Liu, Kelsey_Senior Thesis 2026

Senior Thesis | 2026

AutomatingBiology:ScalableWebInfrastructure fortheDAMPLabWorkflowManager

AldenCarterandKelseyLiu

March2026

1 Introduction

Inanerawhereengineerscansimulaterocketlaunches,airflow dynamics,andentirevirtualenvironmentsfromacomputer, biologyexperimentscontinuetorequiremanualoperationsoneata time.Abiologistconductinganexperimenttosequenceagenetic circuitisconstrainedbyhands-onbenchwork.Despiteadvanced practicesinbiotechnology,sequencingandDNAassemblycanstill requireresearchersandlabtechnicianstomanuallypipette minisculevolumes.Theselimitationsrepresentthebottleneckin thedesign-test-buildcycleinwhichscientistsandengineershave yettoreachthefullpotentialofintersectinghardware,software, andwetware[1].Inrecentyears,effortsinbiodesignautomation haveworkedtoclosethisgap.

Biologyresearchisstillslow,manual,andlabor-intensive,relying ontrial-and-errorratherthanpredictableengineeringworkflows. Therootofthisinefficiencyliesinafundamentaldisconnection: software,labhardware,andbiologicaldesignsoperateinisolation, makingexperimentshardtoautomate,scale,orreliablyreproduce. OliveiraandDensmorecharacterizethisfragmentationasabarrier tothecodesignenvironmentnecessaryforsyntheticbiology[1], whileMilesandLeeemphasizethatwithoutclosed-loop automationandstandardizedprotocols,evenwell-designed experimentssufferfromreproducibilitychallenges[2].Asaresult, thedesign-build-testcycleisbottlenecked,limitingthespeedand

reliabilityofinnovationinsyntheticbiology.

Toaddressthesechallenges,facilitiesliketheDAMPLabhave emergedas"cloudlabs"whichisbasicallyalabthatisaccessible entirelyonline.Insteadofmanuallyperformingeachstep,aclient submitsrequestsforservicessuchasDNAassembly,cloning,and PCRreactionsthroughawebinterface,andtheDAMPLab handlesexecutionautomatically.Thisapproachexcelsathandling routinetaskswithconsistentprocedures,bringingunprecedented standardizationtobiologicalworkflows,thoughMilesandLee noteitremainslesssuitableforexploratoryresearchrequiring frequentadjustments.Theunderlyingphilosophydrawsfrom bio-designautomationandmodularity,whereordersarecreated usingstandardizedbiological"modules"andautomaticallycarried out.DensmoreandBhatiadescribethisconvergenceofsoftware, biology,androboticsasessentialforenablingmorepredictable, reproducible,andscalableexperimentation[3].

Oneofthelimitationsoftheseautomatedlabsisthebarriertoits adoption;manybiologistshavelittleexperiencewithintegrating automationsystemswiththeirexperiments.Platformssuchas DAMPLabarebeingdevelopedtoallowscientiststodesign experimentsintheseautomatedandscalablewayswithoutneeding tolearnhowtocode[2].Ourprojectisatthisinterface.Amongthe manyprojectssupportedbySAIL,theDAMPLabrepresenteda compellingintroductiontotheintersectionofsoftwareengineering andbiology.Theengineeringprinciplesofmodularity,abstraction, andautomationlinkdirectlytotheselimitationsinbiology experimentsthatthelabinfrastructureaimstoaddress.The prototypeoftheoriginalworkfloworderingwebsitelackedseveral criticalfeaturesforascalablecloudlab.Althoughthewebsite displayedservicesofabiologyexperimentandworkflowcreation, manyofthesefeatureswerehardcodeddirectlyintotheinterface,

meaningtheyarenotflexibletouserinputandaretherefore unsuitableforcustomizationandupdates.Andthebackendhadno authenticationsafeguardstoprotectsensitiveoperations.Thus, theselimitationsmotivatedthecentralquestionofthiswork:how cansoftwareengineeringprincipleshelpwithscientificdiscoveries byimprovingspeed,reliability,andautomationofthebiological experimentprocesses?Toinvestigatethislearningandresearch question,ourcontributionstotheDAMPLabcloudworkflow managerfocusedonextendingandrefactoringitscodebaseintoa secure,modular,andscalablesystemusingmodernfull-stack practices.Themethodssectionthatfollowsoutlinesthetechnical foundationofthiswork.

2 Methods

Tocontextualizethetechnicianfoundationofthisproject,this sectionfirstoutlinesamodernfull-stackwebapplication.Atypical stackconsistsofthreeinterdependentlayers(Fig.1),each responsibleforadifferentstageofinteractionbetweentheuser, website,andlong-termdatastorage[4].

Thefrontendisresponsibleforhandlingeverycomponentonthe websiteitselfthattheuserinteractswith,suchaslayouts,buttons, forms,andanimations.Theseinteractionsarekepttrackofusing “states,”representingthecurrentstatusoftheinterface.Aclient programhandlesthesestate-basedinterfaceupdates,commonly builtusingHTML,CSS,andJavaScriptframeworkssuchasReact. Themainchallengeinthislayerisbalancingvisualdesignclarity andperformance.Thedevelopers’jobistofigureoutwaystokeep interfacesresponsive,efficient,andaccessibleacrossdifferent devicesandbrowsers[4].

Thebackendmanagestheapplication’slogic,whichcontrolsthe request-responsecycle,authentication,andcommunication betweentheuserinterfaceanddatabasewherelong-termdatais stored.Thisserverlayer,functionallyanintermediary,ensuresthat auseronlyinteractswithdatatheyarepermittedtoaccess, whetherintentionallyorunintentionally.Thisincludespreventing unauthorizedaccess,verifyingthatincomingrequestsare legitimate,andprotectingagainstcode-injectionattackstothese communicationpointsbetweentheserverandclient[5].Backend architectureisachievedthroughApplicationProgramming Interfaces(APIs),whichallowanddefinestructuredwaysfor differentsoftwareapplicationstocommunicateandinteractwith eachother[6].Runtimeenvironmenttools(theruncodelanguage outsideofthewebsiteitself)suchasNode.jsarethetoolsthat implementAPIs.Withtheexistenceofmanysuchframeworks, choosingthebackendruntimeenvironmentdependson considerationssuchasdata-handling,scalability,andsecurity[7]. Forinstanceinourproject,weusedNode.jsforitsconsistent Javascriptinbothfrontendandbackend,aswellasasynchronous handlingofrequestssuchthatinsteadofwaitingforoperationsto completeoneatatime,itexecutesothertasksuntilacallback[7]. Securityauthenticationformsoneofthemostcrucial

responsibilitiesofthebackend.Defaultsecuritymethods implementencryptedpasswordsthroughhashingtheirstored valuesandtoken-basedauthentication(suchasJSONWeb Tokens).Thesefeaturespreventunauthorizedusersfromviewing oralteringstoredconfidentialdata.Atthesametime,backend developmentrevolvesaroundscalability,inwaysthatensurethe systembehindawebsiteconnectedtovariousserverscanhandle largevolumesofsimultaneousrequestssecurely,allwhilebeing abletobeeasilyaugmentedandtransformedintonewsystem designspecifications.

Theprimarypurposeofawebsiteistoretrieveandstore informationthatauserwantsfromtheservice,suchaslogins, updatinginteractionsforums,andplacingaproductorderwhen shoppingonline.Thedatabaseorganizesinformationsuchas users’information,passwords,andhistoryinthesystem’s long-termmemory.Eachpieceofdataisstoredinastructured formatsuchthatdifferenttypesofinformationcanberetrieved uniformly[4].Thus,theprimarychallengeinthislayeris maintainingdatawithconsistency andintegrityacrosstheentire application. Thisinvolvesvalidatingdatabeforeitissaved, enforcingaccessrules,andstoringinformationofrelated componentsofthesysteminastandardizedway. BeforeinitiatinganyworkontheDAMPLabproject,westarted withalearningphasetoensurethatwehadaworking understandingofthetechnologiesinthefullstack.Ourinitialstep wastocompleteanintroductorytutorialonbuildinga MERN-stackwebapplication.TheMERNstackconsistsof MongoDBasthedocumentdatabase,Expressastheserver-side applicationframework,Reactastheclientinterface,andNode.jsas theruntimeenvironmentthatexecutesJavaScriptontheserver[4]. AlthoughthistutorialdidnotuseNestJS,itestablishedthecore conceptsofthefrontend,backend,andclient–serverinteraction

Aftercompletingthispreliminaryexercise,wetransitionedtoa secondexploratoryproject:theNestJS“catswebsite”tutorial.This stagemirrorsthefulltechnologystackusedintheDAMPLab platformandintroducesframework-specificcomponentssuchas controllers,providers,datatransferobjects(DTOs),and dependencyinjection.Weadditionallypracticedbuildingabasic frontendinterfacewithoutrelyingonTailwindCSS,sincethe DAMPLabplatformusesplainReactforitsuserinterface.

TailwindCSSisastylingframeworkthatprovidessimpleutility classesforlayoutanddesign,butforthisprojectwefocusedon writingourowncomponentsandstylesdirectlyinReacttomatch thelab’sexistingconventions[8].Wethenmovedbeyondthebasic tutorialandbeganlearninghowtointegrateauthenticationintoour systembyusingNestJS’sAuthGuardtoimplementsecurelogin andaccount-creationworkflows.Thisintroducedustoconcepts suchasprotectedroutes,JWT-basedauthorization(JSONWeb Token),androle-restrictedaccesswithintheapplication[5].In addition,weincorporatedMailgun,anemailAPIthatenables automatedmessagedelivery,tosendverificationemailsandother notificationstousers.Finally,wedeployedourapplicationsto AmazonWebServices(AWS),whichinvolvedconfiguringEC2 instances,managingsecuritygroups,andsettingupenvironments thatmirroredreal-worlddeploymentconditions.

Versioncontrolremainsintegraltoourworkflowthroughout development,andasignificantpartofourpreparationinvolved learninghowtouseGiteffectively.Gitprovidesacompleterecord ofcodechanges,enablingustocompareearlierstatesofthe applicationandrevertbreakingmodificationswhenneeded.Its branchingandmergingmodelallowsmultipledeveloperstowork simultaneouslywithoutoverwritingeachother’swork,whichis

essentialinacollaborativeresearchenvironment[9].Branch isolationalsofurthersupportsexperimentaldevelopment,enabling ustoprototypeideassafelyandintegratethemonlyaftertheyare fullytested.Wealsoadoptedaworkflowinwhichnewfeatures weresubmittedthroughpullrequests,allowingmentorstoreview code,providefeedback,andensurequalitybeforechangeswere mergedintothemainbranch.Inaddition,welearnedhowto configure.secureenvironmentvariablessosensitiveinformation–suchasAPIanddatabasekeys–remainedlocalandwasnot exposedinthepublicGitHubrepository.

3 ResultsandDiscussion

3.1

UIStatesandUser-centeredDesign

Usersroutinelydismisswarningdialogueswithoutreadingthem, especiallylongdensetextssuchasconditionsandagreements.A redesigneduserinterfacewasimplementedtoimprovetheoverall site’svisualcoherence,reduceinteractionambiguities,and communicateactionseveritymoreeffectivelytousers.This redesignforcedondesignprinciplesregardingcolorusage,aswell asuserconveniencewithlayoutconsistencyandvisualhierarchy. Intheoriginalinterface,warningsandhigh-impactactionswere notconsistentlydistinguishedfromroutineinteractions.Asa result,criticalmessagescouldbemissed,andirreversibleactions couldbetriggeredwithoutsufficientvisualemphasis.

Therevisedinterfaceintroducedastandardized primary-secondary-tertiary-accentcolorsystemusingtheReact framework’sthemeconfigurations.Primaryinterfaceelements wererecoloredtomatchtheproject’slogopalette,establishinga

consistentvisualidentityaswellasbrandpresenceacrosspages (Fig.2).Thischangeimprovedrecognizabilityandreduced cognitiveloadwhennavigatingdifferentsectionsofthe application.Importantly,visualemphasisisusedtoslowuser interactionatappropriatetimesinordertodrawattentionto consequences(Fig.3).Rediscommonlyreservedfordestructive actionsacrosswebapplications.Thisconventionwasintentionally adoptedintheredesignedinterfacetoreduceaccidentalactivation ofirreversibleoperations,suchasdeletingentireintervalsofa user’swork[10].

Fig.2:Streamlinedvisualconsistencyandcoloringattention

Fig.3:Visualhierarchyandareasofcognitiveloadconcentrations inawebapplication[11] Fromasystemperspective,thefrontendredesignfunctionsasa criticalcommunicationlayerwithoutaffectingthecontrollayer. Noadditionalbackendvalidationlogicwasintroducedasapartof thischange.Thesesurface-leveldesigndecisionsdemonstratehow visualscontributetosystemreliability.Byimprovingclaritywith consistency,theinterfacereducesthelikelihoodofusererrorwhile maintainingflexibilityandresponsiveness.

CheckoutPages

Thecheckoutpagerevampredesignedtheordersubmissionpages tocreateamoreintuitiveuserexperienceandaddedfeatures.The updatedcheckoutinterfacenowdynamicallypullsserviceprices fromthebackendratherthandisplayinghardcodedvalues. Underneaththesummaryitalsoincludesaprominentdisclaimer clarifyingthatdisplayedcostsareestimatesonly,withfinalpricing communicatedviaemailafterlabpersonnelreviewtheorder(Fig. 4).

Fig.4:Finalcheckoutpagebeforesubmittingthejob

Thefinalcheckoutpagereceivedsignificantimprovements includingbetterstylingforvisualconsistencytomatchthe previouscheckoutpage,navigationprotectiontopreventusers fromaccessingthesubmissionpagewithoutproperlycheckingout, andtheremovalofredundantpaymentprocessingfieldssince transactionsarehandledexternallythroughemail.Personal informationfieldswerealsoeliminatedbecausethisdataisalready capturedduringaccountcreation.Intheirplace,newfunctionality wasaddedallowinguserstotitletheirjobs,viewasummaryof theiraccountcontactinformation,andprovideadditionalnotes withtheirorders.

Thisfeatureaddressescriticalusabilityissuesthatexistedinthe previouscheckoutsystemwhilestreamliningtheentireorder creationprocess.Theoriginalcheckoutpagerequiredusersto repeatedlyenterpersonalinformationthatwasalreadystoredin theiraccounts,creatingunnecessaryworkandpotentialdata inconsistency.Moresignificantly,althoughajobsubmitted summarypageexistedinthecodebase,itwaspreviously inaccessiblethroughnormaluserworkflows.Theredesign integratesthispageintothecheckoutprocess,automatically navigatinguserstoitafterjobsubmission.Thepagedisplays createdjobdetails,submissiontimestamps,loadingstatus,and validationwarningsforinvalidIDs(Fig.5).Enhancedwitha completeorderdocumentandPDFdownloadcapability,the systemprovidesclientswithimmediatetrackinginformation similartocommercialplatformslikeAmazon.Thistransparency givesclientsreferenceabledocumentationforcommunicatingwith labpersonnelwhileimprovingoverallorderprocessingclarity.

Fig.5:Jobsubmittedsummarypage

Severalimprovementscouldfurtherrefinethecheckoutandorder managementexperience.Implementingautomatedemailreceipts functionalitywouldensureusersreceiveacopyoforderdetails immediatelyuponsubmission.Adedicateduserdashboard displayingallpastandpendingorderswouldgiveclientsa centralizedviewoftheirorderhistoryratherthanrequiringthemto scrollthroughtheiremails.Additionally,introducingorderediting capabilitieswithinalimitedtimeframebeforelabprocessing beginswouldallowuserstocorrectmistakesorupdate requirementswithoutneedingtocancelandresubmitentireorders, reducingfrictionforbothclientsandlabpersonnel.

3.2 AuthenticationFlows

APIEndpoints

Everyinteractionwithawebsitebeginswitharequestsenttoa URL.WebapplicationssuchastheDAMPLabtoolregularly

handlethousands,uptomillionsofconcurrentrequests,naturally leadingtosomedevelopershavenotexpected.Whenauserclicks buttons,submitsforms,etc.theirbrowsersendsastructured messagetoaspecificaddressontheinternet[13].Fromthe perspectiveoftheserver,thereisnodifferencebetweena legitimateuserandamaliciousattacker.Beyondstandarduser interactions,hackershaveavarietyofmethodstogain unauthorizedaccesstoapplicationpermissions,suchasmanually injecting,modifying,orreplayingrequeststooverloadorcrasha system[14].APIendpointsarethepointsofexposurebetweenthe systemandincomingtraffic,motivatingdefensiveAPIdesignto filterthelegitimateones.

Fig.6:AuthGuardprotocolfromfrontendtoserver[12]

Fig. Unguardedendpointsthrough protecting

Theapplicationiscomposedofmultiplesubpagesandservice routes,whichsensitivedata,suchasloginpasswords,flows through(Fig.6).Toprotectdataintransit,allroutesareserved overHTTPS(secureHTTP),rejectingrequestsmadewithout encryption,preventingpotentialmaliciousinjectionsor modificationsoftransmittedjavascriptdatatotheserver.Browser warningssuchasthosedisplayedbyCloudflarewarnwebsurfers ofincreasedrisksduetotheabsenceofHTTPSorguaranteeof encrypteddata.Directaccesstoprotectedroutes,suchas admin-onlyfeatures,wasrestrictedusinganauthenticationguard (AuthGuard).Beforeimplementingthis,anydemouserwithout specialpermissionswouldhavebeenabletoaccesspagesonly intendedforadminuse.Fig.7showshowURLsarediscoverable bydesign,meaningtheyarenotlimitedbytraversinglegitimately throughabutton.Bygivingauseratime-expirytokenembedded withdifferentaccesspermissionsuponloggingin,theAuthGuard checksincomingrequests,suchasvisitingasubpageURL,for validtokensbeforereachingthebackend[15].

TheformattedrequestsareimplementedthroughGraphQLrather

thanRESTAPI,atypeofarchitecturalstylethatusesHTTPto transferrequests,becausetheschemaspecifiesavailabledata types,queries,andmutations.Thetradeoffconsideredwasthat, comparedtoREST,GraphQLrequiresexplicitmaintenancein ordertoreduceover-fetchingbyreturningonlyrequesteddata fields[6].Inpractice,thisconstraintlimitstheamountof informationrevealedineachresponseandreducesthe effectivenessofmaliciousprobing.Apracticalobservation emergedfromthis:interface-levelrestrictionsarefutile,sinceany requestvisibleinabrowser’snetworkinspectorcanbemanually replicated.Forthisreason,theAPIlayerenforcesallaccesscontrol decisionsinsteadofdependingonthedata’svisibilityonthe frontend.

AnnouncementsFeature

Theannouncementsfeatureprovidesadministratorswitha streamlinedwaytocommunicateimportantinformationtoalllab usersdirectlythroughthewebsite'shomepage.The implementationincludesanadmin-onlybuttonthatnavigatestoa dedicatedannouncementpagewhereadministratorscanviewthe currentannouncement,createnewannouncementsusingatext box,andseeanoteonsupportedMarkdownformattingoptions includingboldtext,italics,andheadings(Fig.8).Oncesubmitted, announcementsappearonthehomepageforalluserswitha timestampindicatingwhentheywereposted.Administratorsalso havetheabilitytohidethecurrentannouncementwhenitisno longerrelevant.

retrievingexistingmessages.Onthefrontend,thesystem integratesReactMarkdownforrenderingformattedtextand establishesthenecessaryqueriesandmutations (CREATE_ANNOUNCEMENT,GET_ANNOUNCEMENT, UPDATE_ANNOUNCEMENT)tocommunicatewiththe backend,allaccessiblethroughanew"/edit_announcements" route.

Thisfeaturesignificantlyimprovestheuserexperiencebyenabling direct,organizedcommunicationbetweenthelabanditsusers. Previously,noformalannouncementsystemexistedonthe

website,creatingagapinhowthelabcouldsharetime-sensitive informationorupdateswiththecommunity.Becausethe organizationalstructureofthecodebasewasalready well-established,implementingthisfeatureprovedrelatively straightforward–addingthenewroute,page,queries,and mutationsintegratedsmoothlyintotheexistingarchitecture.One keydesigndecisionwastoretainallannouncementsinthe databaseratherthanoverwritingpreviousmessages,which preservesacompletehistoryoflabcommunications.However,this historicaldatacurrentlyhasnointerfaceforaccesswithinthe websiteitself,representinganopportunityforfuture improvements.Anotherpotentialadditionwouldbeaddinga previewfunctionthatallowsadministratorstoseehowtheir formattedannouncementwillappearbeforepublishingittoall users.

3.3 DataIntegrityandScalability

ServicesandWorkflows

Theservicepricingfeaturereplacedarigid,hardcodedpricing systemwithaflexible,administrator-controlledapproach. Previously,allserviceswerehardcoded–meaningtheirprices werefixeddirectlyinthesourcecodeat$100regardlessofthe actualcostofeachservice.Thisimplementationaddedanewprice columntotheadmineditpage,allowingadministratorstoset individualpricesforeachservicebasedontheiractualcosts.

Thebackendmodificationsinvolvedupdatingtheservicemodelto includeanoptionalpricefieldwithafloatdatatype,which accommodatesbothserviceswithknownapproximatecostsand thosewithvariable(unknown)prices.Onthefrontend,theprice fieldwasintegratedintoseveralGraphQLoperationsincluding

CREATE_SERVICE,GET_SERVICES,andGET_JOB_BY_ID mutationsandqueries,establishingtheconnectionbetweenthe database-storedpricesandwhatadministratorsconFig.throughthe interface.TheEditServicesTablecomponentreceivedanewprice column,andthepriceinformationwasalsoincorporatedintothe CanvasTypedefinitionsforbothservicesandnodeswithinthe workflowvisualization(Fig.9).

Fig.9:Admineditpageshowingtheservicetablewiththenewly addedpricecolumn

Thisadditionaddressescriticalneedsforgeneralizabilityand scalabilityinthelab'soperations.Whileservicesalreadyexistedin thesystem,updatingtheirmodelandcorrespondingfrontend queriesenabledmoreaccuraterepresentationofactualservice costsratherthanrelyingonplaceholdervalues.Thedesign decisiontomakepricingoptionalreflectspracticaloperational considerations:customersdonotcompletepaymenttransactions directlythroughthewebsite,andsomeserviceshavevariablecosts thatdependonspecificprojectdetailsprovidedduring consultation.Thisflexibilityalignswithbiologicalmodularity

principlesdescribedbyDensmoreandBhatia,wheremodular, adaptablecomponentscanbeconFig.dandrecombinedfor differentapplications[3].Bydoingthisimprovement,thesystem becomesmoremaintainableandbettersuitedtoaccommodatethe lab'sevolvingserviceofferingsandpricingstructureswithout requiringcodemodificationsforeachchange.

Bundlesandcanvasoverhaul

Previously,workflowsandrelatedservicesemployedhardcoded logic;addingormodifyingaworkflowrequiredchangesacross multiplebackendandfrontendfiles,increasingtheriskof producingcompilationerrorandlimitingscalability.Toaddress this,bundleswererestructuredasexplicitdataobjectsthatencode relationshipsbetweenservicesinacustomuser-designedworkflow intheCanvasbuilder(Fig.10).Theadvantageofusersbeingable tocreatetheirownbundlesisplenty.Critically,bundlingservices enablesreproducibilityacrossexperimentsbybecominga ready-madecloudworkflowforotherresearcherstomodifyor replicatewhileeliminatinginconsistenciesposedbyhumanerror [3].Eachbundlecontainsmetadatalinkingitsconstituentservices, whichenablesconsistentpropagationofoperationsinthe experimentalworkflow.Inthedatabaselayer,overhaulingthis featureallowsstorage,queries,validationinfutureupdatesto reducedeveloperoverheadandhumanerrorasneedsscale.

Fig.10:BundlesrelationshiptoServicesandWorkflows[16]

TheCanvasinterfacevisualizeshowtheservicesareconnected. Eachbundleisrenderedasadistinctgrouping,whichsupports bothlinearandtreeencodedstoragestructures.Abundlewitha linearworkflowisshown(Fig.11).Linearworkflowsrepresent sequencesofservicesintendedtoexecuteinorder,andaresuited forsimpleandfixedprocedures.

RestrictedLinearDataStructureofaBundle

Fig.11:

Ontheotherhand,ifanexperimentrequiresservicesthatleadto conditionalorparallelexperimentalsteps(Fig.12),atree workflowisimportantforachievingthisoptiondespiteconsuming morememoryandbeingmoredifficulttoencode.Withthis flexibility,thesystemcansupportfutureautomation,reporting, andvalidationwithoutalteringexistingcode.

Fig.12:TreeDataStructureofaBundle

WhilethebundleandcanvassystemimprovedtheWorkflow Manager’sorganizationandflexibility,itrevealsseveral limitationsinscalability.Linearworkflowsarepredictedtoscale predictably,buttree-encodedworkflowsrequireadditional computationtopropagateacrossbranches,whichexposes inefficienciesinrenderingandstorage.Further,somepartsarestill rigidandrepetitivebecauseoftherenderinglimitationsforeach nodeandedgeofabundle.Ifredesigned,thesystemcould separatelayoutcomputationfromdatalogicentirelyusinga generalizedgraph-processingapproachtosupportarbitrary workflowstructures.Futuresystemsshouldstoreworkflows

consistentwiththebundlestructureinthedatabasefromthestart toreducethetranslationcomplexitybetweentheseconceptually uniformdataobjects.

4 Conclusions

Thisworkdemonstrateshowsoftwareengineeringprinciplescan directlyacceleratescientificdiscoverybyimprovingthespeed, reliability,andautomationofbiologicalexperimentation.Forthe DAMPLab,thecontributionsoutlinedinthisprojecttransforma prototypeworkflowmanagerintoanalmostproduction-ready cloudlabplatform.Theannouncementsfeatureestablishesclear communicationchannelsbetweenlabpersonnelandusers,the flexibleservicepricingsystemenablesaccuratecostrepresentation withoutcodemodifications,andtheredesignedcheckoutprocess providesclientswithprofessionalordertrackingand documentation.Theseimprovementsaddressthefundamental challengeintroducedearlier:bridgingthegapbetweensoftware andbiologicalexperimentationtocreatetheintegratedcodesign environmentnecessaryforscalablesyntheticbiology.

BeyondthetechnicalcontributionstoDAMPLab,thisexperience providedinvaluableprofessionaldevelopmentincollaborative softwareengineering,includingpracticalexperiencewithmodern full-stacktechnologies(MERNstack,Nest.js,GraphQL),version controlworkflowsthroughGitHub,andthecommunicationskills essentialforteam-baseddevelopment–expertisedirectly applicabletofutureinternshipsandcareersattheintersectionof computationandbiology.

TheDAMPlabrepresentsjustoneopenapplicationofsoftware

engineeringinbiologicalresearch,butthebroadertrendisclear: biologyisrapidlybecomingdata-driven,creatingexpanding opportunitiesforcomputationalexperience.Carbonell, Radivojevic,andGarciaMartinidentifythreecriticalareaswhere softwareengineersareessentialtoadvancingsyntheticbiology [17].First,high-volumedatafrommodernsequencingand screeningneedscomputationalpipelinesforanalysis.Second, large-scaleautomationreliesonsoftwaretocoordinaterobotics, sensors,andworkflows,requiringengineerswhounderstandboth biologyandtechnicalsystems.Third,combiningsyntheticbiology, machinelearning,andautomationallowsclosed-loop experimentationwheresoftwareanalyzesresultsandautomatically designsfollow-upexperiments,speedingupthedesign-build-test cycle[2].Inshort,softwarehasbecomecentraltobiological research.

FutureworkontheDAMPLabcouldfocusoncompatibilitywith othercloudlaboratories.IntegratingAPIsfromplatformslike Benchlingwouldenablecross-platformautomationworkflows, allowingresearcherstodesignexperimentsinonesystemand executetheminanother.Thiscapabilityisparticularlyimportant foropen-sourceworkflowmanagerslikeDAMPLab,asitwould createanetworkeffectwheremultiplelabscontributetoand benefitfromsharedautomationprotocolsandstandardized biologicalmodules.Suchintegrationrepresentsasteptowardsthe fullyrealizedbiodesignautomationecosystemenvisionedby Densmore[1].

Lastly,wewouldliketothankZoeforherpatientguidanceand countlesshoursspentdebuggingalongsideus,Asadfororganizing ourprojectsandprovidingdetailedspecificationsthatkeptour workfocused,Dr.Tomlinsonforcreatingtheopportunitytolearn andcontributeatSAIL,andDr.Karnaukhforexpertly coordinatingtheprogram!

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