About
Building mechanistic models in biology is hard for mathematicians who lack field or laboratory experience in biology. This experience is not easy to get in the real world. Biology experiments are difficult to setup and can require a lot of skill and time to collect data. Most of us work around this issue by finding biologists as collaborators. This is great, but it doesn't give us the biological intuition that we need to improve our modeling skills.
This is where virtual laboratories come in. A virtual laboratory is a controlled experiment with a designed biological scenario. The user can do many experiments very quickly in the comfort of his/her office with full access to shelter, air conditioning, and coffee. While the virtual world in a virtual laboratory is not really equivalent to any real-world scenario, it can nevertheless serve as a biological scenario for mathematical modeling.
There are two key principles that must be followed in making and using virtual laboratories.
1) The virtual laboratory creates a world that can be studied by mathematical modeling, but the results one gains from that modeling cannot be expected to apply to any real-world scenario. This does not mean that they can't apply to a real-world scenario, just that this is not something we should expect.
2) A virtual laboratory has to be built from first principles, typically an agent-based model. It cannot be built using the model the user has in mind for the result of the modeling. For example, a density-dependent growth virtual laboratory should implement simple mechanistic rules at an individual level, not a model for logistic growth.
Canonical examples of virtual laboratories are the BUGBOX laboratories created in 2007 and 2008 by Glenn Ledder for the RUTE (Research for Undergraduates in Theoretical Ecology) program at the University of Nebraska-Lincoln. BUGBOX-predator recreates the human simulation described in C. S. Holling's classic 1959 paper that derived what are now called the Holling predation models. The predator in the experiment follows simple rules for movement and handling of prey, producing data that fits the Holling type 2 model with a lot of demographic stochasticity. BUGBOX-population simulates the experiments students did in RUTE to develop a stage-structured population model for aphids, with the considerable advantage that the "boxbugs" in the virtual laboratory have a simpler life history than aphids and stages that are visually distinct.
Anyone interested in using and creating virtual laboratories is welcome to join this project. Creating virtual laboratories in Netlogo is something that students with a knack for programming can use as an undergraduate research project.