INDISIM-YEAST: an individual-based simulator on a website for experimenting and investigating diverse dynamics of yeast populations in liquid media

Abstract

Simulation modelling can be used to capture and mimic real-world microbial systems that, unlike the real-world, can then be experimented upon as a new kind of experimental milieu. Individual-based models, in which individuals interact dynamically with each other as structural elements in the model world, exemplify this view of simulation modelling. These models are more difficult to analyze, understand and communicate than traditional analytical models. It is good practice to provide executable versions that perform simulation results. INDISIM-YEAST, developed to deal with yeast populations in liquid media, models the evolution of a set of yeasts by setting up rules of behavior for each individual cell according to its own biological regulations and characteristics. The aim of this work is to develop and present a website from which INDISIM-YEAST is accessible, and how to carry out yeast simulations to further the skills associated with the use of this individual-based simulator. A good and useful way to analyze this yeast simulator is to experiment and explore the manner in which it reacts to changes in parameter values, initial conditions or assumptions. The application results in a very versatile program that could be used in controlled simulation experiments via the Internet.