Software and data as scaffolds for integrative science

SoftwareandDataasScaffoldsforIntegrativeScience

DavidLeBauer,Ph.D.UniversityofIllinoisatUrbana-Champaign

DepartmentofAgriculturalandBiologicalEngineeringCarlRWoeseInstituteforGenomicBiology

NationalCenterforSupercomputingApplications

Outline

• Overview:ProblemsandApproach

• CombiningInformation

• Models:integrationacrossdomains

• PEcAn:integrationofmodelsanddata

• TERRAREF:automateddatacollectionandanalysis

• FutureDirections

Challengesweface

• AgriculturalProduction:• Feeding9bnby2050• Climateischanging

• Resourcesarebecomingscarce

• ScientificProblems:

• Howdogenescontroltraits?• Howcanleveragedataandcomputing?

3Tilmanetal,Nature2002

Fertilizer

Pesticides

TechnicalSolutionsforScienceandAgriculture

• KnowledgeisSpreadAcrossManyScalesandFormats:• ExpertKnowledge• Data• MechanisticModels

• Integratingthesewillenable:• StrongerInferenceandPrediction• MoreScienceandEngineering

Marshall-Colon et al 2017 Frontiers in Plant Science

105m Whichcropsareviable,…andwhere?

Whatfractionofglobalenergy/fooddemand?

CountylevelmeanyieldsSupplychainoptimization

Localtopography:soil,hydrologySub-fieldmanagement

CropArchitectureRowSpacing/OrientationHarvestingEquipmentShadingresponse

SpatialScale Questions

OpportunitiesAcrossScales

Outline

• ConceptualOverview• ComputationalSolutions

• CropModels

• PEcAn• TERRAREF

• FutureDirections

Zhu,Lynch,LeBauer,Millar,Stitt,Long,2015PlantCell&Environment

EvanDelucia

StartingPoint:ConceptualModels

BioCro:CombiningBiology,Physics,Chemistry

HumphriesandLong2005Miguezetal2009,2012Jaiswal,DeSouza,Larsen,LeBauer,…etal2017Wang,Jaiswal,LeBauer,…etal2015

InputsMeteorology(energy,water)

Soil(physics,carbon,nutrients)

Parameters(e.g.planttraits)

OutputsYield,Biomass,

EnergyBalance

WaterUse

NutrientUse

ScalingPhotosynthesisfromLeaftoCanopy

Temperature

Photosynthesis

Temperature9

ScalingUp&PredictingtheFuture

IPCC AR5 Warszawski et al. PNAS

Temperature Precipitation

ClimateForecasts(2040-2050) CMIP5:5Climatemodelsx4CO

2emissionsScenarios

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

Outline

• CropModels

• PEcAn:LinkingModelsandData

• TERRAREF• FutureDirections

LeBauer et al, 2013

Ecological Model-data Synthesis

LeBauerandTreseder,2008

Thomasetal2013

CombiningDataandModelsIsHard,MostlyaTechnicalChallenge

Traits System States

Prediction

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

DataSources AnalysesEcosystemModels

BioCroED2CLMSIPNET

...n=12

TheStandardApproach:Redundant,LaborIntensive,ErrorProne

Converter

ForMet,needoneconverterperdriver(m)xmodel(n)combination

Prediction

Fluxnet

… m = 10

Met Station

Calibration

Sensitivity

Validation

Visualization

PEcAncommonformats:Manyusersuse,reuse,test,andimprovecomponents

CommonFormat

EcosystemModels

BioCroED2CLMSIPNET

...n=12

Converter

Onlyneedn+m(notn×m)convertersLesswork,morerobustandvalidresults

Diverse Met Data

Fluxnet

… n = 10

Met Station

Analyses

Prediction

Calibration

Sensitivity

Validation

Visualization

ParameterEstimation:CombiningLiteratureandFieldData

LeBaueretal,2013 17

LeBaueretal,2013

Givencurrentdata,whatdrivesuncertainty?3Years,1crop,1location

PEcAnVarianceDecomposition

Bars:ParameterContributiontoUncertaintyinYieldPrediction

Grey=PriorBlack=Posterior

Usedtoinformoptimaldatacollection

LeBaueretal,2013

Automation&Reuse:Uncertaintyanalysisbars/color=ParameterContributiontoPredictiveUncertainty

3Years,1crop,1location

19Dietzeetal,2014

~1Year,8scientists,17PFTs,6biomes

TargetedFieldStudy:WillowWaterUse

Wertin,LeBauer,Volk,Leakey,inprep

Predictions

Before AfterDataCollection

AddData Configure AnalyzeRun

MakingCrop&EcosystemModelsAccessible

LeBaueretal2013,Kooperetal2013,Dietzeetal,201321

PEcAnisacommunityproject

42Contributors>50citationsTextbook100sofstudentstrained

PEcAnRadiativeTransferModelInversion

23Ely,Serbin,Shiklomanov,Dietzeandothers

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

Outline

• CropModels

HighThroughputPhenotyping

• HighThroughputPhenotyping:• Replacemanualwithsensor-basedmeasurements• Measuremoretraitswithhigherfrequency

• But…sensorsareexpensiveanddataaredifficulttointerpret

• Terraprogrammajorinvestmenttopushthisforward

http://bulletin

.ipm.illinois.ed

u/print.ph

p?id=513

TERRAREF

• Motivation:

• AutomatedMeasurements—>StrongerInference

• Software&Data—>FrameworkforInterdisciplinaryCollaboration

• Solutions:• ReferenceDatasets• ModularandInteroperable

• OpenData,Software,Computing

APhenomicsPipelineforCropImprovement

Sensors Traits Genotypes

Selection

Genomics

Higher Yield Yield Stability Nutrition Stress Tolerance and more …

Automated MeasurementsComponent & Aggregate

Genomic Prediction

Pan Genome

DiverseScientificDisciplines

Selection

Genomics

Engineering Robotics Computer Vision

(Eco)Physiology Agronomy

Biology

Breeding

Statistics & Machine Learning

ARPA-ETERRA

OpenDatasetforSixProjects+PublicRelease

TERRAReferenceDataSources

LemnatecScanalyzerDanforth,St.Louis

LemnatecFieldScannerUSDAALRC,Maricopa,AZ

TractorandUAVAZandKansasState

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

Approach:IntegrateSoftwareandDatabases

• Whatdopeoplecurrentlyuse?

• Whatdomainspecificsoftwareanddatabasesexist?

• Howcanweconnectthese?• Whatstandards&conventionstoadopt?

GeneralFrameworkforCross-DomainLinks

Selection

Genomics

LocationTime

Genotype

DataFormats,Standards&Conventions

Selection

CF Conventions OGC

geoTIFF NetCDF-CF LAS

PEcAn Crop Ontology AgMIP/ICASA BRAPI

BAM, FASTQ, VCF, BED, FASTA, GFF

Genomics

TERRAREFDatabases

Selection

Genomics

ModularSoftware

github.com/terraref 37

TERRAREFPipeline

Fieldmeasurements

Metadata

TraitData

PipelineOrchestration

SensorData

Analysis&Development

Genomics

DataAnalysisEnvironmentsAnyLinuxConfiguration+LargeFilesystem+ Databases+ Compute

Workflows:Analyze! Share! PublishDevelop! Deploy

workbench.terraref.org39

~/data~/tutorials

WebApplicationDevelopedwithNDSWorkbench

traitvis.workbench.terraref.org 41

RobertPlessZongyangLiSolmazHajmohammadi

3DLaserScanner

%Reflectance

Nscandirection

HyperspectralImageat543nm

Thermal

AutomatedDetectionAlgorithms(TimeSeriesofPanicleCounts)

ZongyangLiandRobertPless 45

GeoffMorris&ZhenbinHu,KSULOD(LogorithmofOdds)geneslinkedtotrait

GenesThatControlGrowthRate

Getinvolved

• Signupforbetareleaseofsoftwareanddata• terraref.org/data

• Useandprovidefeedbackonsoftwareanddataformats

• github.com/terraref

• Collaborate• Fieldmeasurements

• Software• Algorithms

• ColocatedSensors68

Outline

• CropModels

Baroneetal2017bioRxiv“UnmetNeedsforAnalyzingBiologicalBigData:ASurveyof704NSFPrincipalInvestigators”

SoftwareCarpentryXSEDE.org,SharedClusters

Trainingisthebottleneck

Introductiontodatascience,withexamplesandprojectsfromTERRAREF

HackathonsandTraining

ArkansasStateUniversityIowaStateUniversityPurdueUniversityUniversityofArizonaUniversityofIllinoisUniversityofNebraskaUniversityofArkansas

Toppetal,unpublished72

SensorModelingandModelCoupling

Toppetal.unpublished73

ModularModelComponents

Zhu,Lynch,LeBauer,Millar,Stitt,Long,2015PlantCell&EnvironmentMarshall-Colonetal2017FronsersinPlantSciencecropsinsilico.org

Eachcomponentrepresents>=1hypothesis.

Eachparameteroroutputcanbetreatedasaphenotype

EnvironmentaldriverscanbeintegratedovertoaddressGxE

PurduePhenomics&IoTPlatforms• DevelopCyberinfrastructure

• Makedatauseable

• Facilitateinterdisciplinaryresearch• Assessexistingcapabilities,currentroadblocks,futureneeds• WorkwithLibrary,RCAC,facultytofacilitatedatapublishing

• QA/QC• CommunityStandardsandCommonInterfaces

Funding:

NSFAdvancesinBiologicalInfrastructure

USDANIFAFoodandAgricultureCyberinformaticsandTools

AgriculturalTechnology

Onceweunderstandhowthesesystemswork,wecanengineerforecosystemservicesratherthatsolelyforyield:• Climatecontrol• Soilimprovement,carbonstorage• Roots,mycorrhizae,microbiome• Pharmaceuticals• PetrochemicalSubstitutes• …anythingplantscando

NASA Ames Research Center

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

• MikeDietze,BostonUniversity

• DavidLeBauer,UniversityofIllinois• ShawnSerbin,BrookhavenNationalLab• AnkurDesai,UniversityofWisconsin

• KentonMcHenry,NationalCenterforSupercomputingApplications

• andmanyotheruser/contributors

DavidLeBauer

dlebauer@illinois.edu

TERRAREF

terraref.org

github.com/terraref

@terra_ref

PEcAnProject

pecanproject.org

github.com/pecanproject

@pecanproject79

Software and data as scaffolds for integrative science

Science

Safety : Scaffolds

Scaffolds (61.170) NORMA

Biomaterials and scaffolds

Arch205 building construction I - … · TYPES OF SCAFFOLDING •Putlog Scaffolds •Independent Scaffolds •Mobile Scaffolds •Patent Scaffolding •Birdcage Scaffolds •Slung

Ladders, Scaffolds, 7 & Other Supportwilswood.weebly.com/uploads/1/6/8/8/16880972/ch07_carpentry_se.pdf · Ladders, Scaffolds, ... • Identify various types of ladders and scaffolds

Cyclodextrin Scaffolds

Molecular scaffolds poster

Tower Scaffolds

Suspended Scaffolds

Section Six: Scaffolds

Temporary Scaffolds Guidelines

23627130 Scaffolds Safety

Polymer Scaffolds for Biomaterials Applicationsmolly/Binder/polymer scaffolds for... · Polymer Scaffolds for Biomaterials Applications ... scaffold, the degradation of which is controlled

CFR 1926.450 - SUBPART L SCAFFOLDS CFR 1926.450 - SUBPART L SCAFFOLDS

C 8 Scaffolds

OSHA Rules for ScaffoldingOSHA Rules for Scaffolding · give to erector / user or post on job site frame scaffolds, system scaffolds, tube and clamp scaffolds & rolling scaffolds

Biovascular scaffolds

Scaffolds in Construction.ppt

WSH (Scaffolds) Rgs

PREPARATION OF INTELLIGENT CHITOSAN- COLLAGEN BASED ... · Collagen scaffolds lead to larger porous while chitosan scaffolds originated smaller ones. Collagen scaffolds also showed