Abstract
Food-webs and other classes of ecological network motifs, are a means of describing feeding relationships between consumers and producers in an ecosystem. They have application across scales where they differ only in the underlying characteristics of the organisms and substrates describing the system. 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. 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. We have developed the MI-Sim software for use with MATLAB to allow a rigorous and rapid numerical analysis of several common ecological motifs. MI-Sim contains a series of the most commonly used motifs such as cooperation, competition and predation. 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. The tools available in the current version of MI-Sim include model simulation, steady-state existence and stability analysis, and basin of attraction analysis. The software includes seven ecological interaction motifs and seven growth function models. 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.
Highlights
Network motifs provide an approach to understand and characterise the behaviour of living systems at genomic, metabolic and ecological scales [1,2,3]
More complex thermodynamic models, useful in general microbial ecology modelling, may make the analyses provided here intractable
We have developed the MATLAB based software tool MI-Sim for numerical analysis of ecological interactions
Summary
Network motifs provide an approach to understand and characterise the behaviour of living systems at genomic, metabolic and ecological scales [1,2,3]. 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 microscales [4,5,6]. Mathematical modelling of ecological interactions is affected by the model objective (e.g., observation, prediction, control), the availability of existing knowledge and data, and the PLOS ONE | DOI:10.1371/journal.pone.0173249.
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