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Usingbig“bio-data”todesignbettercellfactoriesThe EU has granted 6.3 million Euros to the project DD-DeCaF,coordinated by the Novo Nordisk Foundation Center forBiosustainability.Theobjective is todevelopa computer tool thatwillallow biotech companies to design and engineer cell factories fasterthaniscurrentlypossibletoday.Thetoolwillacceleratetheproductionof sustainable bio-chemicals and lay the groundwork for design ofhealthierfoodstuff.
Today,manyvaluablemoleculesusedinconsumergoods,forexampleplasticdiapers,cosmeticsandfood canbeproducedby cell factories – genetically engineeredmicrobes suchasbaker’s yeast andEscherichia coli. But engineeringmicrobes toproduce large amounts of a givenbio-chemical is verycomplicated,timeconsumingandexpensive.Socalled“omics”data–genomics,transcriptomics,proteomics,metabolomics,fluxomics–allowlifescientiststoinventoryacell’smolecularcomponentsandthereforeenablesadata-drivenapproachtobiologyandbioengineering.Unfortunately,biotechindustryhasnotyetbeenequippedwithtoolsthatwouldallowthemtomakeeffectiveuseofthisdata.ThescopeoftheDD-DeCaFprojectisthereforetodevelopaneasytousewebapplicationthatcollectsallthisdataandenablesengineerstointegrateitwithcomputationalmodelsofbiologicalpathways.“Thebiotechindustryisingreatneedofacomputationaldesigntoolthatallowsthemtosimulatehowacellwillbehaveifyouengineeritinacertainway–justasengineersdesignandtestbuildingsbeforethey build them” says project coordinator of DD-DeCaF, ProfessorMarkus Herrgard from the NovoNordisk Foundation Center for Biosustainability (DTU Biosustain) at the Technical University ofDenmark.Thewebplatformwillhavean intuitiveanduser friendly interface thatwill enableexploratorydataanalysis through interactive and interconnected visualizations reducing the costs of developing cellfactories and making them able to compete with currently used unsustainable petrochemicalprocesses.The DD-DeCaF project is a collaboration between the Technical University of Denmark, ChalmersUniversity (Sweden), EuropeanMolecular Biology Laboratory, University of Minho (Portugal), EcolePolytechniqueFederaledeLausanne(Switzerland),SilicoLifeLda(Portugal),Genialisd.o.o.(Slovenia),BiobytesolutionsGmbH(Germany),BiosyntiaA/S(Denmark)andDSMN.V.(theNetherlands).ThetoolwillbetestedbytheindustryThreesmallandmediumsizedbioinformaticscompanies–Biobyte(Germany),SilicoLife(Portugal)andGenialis (Slovenia) – will be involved in the development of the software tools and intuitivevisualizationsofbiologicalnetworks thatcanbeusedbynon-experts.Simultaneously, two industrialbiotech partners – the DTU spin-off company Biosyntia and the Dutchmultinational company DSM(>20,000employees)–willutilizethetoolintworeal-worldcellfactoryprojectsandthuscontinuouslyevaluatethetool’susabilityfromtwoverydifferentuserperspectives.
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DD-DeCaFcanleadtohealthierfoodDD-DeCaF also aims at exploring interactions between cell communities and obtaining novel dataabout the interplay betweenmicrobes. For example, the human gut consists ofmany different celltypesthatinteractandcompetewitheachother.If some cell types begin to dominate the gut, or if communities fight each other, thismay lead todiseases.Beingabletodescribethesecellinteractionscomputationally,theindustrywilleventuallybeabletodevelopfoodandpharmaceuticalcompoundswithbeneficialimplicationsonthegut.FactsaboutDD-DeCaf
• DD-DeCaF(BioinformaticsServicesforData-DrivenDesignofCellFactoriesandCommunities)bringstogetherleadingacademicpartnersfromfiveEuropeanuniversitieswithfiveinnovativeEuropeancompaniestoaddressthechallengeofbuildingacomprehensivedesigntool.
• Theacademicpartnerswilldevelopcuttingedgemethodsforusinglargescaledatatodesign
cellfactoriesandcommunitiesforbiotechnologicalapplications.• Theprojectwaslaunched1stofMarch2016andrunsovera4-yearperiod.• The grant was given as part of a call from EU within the Horizon2020 program ‘New
BioinformaticsapproachesinserviceofBiotechnology’.Thisprojecthas received funding from theEuropeanUnion’sHorizon2020 researchand innovationprogrammeundergrantagreementNo.686070.ContactsProjectcoordinatorProfessorMarkusHerrgardE-mail [email protected]ã[email protected]:http://dd-decaf.eu/
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