MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions.

作者: Matthew J. Wade , Jordan Oakley , Sophie Harbisher , Nicholas G. Parker , Jan Dolfing

DOI: 10.1371/JOURNAL.PONE.0173249

关键词: MATLABPopulationDynamical systems theoryEcologyEcological networkSoftwareBiologyTheoretical ecologyGraphical user interfaceStability (learning theory)

摘要: Food-webs and other classes of ecological network motifs, are a means describing feeding relationships between consumers producers in an ecosystem. They have application across scales where they differ only the underlying characteristics organisms substrates system. Mathematical modelling, using mechanistic approaches to describe dynamic behaviour properties system through sets ordinary differential equations, has been used extensively ecology. Models allow simulation dynamics various motifs their numerical analysis provides greater understanding interplay components intrinsic properties. We developed MI-Sim software for use with MATLAB rigorous rapid several common motifs. contains series most commonly such as cooperation, competition predation. It does not require detailed knowledge mathematical analytical techniques is offered single graphical user interface containing all input output options. The tools available current version include model simulation, steady-state existence stability analysis, basin attraction analysis. includes seven interaction growth function models. Unlike tools, designed simple user-friendly tool specific population type models, allowing assessment dynamical behavioural

参考文章(36)
Henry R. Bungay, Microbial interactions in continuous culture. Advances in Applied Microbiology. ,vol. 10, pp. 269- 290 ,(1968) , 10.1016/S0065-2164(08)70194-1
Frank Schilder, Harry Dankowicz, Recipes for Continuation ,(2013)
Roie Levy, Rogan Carr, Anat Kreimer, Shiri Freilich, Elhanan Borenstein, NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation BMC Bioinformatics. ,vol. 16, pp. 164- 164 ,(2015) , 10.1186/S12859-015-0588-Y
Tobias Großkopf, Orkun S Soyer, Synthetic microbial communities. Current Opinion in Microbiology. ,vol. 18, pp. 72- 77 ,(2014) , 10.1016/J.MIB.2014.02.002
Marina Arnaldos, Youri Amerlinck, Usman Rehman, Thomas Maere, Stijn Van Hoey, Wouter Naessens, Ingmar Nopens, From the affinity constant to the half-saturation index: Understanding conventional modeling concepts in novel wastewater treatment processes Water Research. ,vol. 70, pp. 458- 470 ,(2015) , 10.1016/J.WATRES.2014.11.046
Elie Desmond-Le Quéméner, Théodore Bouchez, A thermodynamic theory of microbial growth. The ISME Journal. ,vol. 8, pp. 1747- 1751 ,(2014) , 10.1038/ISMEJ.2014.7
M. E. Gilpin, M. L. Rosenzweig, Enriched predator-prey systems: theoretical stability. Science. ,vol. 177, pp. 902- 904 ,(1972) , 10.1126/SCIENCE.177.4052.902
Gregor F Fussmann, Stephen P Ellner, Kyle W Shertzer, Nelson G Hairston Jr, Crossing the Hopf Bifurcation in a Live Predator-Prey System Science. ,vol. 290, pp. 1358- 1360 ,(2000) , 10.1126/SCIENCE.290.5495.1358