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bioRxiv · 10.1101/412197

Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations

Naylor, J.·Fellermann, H.·Krasnogor, N.
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Abstract

Motivation3D physical modelling is a powerful computational technique which allows for the simulation of complex systems such as consortia of mixed bacterial species. The complexities in physical modelling reside in the knowledge intensive model building process and the computational expense in calculating their numerical solutions. These models can offer insights into microbiology, both in understanding natural systems and as design tools for developing novel synthetic bacteria. Developing a robust synthetic system typically requires multiple iterations around the specify->design->build->test cycle to meet specifications. This process is laborious and expensive for both the computational and laboratory aspects, hence any improvement in any of the workflow steps would be welcomed. We have previously introduced Simbiotics (Naylor, 2017) a powerful and flexible platform for designing and analysing three-dimensional simulations of mixed species bacterial populations. Simbiotics requires programming experience to use which creates barriers to entry for use of the tool.\n\nResultsIn the spirit of enabling biologists who may not have programming skills to install and utilise Simbiotics, we present in this application note Easybiotics, a user-friendly graphical user interface for Simbiotics. Users may design, simulate and analyse models from within the GUI, with features such as live graph plotting and parameter sweeps. Easybiotics provides full access to all of Simbiotics simulation features, such as cell growth, motility and gene regulation.\n\nAvailabilityEasybiotics and Simbiotics are free to use under the GPL3.0 license, and can be found at: https://bitbucket.org/simbiotics/simbiotics/wiki/Home\n\nContactnatalio.krasnogor@newcastle.ac.uk

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Naylor, J., Fellermann, H., Krasnogor, N.. 2018-09-11. Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations. https://doi.org/10.1101/412197

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