A software module to assess the metabolic potential of mutant strains of the bacterium Corynebacterium glutamicum

Technologies for the production of a range of compounds using microorganisms are becoming increas­ingly popular in industry. The creation of highly productive strains whose metabolism is aimed to the synthesis of a specific desired product is impossible without complex directed modifications of the genome using mathematical and computer modeling methods. One of the bacterial species actively used in biotechnological production is Co­rynebacterium glutamicum. There are already 5 whole-genome flux balance models for it, which can be used for me­tabolism research and optimization tasks. The paper presents fluxMicrobiotech, a software module developed at the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, which implements a se­ries of computational protocols designed for high-performance computer analysis of C. glutamicum whole-genome flux balance models. The tool is based on libraries from the opencobra community (https://opencobra.github.io) within the Python programming language (https://www.python.org), using the Pandas (https://pandas.pydata.org) and Escher (https://escher.readthedocs.io) libraries . It is configured to operate on a ‘file-in/file-out’ basis. The model, environmental conditions, and model constraints are specified as separate text table files, which allows one to pre­pare a series of files for each section, creating databases of available test scenarios for variations of the model. Or vice versa, allowing a single model to be tested under a series of different cultivation conditions. Post-processing tools for modeling data are set up, providing visualization of summary charts and metabolic maps.

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