Designing a new way to predict engineering strategies in cells.
SEEK ID: https://fairdomhub.org/investigations/58
Projects: Manchester Institute for Biotechnology
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Created: 5th Sep 2014 at 17:30
Last updated: 8th Dec 2015 at 15:05
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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, FAIRDOM Templates
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.
Projects: Manchester Institute for Biotechnology, ICYSB 2015 - International Practical Course in Systems Biology, iRhythmics, INBioPharm, EmPowerPutida, Systo models, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, Multiscale modelling of state transitions in the host-microbiome-brain network, Extremophiles metabolsim, NAD COMPARTMENTATION, Agro-ecological modelling, Bergen(Ziegler lab) project AF-NADase, NAMPT affinity, Stress granules, Modelling COVID-19 epidemics
Web page: Not specified
Programme: Independent Projects
Public web page: Not specified
RobOKoD algorithm was, designed then implemented 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. It was shown to perform better than similar methods (OptKnock, and RobustKnock).
Submitter: Natalie Stanford
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
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.
Submitter: Natalie Stanford
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
RobustKnock 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.
Submitter: Natalie Stanford
Biological problem addressed: Model Analysis Type
Snapshots: No snapshots
FBA result of flux distribution in butanol producing e.coli strain, which designed using RobOKoD.
Creator: Natalie Stanford
Submitter: Natalie Stanford
Butanol producing iNS142, redesigned using RobOKoD.
Creator: Natalie Stanford
Submitter: Natalie Stanford
Model type: Metabolic network
Model format: SBML
Environment: Matlab
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).
Creator: Natalie Stanford
Submitter: Natalie Stanford
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
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 RobustKnock.
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
