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SoftwareandDataasScaffoldsforIntegrativeScience
DavidLeBauer,Ph.D.UniversityofIllinoisatUrbana-Champaign
DepartmentofAgriculturalandBiologicalEngineeringCarlRWoeseInstituteforGenomicBiology
NationalCenterforSupercomputingApplications
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Outline
• Overview:ProblemsandApproach
• CombiningInformation
• Models:integrationacrossdomains
• PEcAn:integrationofmodelsanddata
• TERRAREF:automateddatacollectionandanalysis
• FutureDirections
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Challengesweface
• AgriculturalProduction:• Feeding9bnby2050• Climateischanging
• Resourcesarebecomingscarce
• ScientificProblems:
• Howdogenescontroltraits?• Howcanleveragedataandcomputing?
3Tilmanetal,Nature2002
Yield
Fertilizer
Pesticides
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TechnicalSolutionsforScienceandAgriculture
• KnowledgeisSpreadAcrossManyScalesandFormats:• ExpertKnowledge• Data• MechanisticModels
• Integratingthesewillenable:• StrongerInferenceandPrediction• MoreScienceandEngineering
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Marshall-Colon et al 2017 Frontiers in Plant Science
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102m
10-3m
103m
104m
105m Whichcropsareviable,…andwhere?
Whatfractionofglobalenergy/fooddemand?
CountylevelmeanyieldsSupplychainoptimization
Localtopography:soil,hydrologySub-fieldmanagement
CropArchitectureRowSpacing/OrientationHarvestingEquipmentShadingresponse
SpatialScale Questions
OpportunitiesAcrossScales
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Outline
• ConceptualOverview• ComputationalSolutions
• CropModels
• PEcAn• TERRAREF
• FutureDirections
Zhu,Lynch,LeBauer,Millar,Stitt,Long,2015PlantCell&Environment
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EvanDelucia
StartingPoint:ConceptualModels
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BioCro:CombiningBiology,Physics,Chemistry
HumphriesandLong2005Miguezetal2009,2012Jaiswal,DeSouza,Larsen,LeBauer,…etal2017Wang,Jaiswal,LeBauer,…etal2015
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InputsMeteorology(energy,water)
Soil(physics,carbon,nutrients)
Parameters(e.g.planttraits)
OutputsYield,Biomass,
EnergyBalance
WaterUse
NutrientUse
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ScalingPhotosynthesisfromLeaftoCanopy
Light
Temperature
Light
Light
Photosynthesis
Photosynthesis
Temperature9
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ScalingUp&PredictingtheFuture
IPCC AR5 Warszawski et al. PNAS
Temperature Precipitation
ClimateForecasts(2040-2050) CMIP5:5Climatemodelsx4CO
2emissionsScenarios
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EffectsofClimateonSugarcaneYieldinBrazil2040-2050 Climate Impact
(metric Tons / ha)
Jaiswal, DeSouza, Larsen, LeBauer, Miguez, Sparovek, Bollero, Buckeridge, Long, 2017
Scaling leaf-level CO2 x T x H2O response11
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Outline
• ConceptualOverview• ComputationalSolutions
• CropModels
• PEcAn:LinkingModelsandData
• TERRAREF• FutureDirections
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PEcAn
LeBauer et al, 2013
Ecological Model-data Synthesis
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LeBauerandTreseder,2008
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Thomasetal2013
CombiningDataandModelsIsHard,MostlyaTechnicalChallenge
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Traits System States
Prediction
Soil
Meteorology
Parameters
Boundary Conditions
Drivers
Publications
Primary Data
Repositories
Wild Data Relevant Information Configuration
Sensitivity
Calibration
Validation
AnalysesRun Model Outputs
JustRunningaModelisHard
Most of this work is model independent, so solutions can be shared
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DataSources AnalysesEcosystemModels
BioCroED2CLMSIPNET
...n=12
TheStandardApproach:Redundant,LaborIntensive,ErrorProne
Converter
ForMet,needoneconverterperdriver(m)xmodel(n)combination
Prediction
NARR
NOAA
Fluxnet
CMIP5
… m = 10
Met Station
Calibration
Sensitivity
Validation
Visualization
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PEcAncommonformats:Manyusersuse,reuse,test,andimprovecomponents
CommonFormat
CommonFormat
EcosystemModels
BioCroED2CLMSIPNET
...n=12
Converter
Onlyneedn+m(notn×m)convertersLesswork,morerobustandvalidresults
Diverse Met Data
NARR
NOAA
Fluxnet
CMIP5
… n = 10
Met Station
Analyses
Prediction
Calibration
Sensitivity
Validation
Visualization
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ParameterEstimation:CombiningLiteratureandFieldData
LeBaueretal,2013 17
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LeBaueretal,2013
Givencurrentdata,whatdrivesuncertainty?3Years,1crop,1location
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PEcAnVarianceDecomposition
Bars:ParameterContributiontoUncertaintyinYieldPrediction
Grey=PriorBlack=Posterior
Usedtoinformoptimaldatacollection
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LeBaueretal,2013
Automation&Reuse:Uncertaintyanalysisbars/color=ParameterContributiontoPredictiveUncertainty
3Years,1crop,1location
19Dietzeetal,2014
~1Year,8scientists,17PFTs,6biomes
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TargetedFieldStudy:WillowWaterUse
Wertin,LeBauer,Volk,Leakey,inprep
Predictions
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Before AfterDataCollection
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AddData Configure AnalyzeRun
MakingCrop&EcosystemModelsAccessible
LeBaueretal2013,Kooperetal2013,Dietzeetal,201321
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PEcAnisacommunityproject
42Contributors>50citationsTextbook100sofstudentstrained
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PEcAnRadiativeTransferModelInversion
23Ely,Serbin,Shiklomanov,Dietzeandothers
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PEcAnnowprovidesaplaceforsharedmodels,dataaccess,andtools
Tools: Web front end PostGIS database* Met Scaling and Gap filling Data Ingest Meta-Analysis* Sensitivity & Uncertainty Analysis* Ensemble Prediction Parameter Data Assimilation State Data Assimilation Benchmarking Visualization* Data Modeling:
Radiative Transfer Photosynthesis Tree Rings
Models: BioCro* CABLE CLM DALEC ED* FATES G’Day JULES Linkages LPJguess MAAT MAESPA PRELES SIPNET
Data: Literature* Field Measurements Expert Priors* Meteorology Soils PalEON Fluxnet ORNL NEON TERRA REF* LTER …
github.com/pecanproject/pecanpecanproject.org
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Outline
• ConceptualOverview• ComputationalSolutions
• CropModels
• PEcAn:LinkingModelsandData
• TERRAREF• FutureDirections
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HighThroughputPhenotyping
• HighThroughputPhenotyping:• Replacemanualwithsensor-basedmeasurements• Measuremoretraitswithhigherfrequency
• But…sensorsareexpensiveanddataaredifficulttointerpret
• Terraprogrammajorinvestmenttopushthisforward
http://bulletin
.ipm.illinois.ed
u/print.ph
p?id=513
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TERRAREF
• Motivation:
• AutomatedMeasurements—>StrongerInference
• Software&Data—>FrameworkforInterdisciplinaryCollaboration
• Solutions:• ReferenceDatasets• ModularandInteroperable
• OpenData,Software,Computing
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APhenomicsPipelineforCropImprovement
Sensors Traits Genotypes
Selection
Genomics
Higher Yield Yield Stability Nutrition Stress Tolerance and more …
Automated MeasurementsComponent & Aggregate
Genomic Prediction
Pan Genome
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DiverseScientificDisciplines
Sensors Traits Genotypes
Selection
Genomics
Engineering Robotics Computer Vision
(Eco)Physiology Agronomy
Biology
Breeding
Statistics & Machine Learning
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ARPA-ETERRA
OpenDatasetforSixProjects+PublicRelease
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TERRAReferenceDataSources
LemnatecScanalyzerDanforth,St.Louis
LemnatecFieldScannerUSDAALRC,Maricopa,AZ
TractorandUAVAZandKansasState
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FieldScannerSensors
terraref.org/articles/lemnatec-scanalyzer-field-sensors/
VNIR Imaging Spectrometer 380-1000nmSWIR Imaging Spectrometer 900-2500 nmIR Temperature SensorNDVI (1 down, 1 up) 650, 800 nmPRI Sensor 531, 570 nmPAR Sensor 410-655 nmColor Sensor 410-655 nm3D Scanners: 2 Side View, 1 DownRGB: 2 Side View, 1 Down (1)Active Reflectance 670, 730, 780 nmPS II Fluorescence Environmental: wind, temperature, humidity, light, rain, CO2
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Approach:IntegrateSoftwareandDatabases
• Whatdopeoplecurrentlyuse?
• Whatdomainspecificsoftwareanddatabasesexist?
• Howcanweconnectthese?• Whatstandards&conventionstoadopt?
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GeneralFrameworkforCross-DomainLinks
Sensors Traits Genotypes
Selection
Genomics
LocationTime
Genotype
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DataFormats,Standards&Conventions
Sensors Traits Genotypes
Selection
CF Conventions OGC
geoTIFF NetCDF-CF LAS
PEcAn Crop Ontology AgMIP/ICASA BRAPI
BAM, FASTQ, VCF, BED, FASTA, GFF
Genomics
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TERRAREFDatabases
Sensors Traits Genotypes
Selection
Genomics
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ModularSoftware
github.com/terraref 37
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TERRAREFPipeline
Fieldmeasurements
Metadata
TraitData
PipelineOrchestration
SensorData
Analysis&Development
1TB/d
<48h
Genomics
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DataAnalysisEnvironmentsAnyLinuxConfiguration+LargeFilesystem+ Databases+ Compute
Workflows:Analyze! Share! PublishDevelop! Deploy
workbench.terraref.org39
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~/data~/tutorials
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WebApplicationDevelopedwithNDSWorkbench
traitvis.workbench.terraref.org 41
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218mm
RobertPlessZongyangLiSolmazHajmohammadi
3DLaserScanner
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%Reflectance
10cm
Nscandirection
HyperspectralImageat543nm
x
y
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Thermal
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AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)
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AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)
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AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)
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AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)
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AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)
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AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)
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AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)
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AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)
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AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)
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AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)
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AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)
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AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)
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GeoffMorris&ZhenbinHu,KSULOD(LogorithmofOdds)geneslinkedtotrait
GenesThatControlGrowthRate
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Getinvolved
• Signupforbetareleaseofsoftwareanddata• terraref.org/data
• Useandprovidefeedbackonsoftwareanddataformats
• github.com/terraref
• Collaborate• Fieldmeasurements
• Software• Algorithms
• ColocatedSensors68
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Outline
• ConceptualOverview• ComputationalSolutions
• CropModels
• PEcAn:LinkingModelsandData
• TERRAREF• FutureDirections
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Baroneetal2017bioRxiv“UnmetNeedsforAnalyzingBiologicalBigData:ASurveyof704NSFPrincipalInvestigators”
SoftwareCarpentryXSEDE.org,SharedClusters
Trainingisthebottleneck
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Introductiontodatascience,withexamplesandprojectsfromTERRAREF
HackathonsandTraining
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ArkansasStateUniversityIowaStateUniversityPurdueUniversityUniversityofArizonaUniversityofIllinoisUniversityofNebraskaUniversityofArkansas
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Toppetal,unpublished72
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SensorModelingandModelCoupling
Toppetal.unpublished73
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ModularModelComponents
Zhu,Lynch,LeBauer,Millar,Stitt,Long,2015PlantCell&EnvironmentMarshall-Colonetal2017FronsersinPlantSciencecropsinsilico.org
Eachcomponentrepresents>=1hypothesis.
Eachparameteroroutputcanbetreatedasaphenotype
EnvironmentaldriverscanbeintegratedovertoaddressGxE
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PurduePhenomics&IoTPlatforms• DevelopCyberinfrastructure
• Makedatauseable
• Facilitateinterdisciplinaryresearch• Assessexistingcapabilities,currentroadblocks,futureneeds• WorkwithLibrary,RCAC,facultytofacilitatedatapublishing
• QA/QC• CommunityStandardsandCommonInterfaces
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Funding:
NSFAdvancesinBiologicalInfrastructure
USDANIFAFoodandAgricultureCyberinformaticsandTools
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AgriculturalTechnology
Onceweunderstandhowthesesystemswork,wecanengineerforecosystemservicesratherthatsolelyforyield:• Climatecontrol• Soilimprovement,carbonstorage• Roots,mycorrhizae,microbiome• Pharmaceuticals• PetrochemicalSubstitutes• …anythingplantscando
NASA Ames Research Center
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ToddMockler ProjectLeadNadiaShakoor ProjectDirector
NoahFahlgren Phenotyping&BioinformaticsEricaFishel TechnologyTransfer
SolmazHajmohammadi SensorFusion
StephenKresovich BreedingJeremySchmutz Sequencing
GeoffMorris Gene-traitAssociationsWilliamRooney Breeding
PedroAndrade-Sanchez Agronomy&PhenomicsMichaelOttman Physiology
MariaNewcomb FieldMeasurementsJeffWhite Agronomy
DavidLeBauer Informatics&ComputingRobertPless ImageAnalysis
RomanGarnett PredictionAlgorithmsWasitWalamu Sensing&Physiology
MaxBurnetteCraigWillis
RobKooperJeffTerstreip
ZongyangLi
ZhenbinHuNickHeyek
CharlieZenderHenryButowsky
Team
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• MikeDietze,BostonUniversity
• DavidLeBauer,UniversityofIllinois• ShawnSerbin,BrookhavenNationalLab• AnkurDesai,UniversityofWisconsin
• KentonMcHenry,NationalCenterforSupercomputingApplications
• andmanyotheruser/contributors
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DavidLeBauer
TERRAREF
terraref.org
github.com/terraref
@terra_ref
PEcAnProject
pecanproject.org
github.com/pecanproject
@pecanproject79