kreft_cvIndividual-Based Models
*
Online resource* has gained a lot of popularity in the 1990's
* are simulations based on the global consequences of local interactions of members of a population. These individuals might represent pretty much everything
* typically consist of an environment or framework in which the interactions occur and some number of individuals defined in terms of teir behaviors and characteristic parameters
* the characteristics of each individual are tracked through time.
* are also known as entity or agent based models, and as individual/entity/agent-based simulations.
* are a subset of multi-agent systems which includes any computational system whose design is fundamentally composed of a collection of interacting parts.
* differences with CA: there is an overlap between ibm and ca. Perhaps the significant difference is whether the simulation's inner loop proceeds cell by cell, or individual by individual. (Although that distinction is muddied by parallel-processing hardware.)) The philosophical issue is whether the simulation is based on a dense and uniform dissection of the space (as in a CA), or based on specific individuals distributed within the space.
The structure of BasSim* Currently using diffusion-reaction algorithm. This was made possible by decoupling growth and diffusion on the basis of the different timescales of these processes.
* was extended to multi-species, multi-substrate systems with biofilm geometry (inert substratum at the bottom and bulk liquid at the top of the vertical dimension, periodic boundaries in the other two dimensions), and the bacteria are now living in a 3D space.
* the ability of bacteria to produce and excrete EPS, where the EPS is essentially treated as inert biomass (no metabolism or growth), subject to the same rules of biomass spreading.
Some screen shots*
Colonies*
Biofilms*
Slimy biofilms
*
Spoiled eggs*
BacSim: The program behind the IbM scenes*
Quantification of biofilm structure*
How biofilms promote altruismSome concepts:ibm: Individual based System
EPS: extracellular polymeric substance
