CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology.
Dias, Joao ML
Microbiology (Reading, England)
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Cankorur-Cetinkaya, A., Dias, J. M., Kludas, J., Slater, N., Rousu, J., Oliver, S., & Dikicioglu, D. (2017). CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology.. Microbiology (Reading, England), 163 829-839. https://doi.org/10.1099/mic.0.000477
Multiple interacting factors affect the performance of engineered biological systems in synthetic biology projects. The complexity of these biological systems means that experimental design should often be treated as a multiparametric optimization problem. However, the available methodologies are either impractical, due to a combinatorial explosion in the number of experiments to be performed, or are inaccessible to most experimentalists due to the lack of publicly available, user-friendly software. Although evolutionary algorithms may be employed as alternative approaches to optimize experimental design, the lack of simple-to-use software again restricts their use to specialist practitioners. In addition, the lack of subsidiary approaches to further investigate critical factors and their interactions prevents the full analysis and exploitation of the biotechnological system. We have addressed these problems and, here, provide a simple-to-use and freely available graphical user interface to empower a broad range of experimental biologists to employ complex evolutionary algorithms to optimize their experimental designs. Our approach exploits a Genetic Algorithm to discover the subspace containing the optimal combination of parameters, and Symbolic Regression to construct a model to evaluate the sensitivity of the experiment to each parameter under investigation. We demonstrate the utility of this method using an example in which the culture conditions for the microbial production of a bioactive human protein are optimized. CamOptimus is available through: (https://doi.org/10.17863/CAM.10257).
EU 7th Framework Programme (BIOLEDGE Contract No: 289126 to S. G. O and J. R), BBSRC (BRIC2.2 to S. G. O. and N. K. H. S.), Synthetic Biology Research Initiative Cambridge (SynBioFund to D. D., A. C. C. and J. M. L. D.)
EC FP7 CP (289126)
External DOI: https://doi.org/10.1099/mic.0.000477
This record's URL: https://www.repository.cam.ac.uk/handle/1810/265211