Our new tool eGUT will come from the existing individual-based Dynamics of Microbial Communities Simulator iDynoMiCS, which we published in Environmental Microbiology (Lardon et al. 2011, Merkey et al. 2011) and released on www.idynomics.org in 2011. The key additions will be: (a) implementing agents for the host cells, (b) scaling to a larger domain size, (c) enabling the simulation of a chain of compartments, (d) building a graphical user interface, and (e) producing full documentation to improve user friendliness to enable non-modellers to use the tool, boosting the user base. We will adopt an approach advocated as eXtreme Programming (Beck & Andres 2004) as short development cycles including code review, unit testing, and feedback from users boost productivity and quality and allow requirements to change or become clearer over time.
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Once this is complete, we will seek to carry out novel experimentation that can be used to predict microbial dynamics in the gut. This could potentially impact our understanding of how the microbiota affects human health, in terms of our energy uptake, nutrition, effects on obesity, and use of probiotics. |
