splicing unix into a

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1、SplicingUNIXintoaGenomeMappingLaboratoryLincolnStein,AndreMarquis,ErtDredge,MaryPatReeve,MarkDaly,SteveRozen,NathanGoodmanWhiteheadInstituteforBiomedicalResearchOneKendallSquareCambridge,MA02139Abstractassignedtouniquepositionsonchromosomes[NationalResearchCouncil,19

2、88].TheavailabilityTheWhiteheadInstitute/MITCenterforGenomeofsuchmapsgreatlysimplifiesthetaskofidentifyingResearchisresponsibleforanumberoflargegenomeandisolatinggenesrelevanttotheunderstandingofmappingefforts,thescaleofwhichcreateproblemsdevelopmentanddisease.Therea

3、retwomainofdataandworkflowmanagementthatdictategenomemappingprojectsattheWI/MITCGR:therelianceoncomputersupport.Twoyearsago,whencreationofageneticmapofthemouse[Dietrichetal.westartedtodesigntheinformaticssupportforthe1992],andthecreationofaphysicalmapofthelaboratory,

4、werealizedthatthefluidandever-human[GreenandOlson,1990].Weestimatethatchangingnatureoftheexperimentalprotocolstheseprojectswillrequirethecompletionofseveralprecludedanyefforttocreateasinglemonolithicmillionindividualexperimentalsteps.Thispaperpieceofsoftware.Insteadw

5、edesignedasystemthatdescribesthedesignoftheWI/MITCGRinformaticsreliedonmultipledistributeddataanalysisandsystemandthelessonswelearnedduringtheprocess.processingtoolsknittogetherbyacentralizeddatabase.Theobviouschoiceofoperatingsystems1.2ChoosingUNIXwasUNIX.Inordertom

6、akethischoicepalatabletothelaboratorybiologists—whorightlyconsideritManaginginformationflowinlaboratoryprojectsoftheirjobtodoexperimentsratherthantointeractwiththisscalepresentsseveralchallenges.Thefirstcomputers,andwhohavecometoexpectallsoftwarechallengeismanagingth

7、elaboratorydataforeachtobeasintuitiveandresponsiveastheAppleproject.Thesecondisdataanalysis.ThethirdisMacintoshesontheirdesks—wedesignedasystemmanagingthedisseminationofinformationboththatrunsautomaticallyandessentiallyinvisibly.withinandoutsidethelaboratory.Inadditi

8、onthereisWheneveritisnecessaryfortheinformaticssystemametarequirement:biomedicalresearchprotocolstointeractwithamemberofthelaborato