A software module to assess the metabolic potential of mutant strains of the bacterium <i>Corynebacterium glutamicum</i>
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...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2025-01-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/4411 |
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| author | F. V. Kazantsev M. F. Trofimova T. M. Khlebodarova Yu. G. Matushkin S. A. Lashin |
| author_facet | F. V. Kazantsev M. F. Trofimova T. M. Khlebodarova Yu. G. Matushkin S. A. Lashin |
| author_sort | F. V. Kazantsev |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-6588fda422204978bca2eb2ea304905e |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-6588fda422204978bca2eb2ea304905e2025-02-01T09:58:14ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592025-01-0128889790310.18699/vjgb-24-971524A software module to assess the metabolic potential of mutant strains of the bacterium <i>Corynebacterium glutamicum</i>F. V. Kazantsev0M. F. Trofimova1T. M. Khlebodarova2Yu. G. Matushkin3S. A. Lashin4Kurchatov Genomic Center of ICG SB RAS; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State UniversityInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesKurchatov Genomic Center of ICG SB RAS; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesKurchatov Genomic Center of ICG SB RAS; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State UniversityKurchatov Genomic Center of ICG SB RAS; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State UniversityTechnologies 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.https://vavilov.elpub.ru/jour/article/view/4411flux modelsbacterial metabolismmetabolic optimizationrational metabolic engineering |
| spellingShingle | F. V. Kazantsev M. F. Trofimova T. M. Khlebodarova Yu. G. Matushkin S. A. Lashin A software module to assess the metabolic potential of mutant strains of the bacterium <i>Corynebacterium glutamicum</i> Вавиловский журнал генетики и селекции flux models bacterial metabolism metabolic optimization rational metabolic engineering |
| title | A software module to assess the metabolic potential of mutant strains of the bacterium <i>Corynebacterium glutamicum</i> |
| title_full | A software module to assess the metabolic potential of mutant strains of the bacterium <i>Corynebacterium glutamicum</i> |
| title_fullStr | A software module to assess the metabolic potential of mutant strains of the bacterium <i>Corynebacterium glutamicum</i> |
| title_full_unstemmed | A software module to assess the metabolic potential of mutant strains of the bacterium <i>Corynebacterium glutamicum</i> |
| title_short | A software module to assess the metabolic potential of mutant strains of the bacterium <i>Corynebacterium glutamicum</i> |
| title_sort | software module to assess the metabolic potential of mutant strains of the bacterium i corynebacterium glutamicum i |
| topic | flux models bacterial metabolism metabolic optimization rational metabolic engineering |
| url | https://vavilov.elpub.ru/jour/article/view/4411 |
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