iDynoR: R Analysis package for iDynoMiCS Simulation Results. iDynoMiCS is a computer program, developed by an international team of researchers, whose purpose is to model and simulate microbial communities in an individual-based way. It is described in detail in the paper ”iDynoMiCS: next-generation individual-based modelling of biofilms” by Lardon et al, published in Environmental Microbiology in 2011. The simulation produces results in XML file format, describing the state of each species in each timestep (agent_State), a summary of the species statistics for a timepoint (agent_Sum), the state of each solute grid in each timestep (env_State) and a summary of the solutes for a timestep (env_Sum). This R package provides a means of reading this XML data into R such that the simulation response can be statistically analysed. iDynoMiCS is available from the website iDynoMiCS.org, where a full tutorial on using both the simulation and this R package is provided.
Keywords for this software
References in zbMATH (referenced in 3 articles )
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- Soleimani, Meisam; Wriggers, Peter; Rath, Henryke; Stiesch, Meike: Numerical simulation and experimental validation of biofilm in a multi-physics framework using an SPH based method (2016)
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- Miller, J.K.; Brantner, Justin S.; Clemons, Curtis; Kreider, K.L.; Milsted, Amy; Wilber, Pat; Yun, Yang H.; Youngs, Wiley J.; Young, Gerald; Badawy, Hope T.; Wagers, Patrick O.: Mathematical modelling of Pseudomonas aeruginosa biofilm growth and treatment in the cystic fibrosis lung (2014)