OptKnock applied to e.coli for butanol production.
OptKnock algorithm was used as part of a study in RobOKoD: microbial strain design for (over)production of target compounds. (http://fairdomhub.org/publications/236). It was used to generate a strain of e.coli for producing butanol, that was then compared to an experimental strain.
SEEK ID: https://fairdomhub.org/assays/270
Modelling analysis
Projects: Manchester Institute for Biotechnology
Investigation: Designing a new way to predict engineering strategies in cells.
Study: Predicting engineering strategies for overproduction of butanol in ecoli.
Assay position:
Biological problem addressed: Model Analysis Type
Organisms: No organisms
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Created: 5th Sep 2014 at 15:56
Last updated: 8th Nov 2017 at 14:21
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Projects: SysMO DB, Whole body modelling of glucose metabolism in malaria patients, Manchester Institute for Biotechnology, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, GenoSysFat, DigiSal, FAIRDOM user meeting
Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester
https://orcid.org/0000-0003-4958-0184
Interested in systems + synthetic biology, biotechnology, mountaineering, swimming, running, and the occasional cup of tea. Once diagnosed as an ENFP.
Projects that do not fall under current programmes.
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Grain Yield, Quality, and Net Photosynthesis When Grown Under Semi-Transparent Cadmium Telluride Photovoltaic Modules Near Maturity, Benefit for All FAIR Data, Implementation of Nanopore Sequencing for Detection of Treatment Induced Transcriptomic and Epitranscriptomic Changes in Leukaemic Tumour Models, DPL, Glycogen Metabolism in bacteria, ILS Ceramide Ring Trial, Project Test, DeepCurate, Revisiting mutational resistance to ampicillin and cefotaxime in Haemophilus influenzae, Cancer Systems Biology Consortium (CSBC), Biochemical characterization of the feedforward loop between CDK1 and FOXM1 in epidermal stem cells, Drug Discovery and Biotechnology Standard Operating Procedures, EDITH (Ecosystem Digital Twins in Health) test project, Fluid flow project, Smart Garden Watering System, The role of different fatty acids, AQUACIRCLE, IDIM, Sampling vicinity of industrial settings for pathogens and GMO identification, RNA-seq data for paper, RNA-seq data
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Matlab script that reproduces the model redesign results outlined in RobOKoD: microbial strain design for (over)production of target compounds (http://fairdomhub.org/publications/236) for OptKnock.
Creator: Natalie Stanford
Submitter: Natalie Stanford
Abstract (Expand)
Authors: N. J. Stanford, P. Millard, N. Swainston
Date Published: 24th Mar 2015
Publication Type: Not specified
