Food-webs, defined as a subset or module of larger, more complex networks, are used to analyse ecological interactions at the community or population level, as first described by mathematicians such as Lotka and Volterra, and have been widely used to explore phenomena observed at both macro- and micro-scales. Network motifs provide an approach to understand and characterise the behaviour of living systems at genomic, metabolic and ecological scales.
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The MI-SIM software is also available directly at the Mathworks File Exchange ( ).įunding: MJW and JD acknowledge the Biotechnology and Biological Sciences Research Council UK (BB/K003240/2 Engineering synthetic microbial communities for biomethane production) for funding the project ( MJW, JO and SH developed the software with funding provided by the Institute of Sustainability, Newcastle University ( ).Ĭompeting interests: The authors have declared that no competing interests exist. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: All Matlab package scripts are available at the Github repository ( ). Received: OctoAccepted: FebruPublished: March 8, 2017Ĭopyright: © 2017 Wade et al. Unlike other system analysis tools, MI-Sim is designed as a simple and user-friendly tool specific to ecological population type models, allowing for rapid assessment of their dynamical and behavioural properties.Ĭitation: Wade MJ, Oakley J, Harbisher S, Parker NG, Dolfing J (2017) MI-Sim: A MATLAB package for the numerical analysis of microbial ecological interactions. The software includes seven ecological interaction motifs and seven growth function models.
The tools available in the current version of MI-Sim include model simulation, steady-state existence and stability analysis, and basin of attraction analysis. It does not require detailed knowledge of mathematical analytical techniques and is offered as a single graphical user interface containing all input and output options.
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MI-Sim contains a series of the most commonly used motifs such as cooperation, competition and predation. We have developed the MI-Sim software for use with MATLAB to allow a rigorous and rapid numerical analysis of several common ecological motifs. Models allow simulation of the dynamics of the various motifs and their numerical analysis provides a greater understanding of the interplay between the system components and their intrinsic properties. Mathematical modelling, using mechanistic approaches to describe the dynamic behaviour and properties of the system through sets of ordinary differential equations, has been used extensively in ecology.
They have application across scales where they differ only in the underlying characteristics of the organisms and substrates describing the system. Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem.
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