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

Bioinformatics
Jonathan NaylorNatalio Krasnogor

Abstract

3D physical modelling is a powerful computational technique that 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 bacterial systems. 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, a powerful and flexible platform for designing and analyzing 3D simulations of mixed species bacterial populations. Simbiotics requires programming experience to use which creates barriers to entry for use of the tool. In the spirit of enabling biologists who may not have programming skills to install and utilize Simbiotics, we present in this application note Easybiotics, a user-friendly graphical user interface f...Continue Reading

References

Mar 18, 2011·Environmental Microbiology·Laurent A LardonBarth F Smets
May 6, 2017·ACS Synthetic Biology·Jonathan NaylorNatalio Krasnogor

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Citations

Mar 7, 2021·Microorganisms·Sherli Koshy-ChenthittayilAnna Dongari-Bagtzoglou

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