Designing a new way to predict engineering strategies in cells. (snapshot 1)

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Created at: 8th Dec 2015 at 17:25

Contents

Predicting engineering strategies for overproduction of butanol in ecoli.

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RobOKoD applied to e.coli for butanol production.

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).

FBA result of RobOKoD designed e.coli strain.

FBA result of flux distribution in butanol producing e.coli strain, which designed using RobOKoD.

  • iNS142_ko_biomass_fba_results_excel.xlsx

iNS142 RobOKoD Redesigned Butanol Producing.

Butanol producing iNS142, redesigned using RobOKoD.

  • iNS142_ko.xml
  • Screen Shot 2015-06-03 at 13.43.02.png

RobOKoD SOP for Redesigning Butanol Producing Strain of E.coli.

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).

  • RobOKoD_SOP.zip

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.

OptKnock SOP for Redesigning Butanol Producing Strain of E.coli.

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.

  • OptKnock_SOP.zip

RobustKnock applied to e.coli for butanol production.

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.

RobustKnock SOP for Redesigning Butanol Producing Strain of E.coli.

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.

  • RobustKnock_SOP.zip
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