SEEK ID: https://fairdomhub.org/investigations/58
Projects: Manchester Institute for Biotechnology
Investigation position:
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Created: 5th Sep 2014 at 17:30
Last updated: 8th Dec 2015 at 15:05
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- People (1)
- Programmes (1)
- Projects (1)
- Studies (1)
- Assays (3)
- Data files (1)
- Models (1)
- SOPs (3)
- Publications (1)
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

Roles: Postdoc
Expertise: Systems Biology, Metabolic Engineering, Stoichiometric modelling, Kinetic modelling, Data Management, Metabolic Networks
Tools: Python, Copasi, Matlab, COBRA toolbox
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, Bio-crop, ORHIZON, Coastal Data, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, hybrid sequencing, HOST-PAR, BioCreative VII, Boolean modeling of Parkinson disease map, Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish, Selective Destruction in Ageing, Viral Metagenomic, Synthetic biology in Synechococcus for bioeconomy applications (SynEco), testproject, SDBV ephemeral data exchanges, Test project, The BeeProject, PHENET, LiceVault, EbN1 Systems Biology
Web page: Not specified
Programme: Independent Projects
Public web page: Not specified
Organisms: Escherichia coli
Submitter: Natalie Stanford
Investigation: Designing a new way to predict engineering stra...
Assays: OptKnock applied to e.coli for butanol production., RobOKoD applied to e.coli for butanol production., RobustKnock applied to e.coli for butanol production.
Snapshots: No snapshots
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
Investigation: Designing a new way to predict engineering stra...
Organisms: No organisms
Models: iNS142 RobOKoD Redesigned Butanol Producing.
SOPs: RobOKoD SOP for Redesigning Butanol Producing S...
Data files: FBA result of RobOKoD designed e.coli strain.
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
Investigation: Designing a new way to predict engineering stra...
Organisms: No organisms
Models: No Models
SOPs: OptKnock SOP for Redesigning Butanol Producing ...
Data files: No Data files
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
Investigation: Designing a new way to predict engineering stra...
Organisms: No organisms
Models: No Models
SOPs: RobustKnock SOP for Redesigning Butanol Produci...
Data files: No Data files
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
Organism: Not specified
Investigations: Designing a new way to predict engineering stra...
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
PubMed ID: 25853130
Citation: Front Cell Dev Biol. 2015 Mar 24;3:17. doi: 10.3389/fcell.2015.00017. eCollection 2015.