{"database":"FAIRDOMHub","file_versions":[],"scores":null,"additional":{"omics_type":["Models"],"submitter":["Natalie Stanford"],"full_dataset_link":["https://fairdomhub.org/models/159?version=1"],"ModelFormat":["SBML"],"submitter_affiliation":["University of Manchester - Department of Computer Science","Manchester Centre for Integrative Systems Biology, University of Manchester"],"repository":["FAIRDOMHub"],"pubmed_abstract":["Sustainable production of target compounds such as biofuels and high-value chemicals for pharmaceutical, agrochemical, and chemical industries is becoming an increasing priority given their current dependency upon diminishing petrochemical resources. Designing these strains is difficult, with current methods focusing primarily on knocking-out genes, dismissing other vital steps of strain design including the overexpression and dampening of genes. The design predictions from current methods also do not translate well-into successful strains in the laboratory. Here, we introduce RobOKoD (Robust, Overexpression, Knockout and Dampening), a method for predicting strain designs for overproduction of targets. The method uses flux variability analysis to profile each reaction within the system under differing production percentages of target-compound and biomass. Using these profiles, reactions are identified as potential knockout, overexpression, or dampening targets. The identified reactions are ranked according to their suitability, providing flexibility in strain design for users. The software was tested by designing a butanol-producing Escherichia coli strain, and was compared against the popular OptKnock and RobustKnock methods. RobOKoD shows favorable design predictions, when predictions from these methods are compared to a successful butanol-producing experimentally-validated strain. Overall RobOKoD provides users with rankings of predicted beneficial genetic interventions with which to support optimized strain design."],"pubmed_title":["RobOKoD: microbial strain design for (over)production of target compounds."],"pubmed_authors":["Stanford Natalie J NJ, Millard Pierre P, Swainston Neil N"],"pubmed_abstract_synonyms":["Agrichemical, Materials, Product, Procedures, determination, Laboratory, Gene, bacterium E3, Computer, Oils, Techniques, method, Method, farmaco, method used in an experiment, Escherchia coli, Pharmaceutical Product, Studies, Strain., Chemical, Software Engineering, Enteroinvasive Escherichia coli, Agrichemicals, Enterococcus coli, agricultural chemicals, Sprains, medicament, Technique, Computer Program, Biofuel Oil, Application, Drugs, Open Source Softwares, anatomical systems, Genetic, Escherichia/Shigella coli, Biofuel, Flexibility, Software Application, Open, Open Source Software, Computer Programs and Programming, E coli, procedures, ecotype, E. coli, Computer Software Application, genetic, Study, Eschericia coli, Enteroaggregative Escherichia coli, reaction, Methodological Studies, Tools, Biogas, Pharmaceutical, Biodiesels, Strains, Preparation, Agricultural Chemical, constitutitional genetic, Pharmaceuticals, Applications Software, Alkalescens-Dispar Group, Products, Open Source, Bacterium coli, Computer Software, Sprain, familial, agrochemicals, EAggEC, Procedure, Cistrons, Enteroaggregative E. coli, Source Softwares, predicted, Software Tools, Tool, strain, Programs, Program, Computer Applications, Software Tool, Diffusely Adherent E. coli, Bacillus coli, Biodiesel, Chemicals, chemical analysis, Computer Applications Software, agrichemical, Strain, Computer Applications Softwares, Genetic Materials, Oil, Agrochemical, Pharmaceutic, cultivar, laboratory, agrichemicals, techniques, Softwares, Software, Genetic Material, Diffusely Adherent Escherichia coli, Software Applications, Enteroinvasive E. coli, Pharmaceutic Preparations, Source Software, Engineering, Methodological, Methodological Study, Drug, plan specification, Computer Programs, Preparations, Applications, Applications Softwares, Agricultural, Bacterium coli commune, Material, Biomasses, Biofuel Oils, pharmaceuticals, Agricultural Chemicals, Cistron, inherited genetic, assay, Pharmaceutical Products, Strains and Sprains, hereditary, Pharmaceutical Preparation, methodology, Computer Software Applications"],"name_synonyms":["Hydroxybutanes, Butylhydroxides, Butanol, Butyl Alcohols, Butyl., Alcohols"],"description_synonyms":["Hydroxybutanes, Butylhydroxides, Butanol, Butyl Alcohols, Butyl., Alcohols"],"pubmed_title_synonyms":["strain, Sprain, Strain., cultivar, Strains, Sprains, Strains and Sprains, ecotype"],"additional_accession":[]},"is_claimable":false,"name":"iNS142 RobOKoD Redesigned Butanol Producing.","description":"iNS142 RobOKoD Redesigned Butanol Producing.","dates":{"created":"2015-06-03","publication":"2018-08-31","submission":"2015-06-03","last_modified":"2018-08-31"},"accession":"159","cross_references":{"pubmed":["25853130"]}}