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ForResearchUseOnly.
Notforuseindiagnosticprocedures.
Copyright2020BionanoGenomicsInc.
AllRightsReservedSaphyrSitePreparationGuideDocumentNumber:30145Revision:KForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage2of18TableofContentsLegalNotice.
3RevisionHistory.
4Chapter1:Introduction5Chapter2:Planning.
6SaphyrSystemOverview.
6HardwareRequirementsandSpecifications7NetworkRequirements10NotCompatiblewithProxyServers11FileStorageRecommendations.
11User-SuppliedMaterials.
11User-SuppliedEquipment.
11User-SuppliedConsumables12AdditionalUser-SuppliedMaterialsforDNAIsolation12AdditionalUser-SuppliedMaterialsforDNALabeling12Chapter3:PreparingforArrival13InstallationGuidelines.
13Dimensions.
13LaboratoryGuidelines.
14LabBenchLayout.
14EnvironmentalConsiderations14Chapter4:PreparingforInstallationandTraining.
15SitePreparationChecklist.
15CrateContents.
15AccessoryKit.
15QualificationKit(Part#90011or90034)16UserTrainingKits(Part#90012–90017,90049)16Chapter5:Post-InstallationFollowUpandResources17AdditionalResources.
17Glossary17TechnicalAssistance18ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage3of18LegalNoticeForResearchUseOnly.
Notforuseindiagnosticprocedures.
ThismaterialisprotectedbyUnitedStatesCopyrightLawandInternationalTreaties.
Unauthorizeduseofthismaterialisprohibited.
Nopartofthepublicationmaybecopied,reproduced,distributed,translated,reverse-engineeredortransmittedinanyformorbyanymedia,orbyanymeans,whethernowknownorunknown,withouttheexpresspriorpermissioninwritingfromBionanoGenomics.
Copying,underthelaw,includestranslatingintoanotherlanguageorformat.
ThetechnicaldatacontainedhereinisintendedforultimatedestinationspermittedbyU.
S.
law.
DiversioncontrarytoU.
S.
lawprohibited.
Thispublicationrepresentsthelatestinformationavailableatthetimeofrelease.
Duetocontinuouseffortstoimprovetheproduct,technicalchangesmayoccurthatarenotreflectedinthisdocument.
BionanoGenomicsreservestherighttomakechangesinspecificationsandotherinformationcontainedinthispublicationatanytimeandwithoutpriornotice.
PleasecontactBionanoGenomicsCustomerSupportforthelatestinformation.
BIONANOGENOMICSDISCLAIMSALLWARRANTIESWITHRESPECTTOTHISDOCUMENT,EXPRESSEDORIMPLIED,INCLUDINGBUTNOTLIMITEDTOTHOSEOFMERCHANTABILITYORFITNESSFORAPARTICULARPURPOSE.
TOTHEFULLESTEXTENTALLOWEDBYLAW,INNOEVENTSHALLBIONANOGENOMICSBELIABLE,WHETHERINCONTRACT,TORT,WARRANTY,ORUNDERANYSTATUTEORONANYOTHERBASISFORSPECIAL,INCIDENTAL,INDIRECT,PUNITIVE,MULTIPLEORCONSEQUENTIALDAMAGESINCONNECTIONWITHORARISINGFROMTHISDOCUMENT,INCLUDINGBUTNOTLIMITEDTOTHEUSETHEREOF,WHETHERORNOTFORESEEABLEANDWHETHERORNOTBIONANOGENOMICSISADVISEDOFTHEPOSSIBILITYOFSUCHDAMAGES.
PatentsProductsofBionanoGenomicsmaybecoveredbyoneormoreU.
S.
orforeignpatents.
TrademarksTheBionanoGenomicslogoandnamesofBionanoGenomicsproductsorservicesareregisteredtrademarksortrademarksownedbyBionanoGenomicsintheUnitedStatesandcertainothercountries.
BionanoGenomics,Irys,IrysView,IrysChip,IrysPrep,IrysSolve,Saphyr,SaphyrChip,BionanoAccess,andBionanoEnFocusTMaretrademarksofBionanoGenomics,Inc.
Allothertrademarksarethesolepropertyoftheirrespectiveowners.
NolicensetouseanytrademarksofBionanoGenomicsisgivenorimplied.
UsersarenotpermittedtousethesetrademarkswithoutthepriorwrittenconsentofBionanoGenomics.
Theuseofthesetrademarksoranyothermaterials,exceptaspermittedherein,isexpresslyprohibitedandmaybeinviolationoffederalorotherapplicablelaws.
Copyright2020BionanoGenomics,Inc.
Allrightsreserved.
ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage4of18RevisionHistoryRevisionReleasedNotesK09/14/2020ComputeOnDemand,CustomServer,SPTissueandTumorKitinformationaddedForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage5of18Chapter1:IntroductionThisdocumentprovidesguidelinesandspecificationstoprepareyoursiteforinstallationandoperationoftheBionanoGenomicsSaphyrSystem.
Pleasereviewtheinformationinthisguidebeforepreparingyoursite.
AuthorizedBionanopersonnelwillassistyouthroughtheinstallationandsamplepreparationprocess.
Thesitepreparationprocesshasfourstages:PreparationStageDescriptionPlanningHardwareandsoftwarerequirementsNetwork,filestorage,andelectricalrequirementsCoordinationofrequirementsbetweentheresearchteam,ITOperations,securitygroups,andanyothergovernanceparties.
User-suppliedmaterialsandequipmentPreparingforInstrumentArrivalInstallationguidelinesLaboratoryguidelinesEnvironmentalconsiderationsPreparingforInstallationandTrainingSitepreparationchecklistsCratecontentsAccessoryandQualificationkitsInstallationandtrainingschedulePostInstallationFollow-UpPreparingforfollow-upreviewThefollowingrolesandresponsibilitiesmustbefollowedtoensureasuccessfulinstallation:RoleResponsibilityBionanoGenomicsFieldServiceEngineer(FSE)CoordinateinstallationdatewiththecustomerPerformfullinstallationandqualificationofSaphyrSystem(InstrumentandAccessServer).
BionanoGenomicsFieldApplicationScientist(FAS)Actascustomerpointofcontact.
Coordinatetrainingdatewiththecustomer.
Arrangesendingtrainingconsumablestothecustomerandensuringthattheyhavearrived.
Trainthecustomerinsamplepreparation,runningtheinstrument,andreviewingdataoutput.
CustomerEnsurethatallrequirementslistedinthisdocumentaremet.
Providealluser-suppliedmaterialslistedinthisdocument.
ITatCustomerSiteRackandconnectSaphyrComputeandBionanoComputeServersProvidestaticIPaddressesasdescribedinthisdocument.
Provideaswitchasdescribedinthisdocument.
ProvideanSSLcertificatefortheBionanoAccessServerForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage6of18Chapter2:PlanningTheplanningstageprovidesguidelinesforconfiguration,networksecurity,andfilestorage.
TheseguidelinesexplaintherequiredinfrastructureforasuccessfulimplementationoftheSaphyrsystemwithinyourorganization.
Successfulplanningrequiresacomprehensivecoordinationbetweenallrelevantpartiesatthesite,suchastheresearchteam,ITOperations,securitygroups,andanyothergovernanceparties.
Itisessentialtoinvolvecomplianceteamsintheprocessasearlyaspossibletoensureefficientinstallation.
SaphyrSystemOverviewTheSaphyrInstrumentcapturesimagesoflabeledDNAmoleculesfromtheSaphyrChip.
TheInstrumentController(whichcontrolsthefunctionoftheSaphyrInstrument)convertstheimagesintomoleculedatafiles(.
bnx)andcomputesreal-timethroughput,moleculeN50,andlabeldensityvalues.
The.
bnxfilesaretransferredtotheBionanoAccessServer,wheremappingmetricsarecalculatedanddisplayedintheInstrumentControlSoftware(ICS)andBionanoAccessdashboards.
Oncethechipruniscomplete,thecompletedmoleculedatafilesareautomaticallyimportedintotheBionanoAccesswebapplication(hostedattheBionanoAccessServer).
Themoleculedatafilescanthenbeusedtoperformvariousbioinformaticsoperationssuchasgeneratingadenovoassembly,rarevariantanalysis,ortargetedFSHDanalysis.
TheCustomerSwitchisolatestrafficfortheComputeServerswhicharedesignedtoworktogetherasaclustertoprocessbioinformaticsjobssubmittedfromtheBionanoAccesswebapplication.
Bionanoalsoofferscloudbasedcomputing(ComputeOnDemand)whichcanbeusedinplaceoflocalcomputeserversortoaugmentlocalcomputeresourcesduringcomputationalpeakperiods.
TheBionanoAccesswebapplicationmonitorstheprogressofeachcomputationjob,capturestheouput,notifiestheuserofcompletion,andallowsthemtoinspecttheresultsintheirbrowserontheCustomerWorkstation.
BionanoComputeOnDemand,apay-per-usecomputingservice,isaccessiblethroughtheBionanoAccessServer,forcomputationneeds.
Figure1:SaphyrSystemConnectivityDiagram1BionanoPurchase2UserProvidedForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage7of18HardwareRequirementsandSpecificationsItisrecommendedthatallSaphyrcomponents(Instrument,SaphyrInstrumentController,BionanoAccessandComputeServers)beconnectedtoauser-supplieduninterruptiblepowersupply(UPS).
Thisrecommendationisforlineconditioningandensuringsufficientpowersupply.
SaphyrInstrumentTypeRequirements/SpecificationsProvidedByBionanoSpaceHeight:38cm(15in)Width:86cm(34in)Depth:71cm(28in)Power100-240VACat50-60HertzPowerConsumption≤300Watts2mlong,IEC60320-C13powercordSaphyrInstrumentController(includedwithinstrumentpurchase)TheInstrumentControllerisdesignedtobelocatedadjacenttotheSaphyrInstrument.
Thetwosystemsaredirectlytetheredforcontrollingtheinstrumentanddirectdatatransferofimagefiles.
TypeRequirements/SpecificationsProvidedByBionanoAccessoriesMonitorKeyboardMouseSoftwareSaphyrInstrumentControllerSoftware(ICS)ChromeGoToAssistClientPuttyFilezillaMemory32GBRAMDataStorage8TB(Ddrive)(x2)256GB(Cdrive)SpaceHeight:46cm(18in)Width:18cm(7in)Depth:47cm(18.
5in)Power100-240VACat50-60HertzPowerConsumption≤300Watts2mlong,IEC60320-C13powercordNetworkOneportisconnectedtotheSaphyrInstrumentat1GBLANconnectioncanbedoneat1GBForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage8of18BionanoAccessServer(includedwithinstrumentpurchase)ThewebserverisdesignedtobelocatedadjacenttotheSaphyrInstrumentController.
Thetwosystemsaredirectlytetheredfordirectdatatransfer.
TypeRequirements/SpecificationsProvidedByBionanoSoftwareCentOSBionanoAccessBionanoToolsPostgresSQLNodejsPerlPythonRDockerMemory128GBRAMDataStorage40TBwithRAIDControllerSpaceHeight:46cm(18in)Width:18cm(7in)Depth:47cm(18.
5in)Power100-240VACat50-60HertzPowerConsumption≤300WattsTheserverisshippedwithaUnitedStatespowercord.
UsersoutsideoftheUnitedStatesarerequiredtosupplya2mlong,countryspecificIEC60320-C13powercord(insomecases,theFSEmaybeabletoprovidethesuitablepowercord).
NetworkOneportisconnectedtotheSaphyrInstrumentcontrollerat10GBLANconnectioncanbedoneat1GBForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage9of18OVERVIEWOFCOMPUTEOPTIONSBionanooffersmultiplesolutionsforprocessingBioinformaticsjobsincludingComputeServersandComputeOn-Demand.
Youmaychooseeitheroptionoracombinationforyourcomputingneeds.
COMPUTESERVERSaphyrComputeServer(additionalpurchase)Thenumberofcomputeserversrequiredforyourinstallationwillbedeterminedbasedonyourcomputerequirementsandenvironmentalconditions.
Thecomputeserversworktogetherasaclustertoperformvariousbioinformaticoperationsincludingdenovoassembly,variantannotation,andscaffoldingtonameafew.
EachcomputeclustermusthaveatleastoneSaphyrComputewhichservesastheheadnodewithstorageandtheSGEmasterinstalled.
AdditionalBionanoComputesareaddedtoscaletheclustertofityourspecificdemands.
AsingleBionanoAccessServercanbeconfiguredtointeractwithmultiplecomputeclustersifrequired.
TypeRequirements/SpecificationsProvidedByBionano(additionalpurchase)SoftwareCentOSPythonPerlRSonofGridEngine(SGE)DockerSpace2Urackmountserver(tobeprovidedbycustomer)RailsandcordssuppliedwithserverPowerDual2000Wpowersupplies(Recommended:APCSmart-UPS3000VALCDRM2UUPS-rackmounted)26'NEMA5-15PtoIEC320-C13powercables.
UsersoutsideoftheUnitedStatesarerequiredtosupplytwo2mlong,countryspecificIEC60320-C13powercord(insomecases,theFSEmaybeabletoprovidethesuitablepowercord).
Network5X1GBEthernetconnectionBionanoComputeServers(additionalpurchase)Ourrecommendedconfigurationincludes,atleast,oneBionanoComputeServer.
YoumusthaveatleastoneSaphyrComputeServerbeforeaddinganyBionanoComputesystems.
TypeRequirements/SpecificationsProvidedByBionano(additionalpurchase)SoftwareCentOSPythonPerlRSonofGridEngine(SGE)Space2Urackmountserver(tobeprovidedbycustomer)RailsandcordssuppliedwithserverPowerDual2000Wpowersupplies(Recommended:APCSmart-UPS3000VALCDRM2UUPS-rackmounted)26'NEMA5-15PtoIEC320-C13powercables.
UsersoutsideoftheUnitedStatesarerequiredtosupplytwo2mlong,countryspecificIEC60320-C13powercord(insomecases,theFSEmaybeabletoprovidethesuitablepowercord).
Network5X1GBEthernetconnectionCAUTION:Donotattachthepowercordtoanextensioncord,powerstriporsurgeprotector.
ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage10of18Switch(customerprovided)TypeRequirements/SpecificationsProvidedByCustomerHardware24-portGB,Layer2+SwitchRack-mountableNETGEARswitchisrecommendedCustomComputeServer(customerprovided)Thebioinformaticspipelinesmayalsoworkoncustomclusters;however,customconfigurationswillbeneeded.
PleaseconsultBionanoformoredetails.
COMPUTEON-DEMAND(additionalpurchase)Apay-per-usesolution(tokens)isaccessiblethroughBionanoAccess.
Itcanbeusedtoperformdenovoassembly,variantannotation,hybridscaffolding,andotherbioinformaticspipelinefunctionsindependentoftheComputeServers.
RefertotheBionanoAccessSoftwareUserGuide(P/N30142)foradditionalinformationaboutconfiguringComputeOnDemand,theBionanoGenomicsDataSecurityGuidelines(P/N30292)forTermsandConditions,andtheBionanoComputeOnDemandReleaseNotes(P/N30293).
NetworkRequirementsThecomponentsintheSaphyrsystemrequirenetworkconnectivitytocommunicatewitheachother.
PoornetworkreliabilityorthroughputcanaffecttheperformanceofyourSaphyrsystem.
TheBionanoAccessServerhasatetheredconnectiontotheSaphyrInstrumentController.
OriginatingFromTargetProtocolSaphyrInstrumentControllerBionanoAccessServerSSH(port22)BionanoAccessServerComputeserversSSH(port22)SCP(port22)BionanoAccessServerEmailserverSMTP(port25)InstrumentController,workstations,andcomputeserversBionanoAccessServerHTTPS*(defaultport3006)*EnableusingavalidSSLcertificateBionanoAccessisinstalledontheBionanoAccessServerandisaccessibleviastandardwebbrowsersfromworkstationsconnectedtothesamenetwork.
Userscanperformvariousactivities,suchasgeneratingexperiments,monitoringinstrumentandrunstatus,performingandsharinganalyses(whenproperlyconfiguredwithBionanocomputationservers),byloggingintoBionanoAccessviaawebbrowser.
OurrecommendedwebbrowserisChrome.
TheSaphyrInstrumentControllershouldenablescreen-sharingsessionswithBionanoifremotesupportisdesired.
ThedefaultconfigurationrequirestwostaticIPaddresses.
OneisfortheBionanoAccessServerinthelabandoneisfortheSaphyrComputeServerinthedatacenter.
Sometimesthelabandthedatacenterareondifferentsubnets.
ThetwoIPaddressesprovidedneedtobeaccessibletoeachother.
Theremainingcomputenodeswillbeonaseparatecustomsubnet.
TheSaphyr1anodewillbedualhomed.
ItwillhaveonestaticIPaccessibletotheBionanoAccessserverandoneIPaddressonthesubnetwiththeothercomputenodes.
IProutingwillbeusedonSaphyr1atodirectresponsesfromthecomputenodesbacktotheBionanoAccessServer.
EachcomputenodealsohasaseparateIPMIport.
IfyouwanttohaveyourIPMItrafficonaseparatenetworkplanforanadditionalconnectionforeachcomputenode.
Eachcomputeserverhasfournodes.
ForamoresecureinstallationitispossibletoswitchfromHTTPtoHTTPScommunication.
ThecustomermustprovideandinstalltheSSLcertificatesothatitisobtainedbytheappropriatepartiesforthatspecificinstallationForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage11of18andorganization.
Duringinstallation,wealwaysconfirminitialinstallationusingHTTPandthenaddtheSSLcertificateonceinitialoperationhasbeenconfirmed.
Theuseofselfsignedcertificatesisnotsupported.
NotCompatiblewithProxyServersBionanoAccessisnotcompatiblewithproxyserversandshouldbeexcludedonalluserworkstationsfromproxyrequirements.
Proxyserverswilloftencacheresultsandpreventdynamicpagessuchasthedashboardfromupdatingproperly.
FileStorageRecommendationsBydefault,theInstrumentControllerdoesnotsaveimagedata.
Usersmaychoosetosavetherawimagesduringrunsetupstagepriortostartingtheirrun.
Ifthisoptionischosen,amaximumofonechipcanberunbeforetheimagedataneedstobedeletedortransferredmanually.
SeeSaphyrSystemUserGuide(P/N30247)fordetails.
Ifyouwanttoarchiveorretainrawimagesforaperiodoftime,werecommendthatyouarchiveimagestoafileserveraftereachrun.
ThecustomerisresponsibleforarchivingandbackinguprawimagesfromtheSaphyrInstrumentControllerifdesired(butthisisnotrequired).
TheBionanoAccessServerwillstoreresultfilessuchasmoleculedatafiles(BNX)anddenovoassemblies.
Thisdatawillcontinuetogrowovertime.
TheBionanoAccessServerhasbeenconfiguredtohavesufficientfilestorageforseveralyears.
WehighlyrecommendthatallcontentintheAccessInstallationfolderisbackeduponaregularbasis.
DependingonsystemutilizationyoumayneedtotransitiontoanenterprisestoragesolutionifyouexceedthecapacityoftheBionanoAccessServer.
Alternatively,userscanexportandarchiveunusedprojectsperiodically.
SeeBionanoAccessUserGuide(P/N30142)fordetails.
User-SuppliedMaterialsThefollowinguser-suppliedmaterialsarerequiredforalltypesofsamplepreparationtraining.
Additional,protocol-specificmaterialsarereferredtoonsubsequentpages.
ConfirmwithyourFASwhenyouhaveallthecorrespondingconsumablesandequipmentavailablebeforeschedulingyourtraining.
User-SuppliedEquipmentEquipmentSupplierCatalog#QubitFluorometerThermoFisherQ33216orsimilarMicrocentrifuge,refrigeratedGenerallabsupplierPipettes(2,10,20,200,and1000μl)Note:lighttouchpipettesarenotcompatibleGenerallabsupplierIcebucketandiceGenerallabsupplierVortexerGenerallabsupplierThermalCyclerwithHeatedLid(10°Caboveblocktemp)Generallabsupplier4°Crefrigeratorand-20°CfreezerGenerallabsupplier-20°CEnzymeBlockGenerallabSupplier4°CAluminumCoolingTubeBlockSigmaAldrichZ740270orsimilarPositive-displacementpipetteMR-10(recommended)Rainin17008575orsimilarBathSonicator(optional)GeneralLabSupplierForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage12of18User-SuppliedConsumablesConsumableSupplierCatalog#ProteinaseKenzyme,Puregene,5mlQiagen158920PCRtubes,thin-walled,DNase-free,0.
2mlThermoFisherAM12225orsimilarQubitBroadRange(BR)dsDNAAssayKitThermoFisherQ32853QubitHighSensitivity(HS)dsDNAKit(recommended)ThermoFisherQ32851QubitAssayTubesThermoFisherorAxygenQ32856or10011-830UltraPurenuclease-freewaterThermoFisher10977015Microcentrifugetubes,0.
5ml,amber,nuclease-freeUSAScientific1605-0007Microcentrifugetubes,1.
5mlVWR87003-294Pipettetips,aerosol-resistant2,10,20,200,and1000μlGenerallabsupplierPipettetips,10μl,C-10forpos.
displacement(recommended)Rainin17008604AdditionalUser-SuppliedMaterialsforDNAIsolationThefollowingprotocolslistmaterialsrequiredforextractingDNAfromvaryingsources.
FASwillhighlighttherequiredmaterialsdependingonsampletypeandprotocolchoice.
Ensurethatyouhavetheappropriatematerialsavailableontrainingday.
IntheUserTrainingKit(seedetailsinChapter4),Bionanoprovides1DNAIsolationKit,percustomers'request.
SampleTypeProtocolHumanCellCultureBionanoPrepSPFreshCellsDNAIsolationProtocol(P/N30257)*BionanoPrepSPFrozenCellPelletDNAIsolationProtocol(P/N30268)*BionanoPrepCellCultureDNAIsolationProtocol(P/N30026)HumanBloodBionanoPrepSPFreshHumanBloodDNAIsolationProtocol(P/N30258)*BionanoPrepSPFrozenHumanBloodDNAIsolationProtocol(P/N30246)*BionanoPrepBloodDNAIsolationProtocol(P/N30033)BionanoPrepFrozenBloodProtocol(P/N30215)BoneMarrowAspiratesBionanoPrepSPBMADNAIsolationProtocol(P/N30298)*AnimalTissueBionanoPrepSPTissueandTumorDNAIsolationProtocol(P/N30339)*BionanoPrepAnimalTissueDNAIsolationFibrousTissueProtocol(P/N30071)BionanoPrepAnimalTissueDNAIsolationSoftTissueProtocol(P/N30077)PlantTissueBionanoPrepPlantTissueDNAIsolationBaseProtocol(P/N30068)*BionanoPrepPlantTissueDNAIsolationHighPolysaccharideProtocol(P/N30128)*BionanoPrepPlantTissueDNAIsolationHighPolyphenolProtocol(P/N30133)*BionanoPrepPlantTissueDNAIsolationLiquidNitrogenGrindingProtocol(P/N30177)*BacterialBionanoPrepCellCultureDNAIsolationProtocol(P/N30026)*Referstomostrecentproductreleaseforthatsampletype.
SPisrecommendedformostsampletypes.
AdditionalUser-SuppliedMaterialsforDNALabelingThefollowingprotocolslistmaterialsrequiredforlabelinggenomicDNA.
FASwillhighlighttherequiredmaterialsdependingonlabelingtype.
Ensurethatyouhavetheappropriatematerialsavailableontrainingday.
IntheUserTrainingKit(seedetailsinChapter4),Bionanoprovides1DNALabelingKit,percustomers'request.
LabelingMethodProtocolDirectLabelandStain(DLS)BionanoPrepDirectLabelandStain(DLS)(P/N30206)*Nick,Label,Repair,andStain(NLRS)BionanoPrepLabelingNLRSProtocol(P/N30024)*Referstomostrecentproductreleaseforthatsampletype.
DLSisrecommendedwhenlabeldensityfallswithinoptimalrange.
ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage13of18Chapter3:PreparingforArrivalInstallationGuidelinesAnauthorizedserviceproviderdeliversthesystem.
Makesurethatthecrateisstoredsecurelyneartheinstallationlabbench.
Theinstrumenthastwotip-tiltindicatorsmountedtotheoutsideofthecrateaswellasoneimpact-shockindicator.
PleaseinspecttheexteriorofthecratefordamageandinformyourFSEifeitheroneofthetwotip-tiltsensors,ortheshock-impactsensorshavebeentriggered.
Figure2:(fromlefttoright)shock-impactsensors(un-triggeredandtriggered)andtip-tiltsensors(un-triggeredandtriggered)CAUTION:OnlyaBionanoFieldServiceEngineer(orpersonnelapprovedbyBionano)canuncrateandinstalltheinstrument.
Atleastthreeweeksbeforeinstallation,confirmwithyourFieldApplicationScientist(FAS)thatyouhavetherequiredconsumablesandequipment.
Ensurethatthelabspaceandbencharereadyforinstallation.
Ensurethatyouhaveapalletjacktosupportthecrateandinstrument.
EnsurethereareatleastthreepeopletoassisttheFSEwithliftingSaphyrinstrument.
InstalltheSaphyrComputeServerandBionanoComputeServer(s)inthedatacenter.
EnsurethatIPaddressesandallnetworkrequirementshavebeenmetasdescribedintheNetworkRequirementssectionabove.
DimensionsMeasurementInstrumentCratesHeight38cm(15in)152cm(60in)Total[~81cm(32in)forTopaccessorycrate+~74cm(29in)forInstrumentcrate]Width86cm(34in)109cm(43in)forTopaccessorycrateandInstrumentcrateDepth71cm(28in)81cm(32in)[~74cm(29in)forTopaccessorycrate,~81cm(32in)forInstrumentcrate]Weight103kg(227lb)254kg(560lbs)[Topaccessorycrateincludingcontroller,monitor,server,andaccessorykit+Instrumentcrateincludinginstrument]ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage14of18LaboratoryGuidelinesPrepareaclean,levelsurfacesuchasasturdylabbenchfortheinstrument.
Keeptheinstrumentawayfromdirectsunlightorheatsource.
Donotplacetheinstrumentonalabbenchthathasliquidsorchemicals.
Donotplaceanyotherequipmentonthebenchthatcouldproducevibrations,includingcentrifuges,compressors,andshakers.
Donotplacetheinstrumentonornearobjectsthatcanproducevibrations,suchasheavydoors.
Donotplaceobjectsontopoftheinstrument.
LabBenchLayoutPositiontheinstrumenttoallowproperventilationandaccesstothepowerswitchandpoweroutlet.
AccessMinimumClearanceLabBenchSpaceAllowatleast150cm(59in)wideby77cm(30in)depth.
TopAllowatleast93cm(37in)abovetheinstrument.
BackAllowatleast5cm(2in)behindtheinstrument.
SidesAllowatleast15cm(6in)oneachsideoftheinstrument.
Connections4standardelectricaloutlets(100~240VAC)andtwo1GBEthernetportCAUTION:Movingtheinstrumentcancompromisedataintegrity.
Insufficientoverheadclearancecandamagethestageaccessdoorandaffectrunperformance.
TheSaphyrInstrumentControllermustbeplacedwithin1m(3ft)oftheinstrument.
EnvironmentalConsiderationsThisinstrumentisdesignedforindooruseonly.
ElementSpecificationTemperatureMaintainalabtemperatureof19°C(66°F)to25°C(77°F).
HumidityMaintainanoncondensingrelativehumiditybetween20–80%.
ElevationPlacetheinstrumentatanaltitudebelow2,000m(6,500ft)abovesealevel.
VentilationAtleast5cm(2in)ofclearancebehindtheinstrumenttoallowproperventilationandaccesstopoweroutlet.
Overheadclearancerequiredforinstallationandserviceis93cm(37inch).
AirQualityOperatetheinstrumentinaPollutionDegreeIIenvironmentorbetterasdefinedbytheInternationalElectrotechnicalCommision(IEC).
ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage15of18Chapter4:PreparingforInstallationandTrainingSitePreparationChecklistEnsurethatyourfacilityisreadyforthedeliveryofthecrate.
Ensurethatyouhavetheappropriateequipmenttosupportthecrateandinstrument(e.
g.
,palletjack).
Ensurethatallrequiredpersonnelarepresentonthescheduledinstallationday(atleastthreepeopletoassisttheFSEwithliftingSaphyrinstrument).
EnsurethatyouhavereceivedandproperlystoredthecontentsintheQualificationKitandAccessoryKit.
Verifythatyoursitehaspropercomputing,network,filestorage,andelectricalrequirements.
CrateContentsItemContentStorageTemperatureInstrument1each15–25°C(59–77°F)Monitor1each15–25°C(59–77°F)Keyboard1each15–25°C(59–77°F)Mouse1each15–25°C(59–77°F)InstrumentController1each15–25°C(59–77°F)BionanoAccessServer1each15–25°C(59–77°F)AccessoryKit1each15–25°C(59–77°F)TheFSEwillunpackthecrateduringtheinstallationvisit.
ComputeServerswillshipinadditionalcrate(StorageTemperature:15–25°C(59–77°F)).
AccessoryKitTheAccessoryKitisincludedinthecrate.
ItemContentStorageTemperatureUS-SpecificPowerCord3each15–25°C(59–77°F)SaphyrChipClip2clips15–25°C(59–77°F)DisplayPortCable1each15–25°C(59–77°F)NetworkCable(Cat3)4each15–25°C(59–77°F)SerialCable(M/F)1each15–25°C(59–77°F)USB2.
0AtoBConnector1each15–25°C(59–77°F)USB3.
0AtoBConnector1each15–25°C(59–77°F)AirFilter3each15–25°C(59–77°F)Sparkle,OpticalCleaner1each15–25°C(59–77°F)LensCleaningPaper2each15–25°C(59–77°F)Mousepad1each15–25°C(59–77°F)ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage16of18QualificationKit(Part#90011or90034)TheSaphyrSystemQualificationKitwillbecoordinatedbyyourFSEtoarriveapproximatelyonetothreeweeksbeforeinstallation.
ItemPart#ContentStorageSaphyrChipG2.
320366or203193each4°CDLSBiologicalControlA,100μl204002each4°CSPLargeGenomeLabelingControl.
5000ng+203991each4°C+Thiscontrolwillbeusedfortraining.
UserTrainingKits(Part#90012–90017,90049)TheSaphyrSystemUserTrainingKitwillbecoordinatedbyyourFAStoarriveapproximatelyonetothreeweeksbeforetrainingbegins.
Itwillcontainacombinationof:1)aDNALabelingKit,2)aDNAIsolationKit.
SaphyrChips&ControlwillbeprovidedwiththeQualificationKit,and3)20tokens(ifCompute-On-Demandwillbeused)CoordinatewithyourFAStosendtheproperLabelingKitandIsolationKitcombinationaslistedbyreferencingoneofthepartnumbersbelow(90012–90017,90049)fordelivery:Part#90049*-DLSLabeling+SPBloodandCellDNAIsolation+BionanoPrepSPMagneticRetrieverPart#90016-DLSLabeling+AnimalTissueDNAIsolationPart#90017-DLSLabeling+PlantTissueDNAIsolation*AccessoriesfortheSPBMADNAIsolationKitorSPTissueandTumorDNAIsolationKitcanbeincludeduponrequestPart#90012-NLRSLabeling+BloodandCellCultureDNAIsolationPart#90013-NLRSLabeling+AnimalTissueDNAIsolationPart#90014-NLRSLabeling+PlantTissueDNAIsolation1)LabelingKitTraining:NLRSKitorDLSKitThetableindicatesthecontentstobeexpecteddependingonwhichoneofthelabelingkitsthatisrequestedfortraining.
LabelingTrainingKitPart#Content#ofBoxesStorageBionanoPrepDLSLabelingKit800051each(10rxn)3-20°C,4°C,RTBionanoPrepNLRSLabelingKit800011each(10rxn)24°C,-20°C2)DNAIsolationTrainingKit:Blood&CellCulture,SPBlood&Cell,AnimalTissueorPlantTissueChooseoneoftheDNAisolationkitsbelowtobeusedduringtraining.
DNAIsolationTrainingKitsPart#Content#ofBoxesStorageSPBlood&CellCultureDNAIsolationKit800301each(10rxn)24°C,RTBlood&CellCultureDNAIsolationKit800041each(10rxn)1RTSPTissueandTumorDNAIsolationKit800381each(10rxn)1RTAnimalTissueDNAIsolationKit800021each(10rxn)1RTPlantTissueDNAIsolationKit800031each(5rxn)24°C,RT3)20tokensforComputeOn-DemandCustomersForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage17of18Chapter5:Post-InstallationFollowUpandResourcesAfteryouhavecompletedthetraining,youwillhaveafollow-upreviewmeetingwithyourFAS.
Thereviewmeetingisusuallyintheformatofaconferencecall.
Forthereview,preparetoprovidethefollowing:DataproducedfromyourfirstrunwithouttheFASonsite.
Listofcustomizationrequestsfortheinstrumentandsoftware.
Listofquestions,concerns,andissues,suchasyourlevelofcomfort,comprehension,andconfidenceonusingtheSaphyrsystem.
AdditionalResourcesThefollowingdocumentationisavailablefordownloadfromtheBionanoSupportpage.
ResourceDescriptionSaphyrSystemSafetyGuide(P/N30253)Providesinformationabouttheinstrumentsafetyconsiderations.
SaphyrSystemUserGuide(P/N30247)Providesanoverviewofinstrumentcomponentsandsoftware,propermaintenance,andtroubleshooting.
BionanoAccessSoftwareGuide(P/N30142)Providesanoverviewofdataanalysis.
BionanoGenomicsDataSecurityGuidelines(P/N30292)ProvidessecurityguidelinesforComputeOnDemandusage.
GlossaryTermDefinitionCIFSCommonInternetFileSystemFASFieldApplicationScientistFSEFieldServiceEngineerGBGigabyteHTTPHypertextTransferProtocolHTTPSHypertextTransferProtocolSecureOSOperatingsystemSGEjobsSonofGridEnginejobsSSDSolid-statedriveSFTPSecureFileTransferProtocolSMTPSimpleMailTransferProtocolSSHSecureShellTBTerabyteIECInternationalElectrotechnicalCommisionForResearchUseOnly.
Notforuseindiagnosticprocedures.
TechnicalAssistanceFortechnicalassistance,contactBionanoGenomicsTechnicalSupport.
YoucanretrievedocumentationonBionanoproducts,SDS's,certificatesofanalysis,andotherrelateddocumentsfromtheSupportwebsiteorbyrequestthroughe-mailandtelephone.
TypeContactEmailsupport@bionanogenomics.
comPhoneHoursofOperation:MondaythroughFriday,9:00a.
m.
to5:00p.
m.
,PSTUS:+1(858)888-7663Websitewww.
bionanogenomics.
com/supportBionanoGenomics,Inc.
9540TowneCentreDrive,Suite100SanDiego,CA92121
Notforuseindiagnosticprocedures.
Copyright2020BionanoGenomicsInc.
AllRightsReservedSaphyrSitePreparationGuideDocumentNumber:30145Revision:KForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage2of18TableofContentsLegalNotice.
3RevisionHistory.
4Chapter1:Introduction5Chapter2:Planning.
6SaphyrSystemOverview.
6HardwareRequirementsandSpecifications7NetworkRequirements10NotCompatiblewithProxyServers11FileStorageRecommendations.
11User-SuppliedMaterials.
11User-SuppliedEquipment.
11User-SuppliedConsumables12AdditionalUser-SuppliedMaterialsforDNAIsolation12AdditionalUser-SuppliedMaterialsforDNALabeling12Chapter3:PreparingforArrival13InstallationGuidelines.
13Dimensions.
13LaboratoryGuidelines.
14LabBenchLayout.
14EnvironmentalConsiderations14Chapter4:PreparingforInstallationandTraining.
15SitePreparationChecklist.
15CrateContents.
15AccessoryKit.
15QualificationKit(Part#90011or90034)16UserTrainingKits(Part#90012–90017,90049)16Chapter5:Post-InstallationFollowUpandResources17AdditionalResources.
17Glossary17TechnicalAssistance18ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage3of18LegalNoticeForResearchUseOnly.
Notforuseindiagnosticprocedures.
ThismaterialisprotectedbyUnitedStatesCopyrightLawandInternationalTreaties.
Unauthorizeduseofthismaterialisprohibited.
Nopartofthepublicationmaybecopied,reproduced,distributed,translated,reverse-engineeredortransmittedinanyformorbyanymedia,orbyanymeans,whethernowknownorunknown,withouttheexpresspriorpermissioninwritingfromBionanoGenomics.
Copying,underthelaw,includestranslatingintoanotherlanguageorformat.
ThetechnicaldatacontainedhereinisintendedforultimatedestinationspermittedbyU.
S.
law.
DiversioncontrarytoU.
S.
lawprohibited.
Thispublicationrepresentsthelatestinformationavailableatthetimeofrelease.
Duetocontinuouseffortstoimprovetheproduct,technicalchangesmayoccurthatarenotreflectedinthisdocument.
BionanoGenomicsreservestherighttomakechangesinspecificationsandotherinformationcontainedinthispublicationatanytimeandwithoutpriornotice.
PleasecontactBionanoGenomicsCustomerSupportforthelatestinformation.
BIONANOGENOMICSDISCLAIMSALLWARRANTIESWITHRESPECTTOTHISDOCUMENT,EXPRESSEDORIMPLIED,INCLUDINGBUTNOTLIMITEDTOTHOSEOFMERCHANTABILITYORFITNESSFORAPARTICULARPURPOSE.
TOTHEFULLESTEXTENTALLOWEDBYLAW,INNOEVENTSHALLBIONANOGENOMICSBELIABLE,WHETHERINCONTRACT,TORT,WARRANTY,ORUNDERANYSTATUTEORONANYOTHERBASISFORSPECIAL,INCIDENTAL,INDIRECT,PUNITIVE,MULTIPLEORCONSEQUENTIALDAMAGESINCONNECTIONWITHORARISINGFROMTHISDOCUMENT,INCLUDINGBUTNOTLIMITEDTOTHEUSETHEREOF,WHETHERORNOTFORESEEABLEANDWHETHERORNOTBIONANOGENOMICSISADVISEDOFTHEPOSSIBILITYOFSUCHDAMAGES.
PatentsProductsofBionanoGenomicsmaybecoveredbyoneormoreU.
S.
orforeignpatents.
TrademarksTheBionanoGenomicslogoandnamesofBionanoGenomicsproductsorservicesareregisteredtrademarksortrademarksownedbyBionanoGenomicsintheUnitedStatesandcertainothercountries.
BionanoGenomics,Irys,IrysView,IrysChip,IrysPrep,IrysSolve,Saphyr,SaphyrChip,BionanoAccess,andBionanoEnFocusTMaretrademarksofBionanoGenomics,Inc.
Allothertrademarksarethesolepropertyoftheirrespectiveowners.
NolicensetouseanytrademarksofBionanoGenomicsisgivenorimplied.
UsersarenotpermittedtousethesetrademarkswithoutthepriorwrittenconsentofBionanoGenomics.
Theuseofthesetrademarksoranyothermaterials,exceptaspermittedherein,isexpresslyprohibitedandmaybeinviolationoffederalorotherapplicablelaws.
Copyright2020BionanoGenomics,Inc.
Allrightsreserved.
ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage4of18RevisionHistoryRevisionReleasedNotesK09/14/2020ComputeOnDemand,CustomServer,SPTissueandTumorKitinformationaddedForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage5of18Chapter1:IntroductionThisdocumentprovidesguidelinesandspecificationstoprepareyoursiteforinstallationandoperationoftheBionanoGenomicsSaphyrSystem.
Pleasereviewtheinformationinthisguidebeforepreparingyoursite.
AuthorizedBionanopersonnelwillassistyouthroughtheinstallationandsamplepreparationprocess.
Thesitepreparationprocesshasfourstages:PreparationStageDescriptionPlanningHardwareandsoftwarerequirementsNetwork,filestorage,andelectricalrequirementsCoordinationofrequirementsbetweentheresearchteam,ITOperations,securitygroups,andanyothergovernanceparties.
User-suppliedmaterialsandequipmentPreparingforInstrumentArrivalInstallationguidelinesLaboratoryguidelinesEnvironmentalconsiderationsPreparingforInstallationandTrainingSitepreparationchecklistsCratecontentsAccessoryandQualificationkitsInstallationandtrainingschedulePostInstallationFollow-UpPreparingforfollow-upreviewThefollowingrolesandresponsibilitiesmustbefollowedtoensureasuccessfulinstallation:RoleResponsibilityBionanoGenomicsFieldServiceEngineer(FSE)CoordinateinstallationdatewiththecustomerPerformfullinstallationandqualificationofSaphyrSystem(InstrumentandAccessServer).
BionanoGenomicsFieldApplicationScientist(FAS)Actascustomerpointofcontact.
Coordinatetrainingdatewiththecustomer.
Arrangesendingtrainingconsumablestothecustomerandensuringthattheyhavearrived.
Trainthecustomerinsamplepreparation,runningtheinstrument,andreviewingdataoutput.
CustomerEnsurethatallrequirementslistedinthisdocumentaremet.
Providealluser-suppliedmaterialslistedinthisdocument.
ITatCustomerSiteRackandconnectSaphyrComputeandBionanoComputeServersProvidestaticIPaddressesasdescribedinthisdocument.
Provideaswitchasdescribedinthisdocument.
ProvideanSSLcertificatefortheBionanoAccessServerForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage6of18Chapter2:PlanningTheplanningstageprovidesguidelinesforconfiguration,networksecurity,andfilestorage.
TheseguidelinesexplaintherequiredinfrastructureforasuccessfulimplementationoftheSaphyrsystemwithinyourorganization.
Successfulplanningrequiresacomprehensivecoordinationbetweenallrelevantpartiesatthesite,suchastheresearchteam,ITOperations,securitygroups,andanyothergovernanceparties.
Itisessentialtoinvolvecomplianceteamsintheprocessasearlyaspossibletoensureefficientinstallation.
SaphyrSystemOverviewTheSaphyrInstrumentcapturesimagesoflabeledDNAmoleculesfromtheSaphyrChip.
TheInstrumentController(whichcontrolsthefunctionoftheSaphyrInstrument)convertstheimagesintomoleculedatafiles(.
bnx)andcomputesreal-timethroughput,moleculeN50,andlabeldensityvalues.
The.
bnxfilesaretransferredtotheBionanoAccessServer,wheremappingmetricsarecalculatedanddisplayedintheInstrumentControlSoftware(ICS)andBionanoAccessdashboards.
Oncethechipruniscomplete,thecompletedmoleculedatafilesareautomaticallyimportedintotheBionanoAccesswebapplication(hostedattheBionanoAccessServer).
Themoleculedatafilescanthenbeusedtoperformvariousbioinformaticsoperationssuchasgeneratingadenovoassembly,rarevariantanalysis,ortargetedFSHDanalysis.
TheCustomerSwitchisolatestrafficfortheComputeServerswhicharedesignedtoworktogetherasaclustertoprocessbioinformaticsjobssubmittedfromtheBionanoAccesswebapplication.
Bionanoalsoofferscloudbasedcomputing(ComputeOnDemand)whichcanbeusedinplaceoflocalcomputeserversortoaugmentlocalcomputeresourcesduringcomputationalpeakperiods.
TheBionanoAccesswebapplicationmonitorstheprogressofeachcomputationjob,capturestheouput,notifiestheuserofcompletion,andallowsthemtoinspecttheresultsintheirbrowserontheCustomerWorkstation.
BionanoComputeOnDemand,apay-per-usecomputingservice,isaccessiblethroughtheBionanoAccessServer,forcomputationneeds.
Figure1:SaphyrSystemConnectivityDiagram1BionanoPurchase2UserProvidedForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage7of18HardwareRequirementsandSpecificationsItisrecommendedthatallSaphyrcomponents(Instrument,SaphyrInstrumentController,BionanoAccessandComputeServers)beconnectedtoauser-supplieduninterruptiblepowersupply(UPS).
Thisrecommendationisforlineconditioningandensuringsufficientpowersupply.
SaphyrInstrumentTypeRequirements/SpecificationsProvidedByBionanoSpaceHeight:38cm(15in)Width:86cm(34in)Depth:71cm(28in)Power100-240VACat50-60HertzPowerConsumption≤300Watts2mlong,IEC60320-C13powercordSaphyrInstrumentController(includedwithinstrumentpurchase)TheInstrumentControllerisdesignedtobelocatedadjacenttotheSaphyrInstrument.
Thetwosystemsaredirectlytetheredforcontrollingtheinstrumentanddirectdatatransferofimagefiles.
TypeRequirements/SpecificationsProvidedByBionanoAccessoriesMonitorKeyboardMouseSoftwareSaphyrInstrumentControllerSoftware(ICS)ChromeGoToAssistClientPuttyFilezillaMemory32GBRAMDataStorage8TB(Ddrive)(x2)256GB(Cdrive)SpaceHeight:46cm(18in)Width:18cm(7in)Depth:47cm(18.
5in)Power100-240VACat50-60HertzPowerConsumption≤300Watts2mlong,IEC60320-C13powercordNetworkOneportisconnectedtotheSaphyrInstrumentat1GBLANconnectioncanbedoneat1GBForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage8of18BionanoAccessServer(includedwithinstrumentpurchase)ThewebserverisdesignedtobelocatedadjacenttotheSaphyrInstrumentController.
Thetwosystemsaredirectlytetheredfordirectdatatransfer.
TypeRequirements/SpecificationsProvidedByBionanoSoftwareCentOSBionanoAccessBionanoToolsPostgresSQLNodejsPerlPythonRDockerMemory128GBRAMDataStorage40TBwithRAIDControllerSpaceHeight:46cm(18in)Width:18cm(7in)Depth:47cm(18.
5in)Power100-240VACat50-60HertzPowerConsumption≤300WattsTheserverisshippedwithaUnitedStatespowercord.
UsersoutsideoftheUnitedStatesarerequiredtosupplya2mlong,countryspecificIEC60320-C13powercord(insomecases,theFSEmaybeabletoprovidethesuitablepowercord).
NetworkOneportisconnectedtotheSaphyrInstrumentcontrollerat10GBLANconnectioncanbedoneat1GBForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage9of18OVERVIEWOFCOMPUTEOPTIONSBionanooffersmultiplesolutionsforprocessingBioinformaticsjobsincludingComputeServersandComputeOn-Demand.
Youmaychooseeitheroptionoracombinationforyourcomputingneeds.
COMPUTESERVERSaphyrComputeServer(additionalpurchase)Thenumberofcomputeserversrequiredforyourinstallationwillbedeterminedbasedonyourcomputerequirementsandenvironmentalconditions.
Thecomputeserversworktogetherasaclustertoperformvariousbioinformaticoperationsincludingdenovoassembly,variantannotation,andscaffoldingtonameafew.
EachcomputeclustermusthaveatleastoneSaphyrComputewhichservesastheheadnodewithstorageandtheSGEmasterinstalled.
AdditionalBionanoComputesareaddedtoscaletheclustertofityourspecificdemands.
AsingleBionanoAccessServercanbeconfiguredtointeractwithmultiplecomputeclustersifrequired.
TypeRequirements/SpecificationsProvidedByBionano(additionalpurchase)SoftwareCentOSPythonPerlRSonofGridEngine(SGE)DockerSpace2Urackmountserver(tobeprovidedbycustomer)RailsandcordssuppliedwithserverPowerDual2000Wpowersupplies(Recommended:APCSmart-UPS3000VALCDRM2UUPS-rackmounted)26'NEMA5-15PtoIEC320-C13powercables.
UsersoutsideoftheUnitedStatesarerequiredtosupplytwo2mlong,countryspecificIEC60320-C13powercord(insomecases,theFSEmaybeabletoprovidethesuitablepowercord).
Network5X1GBEthernetconnectionBionanoComputeServers(additionalpurchase)Ourrecommendedconfigurationincludes,atleast,oneBionanoComputeServer.
YoumusthaveatleastoneSaphyrComputeServerbeforeaddinganyBionanoComputesystems.
TypeRequirements/SpecificationsProvidedByBionano(additionalpurchase)SoftwareCentOSPythonPerlRSonofGridEngine(SGE)Space2Urackmountserver(tobeprovidedbycustomer)RailsandcordssuppliedwithserverPowerDual2000Wpowersupplies(Recommended:APCSmart-UPS3000VALCDRM2UUPS-rackmounted)26'NEMA5-15PtoIEC320-C13powercables.
UsersoutsideoftheUnitedStatesarerequiredtosupplytwo2mlong,countryspecificIEC60320-C13powercord(insomecases,theFSEmaybeabletoprovidethesuitablepowercord).
Network5X1GBEthernetconnectionCAUTION:Donotattachthepowercordtoanextensioncord,powerstriporsurgeprotector.
ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage10of18Switch(customerprovided)TypeRequirements/SpecificationsProvidedByCustomerHardware24-portGB,Layer2+SwitchRack-mountableNETGEARswitchisrecommendedCustomComputeServer(customerprovided)Thebioinformaticspipelinesmayalsoworkoncustomclusters;however,customconfigurationswillbeneeded.
PleaseconsultBionanoformoredetails.
COMPUTEON-DEMAND(additionalpurchase)Apay-per-usesolution(tokens)isaccessiblethroughBionanoAccess.
Itcanbeusedtoperformdenovoassembly,variantannotation,hybridscaffolding,andotherbioinformaticspipelinefunctionsindependentoftheComputeServers.
RefertotheBionanoAccessSoftwareUserGuide(P/N30142)foradditionalinformationaboutconfiguringComputeOnDemand,theBionanoGenomicsDataSecurityGuidelines(P/N30292)forTermsandConditions,andtheBionanoComputeOnDemandReleaseNotes(P/N30293).
NetworkRequirementsThecomponentsintheSaphyrsystemrequirenetworkconnectivitytocommunicatewitheachother.
PoornetworkreliabilityorthroughputcanaffecttheperformanceofyourSaphyrsystem.
TheBionanoAccessServerhasatetheredconnectiontotheSaphyrInstrumentController.
OriginatingFromTargetProtocolSaphyrInstrumentControllerBionanoAccessServerSSH(port22)BionanoAccessServerComputeserversSSH(port22)SCP(port22)BionanoAccessServerEmailserverSMTP(port25)InstrumentController,workstations,andcomputeserversBionanoAccessServerHTTPS*(defaultport3006)*EnableusingavalidSSLcertificateBionanoAccessisinstalledontheBionanoAccessServerandisaccessibleviastandardwebbrowsersfromworkstationsconnectedtothesamenetwork.
Userscanperformvariousactivities,suchasgeneratingexperiments,monitoringinstrumentandrunstatus,performingandsharinganalyses(whenproperlyconfiguredwithBionanocomputationservers),byloggingintoBionanoAccessviaawebbrowser.
OurrecommendedwebbrowserisChrome.
TheSaphyrInstrumentControllershouldenablescreen-sharingsessionswithBionanoifremotesupportisdesired.
ThedefaultconfigurationrequirestwostaticIPaddresses.
OneisfortheBionanoAccessServerinthelabandoneisfortheSaphyrComputeServerinthedatacenter.
Sometimesthelabandthedatacenterareondifferentsubnets.
ThetwoIPaddressesprovidedneedtobeaccessibletoeachother.
Theremainingcomputenodeswillbeonaseparatecustomsubnet.
TheSaphyr1anodewillbedualhomed.
ItwillhaveonestaticIPaccessibletotheBionanoAccessserverandoneIPaddressonthesubnetwiththeothercomputenodes.
IProutingwillbeusedonSaphyr1atodirectresponsesfromthecomputenodesbacktotheBionanoAccessServer.
EachcomputenodealsohasaseparateIPMIport.
IfyouwanttohaveyourIPMItrafficonaseparatenetworkplanforanadditionalconnectionforeachcomputenode.
Eachcomputeserverhasfournodes.
ForamoresecureinstallationitispossibletoswitchfromHTTPtoHTTPScommunication.
ThecustomermustprovideandinstalltheSSLcertificatesothatitisobtainedbytheappropriatepartiesforthatspecificinstallationForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage11of18andorganization.
Duringinstallation,wealwaysconfirminitialinstallationusingHTTPandthenaddtheSSLcertificateonceinitialoperationhasbeenconfirmed.
Theuseofselfsignedcertificatesisnotsupported.
NotCompatiblewithProxyServersBionanoAccessisnotcompatiblewithproxyserversandshouldbeexcludedonalluserworkstationsfromproxyrequirements.
Proxyserverswilloftencacheresultsandpreventdynamicpagessuchasthedashboardfromupdatingproperly.
FileStorageRecommendationsBydefault,theInstrumentControllerdoesnotsaveimagedata.
Usersmaychoosetosavetherawimagesduringrunsetupstagepriortostartingtheirrun.
Ifthisoptionischosen,amaximumofonechipcanberunbeforetheimagedataneedstobedeletedortransferredmanually.
SeeSaphyrSystemUserGuide(P/N30247)fordetails.
Ifyouwanttoarchiveorretainrawimagesforaperiodoftime,werecommendthatyouarchiveimagestoafileserveraftereachrun.
ThecustomerisresponsibleforarchivingandbackinguprawimagesfromtheSaphyrInstrumentControllerifdesired(butthisisnotrequired).
TheBionanoAccessServerwillstoreresultfilessuchasmoleculedatafiles(BNX)anddenovoassemblies.
Thisdatawillcontinuetogrowovertime.
TheBionanoAccessServerhasbeenconfiguredtohavesufficientfilestorageforseveralyears.
WehighlyrecommendthatallcontentintheAccessInstallationfolderisbackeduponaregularbasis.
DependingonsystemutilizationyoumayneedtotransitiontoanenterprisestoragesolutionifyouexceedthecapacityoftheBionanoAccessServer.
Alternatively,userscanexportandarchiveunusedprojectsperiodically.
SeeBionanoAccessUserGuide(P/N30142)fordetails.
User-SuppliedMaterialsThefollowinguser-suppliedmaterialsarerequiredforalltypesofsamplepreparationtraining.
Additional,protocol-specificmaterialsarereferredtoonsubsequentpages.
ConfirmwithyourFASwhenyouhaveallthecorrespondingconsumablesandequipmentavailablebeforeschedulingyourtraining.
User-SuppliedEquipmentEquipmentSupplierCatalog#QubitFluorometerThermoFisherQ33216orsimilarMicrocentrifuge,refrigeratedGenerallabsupplierPipettes(2,10,20,200,and1000μl)Note:lighttouchpipettesarenotcompatibleGenerallabsupplierIcebucketandiceGenerallabsupplierVortexerGenerallabsupplierThermalCyclerwithHeatedLid(10°Caboveblocktemp)Generallabsupplier4°Crefrigeratorand-20°CfreezerGenerallabsupplier-20°CEnzymeBlockGenerallabSupplier4°CAluminumCoolingTubeBlockSigmaAldrichZ740270orsimilarPositive-displacementpipetteMR-10(recommended)Rainin17008575orsimilarBathSonicator(optional)GeneralLabSupplierForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage12of18User-SuppliedConsumablesConsumableSupplierCatalog#ProteinaseKenzyme,Puregene,5mlQiagen158920PCRtubes,thin-walled,DNase-free,0.
2mlThermoFisherAM12225orsimilarQubitBroadRange(BR)dsDNAAssayKitThermoFisherQ32853QubitHighSensitivity(HS)dsDNAKit(recommended)ThermoFisherQ32851QubitAssayTubesThermoFisherorAxygenQ32856or10011-830UltraPurenuclease-freewaterThermoFisher10977015Microcentrifugetubes,0.
5ml,amber,nuclease-freeUSAScientific1605-0007Microcentrifugetubes,1.
5mlVWR87003-294Pipettetips,aerosol-resistant2,10,20,200,and1000μlGenerallabsupplierPipettetips,10μl,C-10forpos.
displacement(recommended)Rainin17008604AdditionalUser-SuppliedMaterialsforDNAIsolationThefollowingprotocolslistmaterialsrequiredforextractingDNAfromvaryingsources.
FASwillhighlighttherequiredmaterialsdependingonsampletypeandprotocolchoice.
Ensurethatyouhavetheappropriatematerialsavailableontrainingday.
IntheUserTrainingKit(seedetailsinChapter4),Bionanoprovides1DNAIsolationKit,percustomers'request.
SampleTypeProtocolHumanCellCultureBionanoPrepSPFreshCellsDNAIsolationProtocol(P/N30257)*BionanoPrepSPFrozenCellPelletDNAIsolationProtocol(P/N30268)*BionanoPrepCellCultureDNAIsolationProtocol(P/N30026)HumanBloodBionanoPrepSPFreshHumanBloodDNAIsolationProtocol(P/N30258)*BionanoPrepSPFrozenHumanBloodDNAIsolationProtocol(P/N30246)*BionanoPrepBloodDNAIsolationProtocol(P/N30033)BionanoPrepFrozenBloodProtocol(P/N30215)BoneMarrowAspiratesBionanoPrepSPBMADNAIsolationProtocol(P/N30298)*AnimalTissueBionanoPrepSPTissueandTumorDNAIsolationProtocol(P/N30339)*BionanoPrepAnimalTissueDNAIsolationFibrousTissueProtocol(P/N30071)BionanoPrepAnimalTissueDNAIsolationSoftTissueProtocol(P/N30077)PlantTissueBionanoPrepPlantTissueDNAIsolationBaseProtocol(P/N30068)*BionanoPrepPlantTissueDNAIsolationHighPolysaccharideProtocol(P/N30128)*BionanoPrepPlantTissueDNAIsolationHighPolyphenolProtocol(P/N30133)*BionanoPrepPlantTissueDNAIsolationLiquidNitrogenGrindingProtocol(P/N30177)*BacterialBionanoPrepCellCultureDNAIsolationProtocol(P/N30026)*Referstomostrecentproductreleaseforthatsampletype.
SPisrecommendedformostsampletypes.
AdditionalUser-SuppliedMaterialsforDNALabelingThefollowingprotocolslistmaterialsrequiredforlabelinggenomicDNA.
FASwillhighlighttherequiredmaterialsdependingonlabelingtype.
Ensurethatyouhavetheappropriatematerialsavailableontrainingday.
IntheUserTrainingKit(seedetailsinChapter4),Bionanoprovides1DNALabelingKit,percustomers'request.
LabelingMethodProtocolDirectLabelandStain(DLS)BionanoPrepDirectLabelandStain(DLS)(P/N30206)*Nick,Label,Repair,andStain(NLRS)BionanoPrepLabelingNLRSProtocol(P/N30024)*Referstomostrecentproductreleaseforthatsampletype.
DLSisrecommendedwhenlabeldensityfallswithinoptimalrange.
ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage13of18Chapter3:PreparingforArrivalInstallationGuidelinesAnauthorizedserviceproviderdeliversthesystem.
Makesurethatthecrateisstoredsecurelyneartheinstallationlabbench.
Theinstrumenthastwotip-tiltindicatorsmountedtotheoutsideofthecrateaswellasoneimpact-shockindicator.
PleaseinspecttheexteriorofthecratefordamageandinformyourFSEifeitheroneofthetwotip-tiltsensors,ortheshock-impactsensorshavebeentriggered.
Figure2:(fromlefttoright)shock-impactsensors(un-triggeredandtriggered)andtip-tiltsensors(un-triggeredandtriggered)CAUTION:OnlyaBionanoFieldServiceEngineer(orpersonnelapprovedbyBionano)canuncrateandinstalltheinstrument.
Atleastthreeweeksbeforeinstallation,confirmwithyourFieldApplicationScientist(FAS)thatyouhavetherequiredconsumablesandequipment.
Ensurethatthelabspaceandbencharereadyforinstallation.
Ensurethatyouhaveapalletjacktosupportthecrateandinstrument.
EnsurethereareatleastthreepeopletoassisttheFSEwithliftingSaphyrinstrument.
InstalltheSaphyrComputeServerandBionanoComputeServer(s)inthedatacenter.
EnsurethatIPaddressesandallnetworkrequirementshavebeenmetasdescribedintheNetworkRequirementssectionabove.
DimensionsMeasurementInstrumentCratesHeight38cm(15in)152cm(60in)Total[~81cm(32in)forTopaccessorycrate+~74cm(29in)forInstrumentcrate]Width86cm(34in)109cm(43in)forTopaccessorycrateandInstrumentcrateDepth71cm(28in)81cm(32in)[~74cm(29in)forTopaccessorycrate,~81cm(32in)forInstrumentcrate]Weight103kg(227lb)254kg(560lbs)[Topaccessorycrateincludingcontroller,monitor,server,andaccessorykit+Instrumentcrateincludinginstrument]ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage14of18LaboratoryGuidelinesPrepareaclean,levelsurfacesuchasasturdylabbenchfortheinstrument.
Keeptheinstrumentawayfromdirectsunlightorheatsource.
Donotplacetheinstrumentonalabbenchthathasliquidsorchemicals.
Donotplaceanyotherequipmentonthebenchthatcouldproducevibrations,includingcentrifuges,compressors,andshakers.
Donotplacetheinstrumentonornearobjectsthatcanproducevibrations,suchasheavydoors.
Donotplaceobjectsontopoftheinstrument.
LabBenchLayoutPositiontheinstrumenttoallowproperventilationandaccesstothepowerswitchandpoweroutlet.
AccessMinimumClearanceLabBenchSpaceAllowatleast150cm(59in)wideby77cm(30in)depth.
TopAllowatleast93cm(37in)abovetheinstrument.
BackAllowatleast5cm(2in)behindtheinstrument.
SidesAllowatleast15cm(6in)oneachsideoftheinstrument.
Connections4standardelectricaloutlets(100~240VAC)andtwo1GBEthernetportCAUTION:Movingtheinstrumentcancompromisedataintegrity.
Insufficientoverheadclearancecandamagethestageaccessdoorandaffectrunperformance.
TheSaphyrInstrumentControllermustbeplacedwithin1m(3ft)oftheinstrument.
EnvironmentalConsiderationsThisinstrumentisdesignedforindooruseonly.
ElementSpecificationTemperatureMaintainalabtemperatureof19°C(66°F)to25°C(77°F).
HumidityMaintainanoncondensingrelativehumiditybetween20–80%.
ElevationPlacetheinstrumentatanaltitudebelow2,000m(6,500ft)abovesealevel.
VentilationAtleast5cm(2in)ofclearancebehindtheinstrumenttoallowproperventilationandaccesstopoweroutlet.
Overheadclearancerequiredforinstallationandserviceis93cm(37inch).
AirQualityOperatetheinstrumentinaPollutionDegreeIIenvironmentorbetterasdefinedbytheInternationalElectrotechnicalCommision(IEC).
ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage15of18Chapter4:PreparingforInstallationandTrainingSitePreparationChecklistEnsurethatyourfacilityisreadyforthedeliveryofthecrate.
Ensurethatyouhavetheappropriateequipmenttosupportthecrateandinstrument(e.
g.
,palletjack).
Ensurethatallrequiredpersonnelarepresentonthescheduledinstallationday(atleastthreepeopletoassisttheFSEwithliftingSaphyrinstrument).
EnsurethatyouhavereceivedandproperlystoredthecontentsintheQualificationKitandAccessoryKit.
Verifythatyoursitehaspropercomputing,network,filestorage,andelectricalrequirements.
CrateContentsItemContentStorageTemperatureInstrument1each15–25°C(59–77°F)Monitor1each15–25°C(59–77°F)Keyboard1each15–25°C(59–77°F)Mouse1each15–25°C(59–77°F)InstrumentController1each15–25°C(59–77°F)BionanoAccessServer1each15–25°C(59–77°F)AccessoryKit1each15–25°C(59–77°F)TheFSEwillunpackthecrateduringtheinstallationvisit.
ComputeServerswillshipinadditionalcrate(StorageTemperature:15–25°C(59–77°F)).
AccessoryKitTheAccessoryKitisincludedinthecrate.
ItemContentStorageTemperatureUS-SpecificPowerCord3each15–25°C(59–77°F)SaphyrChipClip2clips15–25°C(59–77°F)DisplayPortCable1each15–25°C(59–77°F)NetworkCable(Cat3)4each15–25°C(59–77°F)SerialCable(M/F)1each15–25°C(59–77°F)USB2.
0AtoBConnector1each15–25°C(59–77°F)USB3.
0AtoBConnector1each15–25°C(59–77°F)AirFilter3each15–25°C(59–77°F)Sparkle,OpticalCleaner1each15–25°C(59–77°F)LensCleaningPaper2each15–25°C(59–77°F)Mousepad1each15–25°C(59–77°F)ForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage16of18QualificationKit(Part#90011or90034)TheSaphyrSystemQualificationKitwillbecoordinatedbyyourFSEtoarriveapproximatelyonetothreeweeksbeforeinstallation.
ItemPart#ContentStorageSaphyrChipG2.
320366or203193each4°CDLSBiologicalControlA,100μl204002each4°CSPLargeGenomeLabelingControl.
5000ng+203991each4°C+Thiscontrolwillbeusedfortraining.
UserTrainingKits(Part#90012–90017,90049)TheSaphyrSystemUserTrainingKitwillbecoordinatedbyyourFAStoarriveapproximatelyonetothreeweeksbeforetrainingbegins.
Itwillcontainacombinationof:1)aDNALabelingKit,2)aDNAIsolationKit.
SaphyrChips&ControlwillbeprovidedwiththeQualificationKit,and3)20tokens(ifCompute-On-Demandwillbeused)CoordinatewithyourFAStosendtheproperLabelingKitandIsolationKitcombinationaslistedbyreferencingoneofthepartnumbersbelow(90012–90017,90049)fordelivery:Part#90049*-DLSLabeling+SPBloodandCellDNAIsolation+BionanoPrepSPMagneticRetrieverPart#90016-DLSLabeling+AnimalTissueDNAIsolationPart#90017-DLSLabeling+PlantTissueDNAIsolation*AccessoriesfortheSPBMADNAIsolationKitorSPTissueandTumorDNAIsolationKitcanbeincludeduponrequestPart#90012-NLRSLabeling+BloodandCellCultureDNAIsolationPart#90013-NLRSLabeling+AnimalTissueDNAIsolationPart#90014-NLRSLabeling+PlantTissueDNAIsolation1)LabelingKitTraining:NLRSKitorDLSKitThetableindicatesthecontentstobeexpecteddependingonwhichoneofthelabelingkitsthatisrequestedfortraining.
LabelingTrainingKitPart#Content#ofBoxesStorageBionanoPrepDLSLabelingKit800051each(10rxn)3-20°C,4°C,RTBionanoPrepNLRSLabelingKit800011each(10rxn)24°C,-20°C2)DNAIsolationTrainingKit:Blood&CellCulture,SPBlood&Cell,AnimalTissueorPlantTissueChooseoneoftheDNAisolationkitsbelowtobeusedduringtraining.
DNAIsolationTrainingKitsPart#Content#ofBoxesStorageSPBlood&CellCultureDNAIsolationKit800301each(10rxn)24°C,RTBlood&CellCultureDNAIsolationKit800041each(10rxn)1RTSPTissueandTumorDNAIsolationKit800381each(10rxn)1RTAnimalTissueDNAIsolationKit800021each(10rxn)1RTPlantTissueDNAIsolationKit800031each(5rxn)24°C,RT3)20tokensforComputeOn-DemandCustomersForResearchUseOnly.
Notforuseindiagnosticprocedures.
30145RevK,SaphyrSitePreparationGuidePage17of18Chapter5:Post-InstallationFollowUpandResourcesAfteryouhavecompletedthetraining,youwillhaveafollow-upreviewmeetingwithyourFAS.
Thereviewmeetingisusuallyintheformatofaconferencecall.
Forthereview,preparetoprovidethefollowing:DataproducedfromyourfirstrunwithouttheFASonsite.
Listofcustomizationrequestsfortheinstrumentandsoftware.
Listofquestions,concerns,andissues,suchasyourlevelofcomfort,comprehension,andconfidenceonusingtheSaphyrsystem.
AdditionalResourcesThefollowingdocumentationisavailablefordownloadfromtheBionanoSupportpage.
ResourceDescriptionSaphyrSystemSafetyGuide(P/N30253)Providesinformationabouttheinstrumentsafetyconsiderations.
SaphyrSystemUserGuide(P/N30247)Providesanoverviewofinstrumentcomponentsandsoftware,propermaintenance,andtroubleshooting.
BionanoAccessSoftwareGuide(P/N30142)Providesanoverviewofdataanalysis.
BionanoGenomicsDataSecurityGuidelines(P/N30292)ProvidessecurityguidelinesforComputeOnDemandusage.
GlossaryTermDefinitionCIFSCommonInternetFileSystemFASFieldApplicationScientistFSEFieldServiceEngineerGBGigabyteHTTPHypertextTransferProtocolHTTPSHypertextTransferProtocolSecureOSOperatingsystemSGEjobsSonofGridEnginejobsSSDSolid-statedriveSFTPSecureFileTransferProtocolSMTPSimpleMailTransferProtocolSSHSecureShellTBTerabyteIECInternationalElectrotechnicalCommisionForResearchUseOnly.
Notforuseindiagnosticprocedures.
TechnicalAssistanceFortechnicalassistance,contactBionanoGenomicsTechnicalSupport.
YoucanretrievedocumentationonBionanoproducts,SDS's,certificatesofanalysis,andotherrelateddocumentsfromtheSupportwebsiteorbyrequestthroughe-mailandtelephone.
TypeContactEmailsupport@bionanogenomics.
comPhoneHoursofOperation:MondaythroughFriday,9:00a.
m.
to5:00p.
m.
,PSTUS:+1(858)888-7663Websitewww.
bionanogenomics.
com/supportBionanoGenomics,Inc.
9540TowneCentreDrive,Suite100SanDiego,CA92121
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