BigDataandNeuroscience

November2016

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Neuroscienceareas• Relativelynewscience

– Datesfromthe1960’s:beforethatsimplypartofbiology• Manydifferenttypesofneuroscience• Developmentalneuroscience describeshowthebraingrowsand

changes.• Cognitiveneuroscience involvesstudyinghowthebraincreatesand

controlsthought,language,problemsolving,andmemory.• Molecularandcellularneuroscience exploresthegenes,proteins,

andothermoleculesinvolvedinthefunctioningofneurons.• Behavioralneuroscience examinesthebrainareasandprocesses

underlyingthebehaviorofanimalsandhumans.• Clinicalneuroscience istheareaofstudyinwhichmedical

specialistssuchasneurologistsandpsychiatristsusebasicneuroscienceresearchfindingstoexplorehowtotreatandpreventneurologicaldisordersandtorehabilitatepatientswhosenervoussystemhasbeendamagedorinjured.– Source:USNIH

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Neuroscienceareas:alternativeview

• Experimentalneuroscience– Experimentalinthesensethatitproducesdata

• Notnecessarilytryinganexperiment– Clinicalandanimalstudies

• Humanandanimal:invivoandinvitro

• Cognitiveandcomputationalneuroscience– Concernedwithmodellingdata,understandinghowitlinkstobehaviour,includingcognition.

• Neuroinformatics– Concernedwithanalysingdatacomputationally,andwithcreatingmathematicalandcomputationalmodelsofdata

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Whybigdataandneuroscience?

• Hundredsofmillionsofpeopleintheworldsufferfromsomekindofneurologicaldisease:50millionpeoplehaveepilepsy;62millionareaffectedbycerebrovasculardisease;326millionpeoplesufferfrommigraine;24millionareaffectedbyAlzheimerdiseaseandotherdementias(WHO,"Neurologicaldisorders- publichealthchallenges",2006).(2011:Dementiaestimatenow35.6million,expectedtodoubleby2030)– Andthatomitsmentalillnessentirely

• Neuroscienceresearchisdependentonawiderangeofmethodsforunderstandinghowthebrainworks.Suchresearchincludecomputermodeling,imagingtechniques,andothermethodswhichgeneratesenormousamountsofdata.

• Inordertofullyutilizetheselargedatasets,researchersneedaccesstoinfrastructure,includingphysicalresources(computergrids);standardsfordataandexperiments;andstructuresforcollaboration.– Source:primarilyINCFwebsite.

• Neuroinformatics:https://www.youtube.com/watch?v=nuSdhaGGlAg

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Neuroscienceandbigdata:inputs• Clinicaldata

– Measurementsfrompatients:• Electroencephalogram(EEG),tomography(CT,MRI,PETscans)• Differentformsofopenskullrecordings(duringoperations)• Behavioural measurements• Nearinfra-redspectroscopy(NIRS)

– Measurementsfromanimals• Tomography,Electrophysiologyfromliveanimals,frombrainslices,fromculturedneurons.

• Behavioural measurements• Molecularandcellular

– Geneticsofbrains– Neurochemicalsinvolved(insynapses,inionchannels,in

neuronsandglia)

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Metadatainneuroscience• Therearemanydifferenttypesofmetadatainthis

discipline• Structuralmetadata:fileformats,etc.

– Relativelystraightforward(sometimes…seehttp://www.buzsakilab.com/content/PDFs/Teeters2015.pdf)

• Clinicalmetadata:– patientidentity,symptoms,co-morbidities,….– Importantethicalandlegalconsiderations

• Experimentalmetadata:– What’sbeingrecordedfrom(animal,tissuetype,plusother

information,e.g.Recordingapparatus,perfusion,...)– Behaviouralmetadata:whatstimuliarebeingprovided,what

behaviourisbeingexhibited...

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Aims(outputs)ofBigDatainNeuroscience

• Clinicalaims– Appropriatetreatments

• Measurementofeffectivenessindifferentpatients– Predictionoftreatmenteffects,understandingwhat’shappeningtothepatient.

• Experimentalneuroscience?– Deeperunderstandingofwhatneuralsystemsaredoing

• Understandingcognitivecapabilities• Developingcomputersthathavebrain-likeabilities

– Effectsofneurochemicalsontargetsystems(modelsystems)• Drugdevelopmentandassessment

– Oftenattemptingtoreduceanimalexperiments

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Somespecificprojects

• TraumaticBrainInjury:InTBIR,Center-TBI• TheHumanBrainProject(HBP)• CARMEN

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TraumaticBrainInjury• InTBIR:Internationalinitiativefortraumaticbraininitiativeresearch

– http://intbir.nih.gov• EU:Center-TBI:

– https://www.center-tbi.euAfewfactsaboutTBIinEurope:• 2.5millionpeoplesufferaTBIeachyear• 1millionareadmittedtohospital• 75,000willdie• TBIistheleadingcauseofdeathanddisabilityinyoungadults.• Theincidenceinelderlypatientsisincreasing.• TBIcanstrikeusall,butmalesareabouttwiceaslikelyasfemalestoexperiencea

TBI.• InyoungerpatientsRoadTrafficAccidentsarethemostfrequentcauseofinjury;in

olderpatientsfalls.• Moderateandsevereheadinjury(respectively)areassociatedwitha2.3and4.5

timesincreasedriskofAlzheimer’sdisease.

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TheCENTER-TBIdatabaseandrepositoriesonTBIwillbeaninvaluableresourceforfurtherresearchwhichwewouldwishtoencourage.Thedatabaseandrepositorieshavebeenfacilitatedbypublicfunding.Hence,itisnotonlyfromadesiretofacilitateresearchtoimprovethecareofTBIpatientsbutalsofromamoralobligationtothecommunitytoensurethemostoptimalreturnoninvestedfunding,thattheCENTER-TBIinvestigatorssupporttheconceptofdatasharing.Withtheaimtoensureanoptimaluseofthedataandtopreventpossiblemisuse,theCENTER-TBImanagementcommitteehasestablishedpoliciesfordatasharingaswellaspoliciesforpublicationandpublicationcreditsforthosewhouseCENTER-TBIdata.Thesepoliciesfurtheraimtoencourageacademicproductivityandtoprovideamechanismfortrackingandarchivingdatarequests,intendedanalysesandpublicationsrelatedtoandresultingfromtheCENTER-TBIdata.

TheexpectationoftheCENTER-TBImanagementcommitteeisthatde-identifieddataoftheCENTER-TBIstudycanbemadeavailabletothegeneralscientificcommunitywithinarelativelyshorttimeframeafterclosingandcheckingofthedatabase.

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FITBIR• FederalInteragencyTraumaticBrainInjuryResearchinformatics

system• “TheFederalInteragencyTraumaticBrainInjuryResearch(FITBIR)

informaticssystemwasdevelopedtosharedataacrosstheentireTBIresearchfieldandtofacilitatecollaborationbetweenlaboratories,aswellasinterconnectivitywithotherinformaticsplatforms.Sharingdata,methodologies,andassociatedtools,ratherthansummariesorinterpretationsofthisinformation,canaccelerateresearchprogressbyallowingre-analysisofdata,aswellasre-aggregation,integration,andrigorouscomparisonwithotherdata,tools,andmethods.Thiscommunity-widesharingrequirescommondatadefinitionsandstandards,aswellascomprehensiveandcoherentinformaticsapproaches.”

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Datadictionaries

• Commondataelements– Datadictionary:clearlydefinedtermsanddefinitions,internationallyshared

– Notstatic!Newmeasurementtypes,newinstruments,makesuchsystemsdynamic

– Seehttps://www.nlm.nih.gov/cde/index.html

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Status

• Running:collectingdatasetsinternationally.– InEU:https://www.center-tbi.eu/project/timeline#0

– InUS:callsforinvestigators:seehttps://www.center-tbi.eu/files/press/TED%20Seed%20Project%20RFA_Final_6-25-2015.pdf

– Verymuchalivebigdataproject!

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HumanBrainProject

• Large(“flagship”)EUproject– TheHumanBrainProject(HBP)isaEuropeanCommissionFutureandEmergingTechnologiesFlagshipthataimstoaccelerateourunderstandingofthehumanbrain,makeadvancesindefininganddiagnosingbraindisorders,anddevelopnewbrain-liketechnologies.

• 10-yearinitiative.Fundedtotallingabout€1,000,000,000altogether.

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HBP:Organisation• TheHBPisorganizedinthirteensubprojects,spanningstrategicneuroscience

data,cognitivearchitectures,theory,ethicsandsociety,managementandthedevelopmentofsixnewinformatics-basedplatformsincluding:

• Neuroinformatics(searchableatlasesandanalysisofbraindata)• BrainSimulation(buildingandsimulatingmulti-levelmodelsofbraincircuits

andfunctions)• MedicalInformatics(analyzing clinicaldatatobetterunderstandbrain

diseases)• NeuromorphicComputing(brain-likefunctionsimplementedinhardware)• Neurorobotics (testingbrainmodelsandsimulationsinvirtualenvironments)• HighPerformanceComputing(providingthenecessarycomputingpower)• TheseplatformswillbeaccessiblethroughtheHBPCollaboratory– aninternet

portalspecificallydesignedtoenableandenhancecollaborationandteamscience.Theseplatformswillalsoserveasthefocalpointforaneducationalprogrammedesignedtoengageandtrainthenextgenerationofscientists.Allthisresearchwillbecloselymonitoredtoensuretheethicaluseofdataandresponsibleresearchandinnovationwithactiverolesforscientists,philosophers,ethicists,policymakersandmembersofsociety.ITNPBD4 16

HBPCollaboratory• Underconstruction– Alpha-versionisreleased:HBPcollaboratory

• Onlineplatformthatlinksuserstovariousresources,data,anduserstooneanother

• Ahubforwebbasedscientificcollaboration,wheresharingandcollaborationhappenarounddata,softwareandservices.

• TheHBPisdevelopinghalfadozencomputingplatformprojectsthatareintendedtosupportneuroscience– Theaimofthecollaboratoryistotieallofthesetogether,andmakethemusablethroughouttheproject

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Whatkindsofplatform?• Neuroinformatics

– Includesbrainatlases,andelectrophysiology– Interconnectionstudiesofneurons– Largevolumeofimage-based(3-d)data

• BrainSimulation:buildingICTmodelsandsimulationsofbrainsandbraincomponents

• MedicalInformatics:bringingtogetherinformationonbraindiseases

• NeuromorphicComputing:ICTthatmimicsthefunctioningofthebrain

• Neurorobotics:testingbrainmodelsandsimulationsinvirtualenvironments

• HighPerformanceComputing:hardwareandsoftwaretosupporttheotherPlatforms

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CARMEN

• UnlikeHBPandInTBIR,CARMEN– CodeAnalysisRepository&Modellingfore-Neuroscience

• …isamature(=old?outdated?)neuroinformaticsproject

• Startedin2006,initiallyfundedbyEPSRC,andlaterbyBBSRC:

• Ane-Scienceprojecttoenhancecollaborationinneuroscience.

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