6/8/2015 TheFutureofBiodiversity:MappingandPredictingtheDistributionofLifewithDistributedComputation

TheFutureofBiodiversity:MappingandPredictingthe
DistributionofLifewithDistributedComputation

JamesH.Beach,AimeeM.Stewart,GregoryY.Vorontsov,RicardoScachettiPereira,DavidR.B.Stockwell,DavidA.Vieglais,
ScottR.Downie

Lifemapperisadigitallibrarythatservesspeciesdistributiondataonaglobalscale.UsingadistributedInternetquery
architecturetoretrievegeoreferencesfrombiologicalspecimendatabasesinmuseumsworldwide,wecreatemapsand
predictivemodelsofspeciesrangesbasedonenvironmentalcorrelationswithlocaleswherespeciesareknowntooccur.To
parallelizethecomputationofeachindependentspeciespredictionwecreatedascreensaverclientthatperformspredictive
analysesondesktopcomputersbeforeuploadingtheresultingmodeltotheLifemapperserver(http://Lifemapper.org).
LifemapperusesSanDiegoSupercomputerCentersGARPalgorithm,EsrisArcIMS,ArcSDEandMicrosoftsSQLServerasits
primarysoftwarecomponents.

Introduction

Conservationandunderstandingoftheearthsbiologicaldiversityisamultidisciplinary,multisectorandmultinational
activity.Museumsaroundtheworldhavebeensurveyingandcataloginglifeforthelast250years,primarilyforthepurposes
ofspeciesdiscoveryanddescription.Nonscientistsarelargelyunawareofvastamountofinformationrepresentedbyan
estimated3billionmuseumspecimensworldwide,andthegeospatialinformationfromthecollectionsthemselveshavebeen
underutilizedbeyondtheprimarycatalogingneedsoftheoriginalcollectors.Lifemapperharveststhegeographical
informationassociatedwithspecimensandrepurposesitasinputdataforpredictivemodelingofspeciesdistributions.The
Lifemapperprojectaimstohighlighttheroleofbiologicalcollectionsinstitutionsinthedocumentationofbiologicaldiversity
bydeliveringspecimendatatothedesktopsofPCusersworldwide.Lifemapperthenusesadesktopscreensavertocalculate
speciesdistributionpredictionmodels.Finally,wearchivethemodelsonanInternetserverandmakethemavailabletothe
publicontheLifemapperwebsite(http://Lifemapper.org).

UsingtheSpeciesAnalystnetwork(Vieglaisetal.,1998,http://tsadev.speciesanalyst.net),weregularlyquery
participatingmuseumdatabasesforgeospatialinformationandcachetheresults.Museumsmaintainownershipandcontrol
locallyoftheirdata,buttheyallowusdirectliveaccesstothem.Thecombinedspecimendataisthenanalyzedwith
environmentalvariablestoproducedistributionmapsforspecies.Itisthisanalysisthatconstitutesthebulkofthecomputing
powerrequired.Startingwithoveronemilliongeoreferencedspecimenrecordsand30,000uniquegeoreferencedtaxa,the
amountofcomputationrequiredissignificant.Toscaleourcomputationalpowertomeetthechallenge,wefollowedthe
embarrassinglyparallelcomputationmodeloftheSETI@Homeproject,whichenlistedpersonalcomputerstoanalyzeradio
signalsforindicationsofextraterrestriallife.Inourdistributedcomputingmodel,usersorLifemappersrunascreensaverin
thebackgroundoftheircomputerthatanalyzesdatadownloadedfromourserveraboutlifeonearth.Thedownloadeddata
packetconsistsofmuseumspecimenoccurrencepointsandenvironmentalvariables.Thescreensaverusesanalgorithmcalled
GARP,theGeneticAlgorithmforRulesetPrediction,toperformtheanalysis.GARPisaniterative,nondeterministicalgorithm
thatanalyzestherelationshipsbetweenpointlocationsandenvironmentalvariablesassociatedwiththoselocations.Thescreen
saverthenreturnsthedatapackettoourserverforsomepostprocessing,spatialdataarchiving,andwebpresentation.

TojointheLifemappereffort,usersregisteranddownloadthescreensaver.Withregistration,Lifemapperscanspecify
preferences,forexample,fortheclassoforganismforwhichtheyprefertocomputemodels.Lifemapperscanalsocreateand
joincomputinggroups.TheservertrackscomputingtimeandmodelscomputedforindividualLifemappersandforgroups
andpresentsthosestatisticsontheserver.

Methodology

Lifemappermodelsthecorrelationsbetweenknownspecieslocationsandenvironmentalvariablesatthoselocationsto
producespeciesdistributionmaps.Theessentialdatasetsoftheprojectarespeciesoccurrencesandenvironmentaldatasetsor
layers.Speciesoccurrencesarebasedonpointlocalitydataassociatedwithmuseumspecimenrecords.

Thesecondclassofdataisasetofglobalgeographiclayerscorrespondingtodifferentenvironmentalparameters,suchas
temperature,rainfall,treecover,andothers.Thelayersarestoredasgrids,whereeachcellcontainsthevalueofan
environmentalparameteratthatlocation.Lifemappercurrentlyusesabout30differentenvironmentallayers.TheUniversity
ofMarylandprovidedtwovariables,percentageoftreecoverandlanduse/landcover,at1kmresolution.TheUSGSprovided
terraindata(aspect,flowdirections,flowaccumulation,slope,andwetnessindex)atascaleof1:250,000thatwereresampledto
1kmresolution.ClimatedatawasobtainedfromtheIntergovernmentalPanelonClimateChange(IPCC)ataresolutionof0.5
degrees,whichwasthenresampledto1kmtomatchtheotherdatasets.ClimatevariablesconsistofJanuary,July,andyear
averagesfor19611990ofcloudcover,diurnaltemperaturerange,groundfrostfrequency,maximum,minimumandmean
temperature,precipitation,solarradiation,vaporpressure,wetdayfrequency,andwinds.

ThethreestagesofdataprocessingforLifemapper,preprocessing,clientprocessing,andserverpostprocessing,are

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6/8/2015 TheFutureofBiodiversity:MappingandPredictingtheDistributionofLifewithDistributedComputation

summarizedinFigure1.

Figure1:Lifemapperdataprocessing.ServerpreprocessingconsistsofdatacollectionviadistributedInternetquery.Client
processingisaccomplishedwithdistributedscreensaverclients.Serverpostprocessingaggregates,storesandservesthe
resultsinanInternetarchiveofspecimendatapointsanddistributionmodels.Theserveralsocombinesancillaryspeciesdata
suchascommonnamesfromotherbiodiversitywebservices.

ServerPreprocessing

Preprocessingconsistsofdatapreparation.TheTaxonSnifferapplicationharvestsdatafrombiodiversitydatabaseswiththe
SpeciesAnalyst(TSA)architecturethenusesArcObjectstostoretheminArcSDE.TSAusesZ39.50protocolandXMLfordata
retrievalfromanetworkofparticipatinginstitutionsthatareaccessibleovertheInternet.Asecondapplication,the
PreProcessor,combinesgeoreferencedspeciesdatapointsforindividualspecies,calculatesthegeographicextentofthepoints,
andthenpreparesapacketofdata(ajobpacket)inXMLformatfordistributiontoLifemapperclients.

ClientProcessing

TheLifemapperscreensaver(Figure2)implementsanevolutionaryalgorithmcalledtheGeneticAlgorithmforRuleset
Prediction(http://biodi.sdsc.edu),orGARP(StockwellandPeters,1999).Thismethodhasbeenshowntobethebestavailable
methodforreliablespeciespredictionsusingsmallsetsofadhocdatatypicallyreturnedfrommuseumdatabases(Stockwell
andPeterson,2002).Thealgorithmcreatesasetofrulestopredictpresenceorabsenceofaspeciesatacell,theniterativelytests
andmodifiesthem.

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Figure2.LifemapperScreenSaver.Thescreensaverpredictsspecieshabitatdistributionforasetofoccurrencedataand
environmentallayersusingtheGARPalgorithm.

Whenthescreensaverapplicationbegins,itrequestsajobpacketfromtheserver.Uponreceipt,theapplicationchecksthe
geographicextentofthejobpacketand,iftheenvironmentaldatasetwiththematchingextentisnotpresent,itrequeststhat
dataset.Thescreensaverprocessesthejobusingthedatapoints,theenvironmentaldataset,andtheGARPalgorithm.Once
thejobiscomplete,thescreensaversubmitsthejobbacktotheLifemapperserver.

ServerPostprocessing

Afteracompletedjobissubmittedtotheserver,thePostProcessor,anapplicationusingArcObjectsandVisualBasic6,creates
agridbyprojectingtherulesofthemodelbackontotheenvironmentallayers.Theapplicationthenaddsthegridtoan
aggregategridforthatspeciesandstoresitonthefilesystem.Asecondapplication,theModelStorer,convertsaggregategrids
tovectorformatandthenaddsthepolygonstoasingleArcSDElayerthatstoresallspeciesmodels.

Display

TheresultsoftheprocessingpipelinearegraphicallydisplayedontheLifemapperwebsite(http://www.lifemapper.org)from
theMapsandModelsmenu.ThemappingapplicationwascreatedusingtheArcIMS,ArcSDE,ArcIMSActiveXConnectorand
VBScript.Thisapplicationallowstheusertoquerythedatabaseforaspeciesbyscientificorcommonname,thenmapthepoint
locationsandaggregatedistributionmodelsforeachspecies.Otherservicesprovidedbythisapplicationincludeopportunities
forusers:toviewcurrentdatabasestatisticsonpointsandmodelsforthatspecies,toviewpointsbycontributinginstitution,
andtoreviewdistributionpointsormodels.

Figure3.LifemapperMappingApplication.TheLifemappermappagedisplaysspeciesdatapointsandaggregate
distributionmodelsarchivedarchivedontheserver.

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AsecondgraphicalapplicationcreatedincompliancewiththeOpenGISConsortiums(OGC)WebMappingServicestandard,
WMS,isawebservicethatwillreturnanXMLfiledescribingthecapabilitiesofthemapserviceoramapimagethatcanbe
insertedintoanotherwebpage.ToreturnthecapabilitiesXMLfile,aquerystring(theportionfollowingthe?)mustbe
attachedtothebaseURL(i.e.http://www.lifemapper.org/lmapps/MapWMS/?Service=WMS&Request=GetCapabilities).There
areseveralrequiredandoptionalparametersforconstructingamapquerythataredescribedattheWebMappingService
undertheDownloadsmenuoftheLifemapperwebsite.ThisapplicationwasbuiltwithArcIMSActiveXConnectorand
VisualC#.

Discussion

Lifemapperrecoversunderutilizedgeospatialdataassociatedwithbiologicalcollectionsandbringsthemintoa
predictivescienceframework.Bycombiningmuseumdatawithglobalenvironmentaldatalayersweareabletopredictthe
presentandfuturespreadofspeciesranges.Bychangingenvironmentalregimes,suchasbyapplyingglobalclimatechange
scenariostobaselineenvironmentalcoverages,wecanpredicttheinfluenceofchangesintemperatureandrainfallonthe
distributionofspecies.Bybringingtheresultsofthesesimulationstoanopenaccesswebserverandwebmappingservice,we
canpromoteabetterandwiderunderstandingofbiologicaldiversityandenvironmentalinfluencesonit.

FuturedirectionsfortheLifemapperProjectincludeevolvingitintoawebbased,workbenchanalysistool,addingmore
classesofenvironmentaldata,includingremotesensinginformationandadditionalkindsofbiologicalandhumanimpactdata
setsasinputstothepredictionprocess.WealsoplantoextendLifemappertoprovidevalueaddedservicesformuseumdata
providers,suchasgeographicaldatavalidationfornewlyenteredspecimenrecords.Forexamplewecouldrespondtoanew
museumdatarecordwith:YourspecimenoforchidspeciesXappearstobeinthewronghemisphere,orThisparasite
speciesisseveralcountriesawayfromitspredictedrange,andmaybeaninvasive.Anotherexciting,broadareafor
developmentistheincorporationLifemapperintoformalandinformalscienceeducationprojects.Wearenowplanningfor
thoseactivities.

Acknowledgements

WethanktheNationalScienceFoundationforitssupportviaagrantfromtheDivisionofBiologicalInfrastructureKDI
Program(DBI9873021).LifemapperwascreatedattheBiodiversityResearchCenterattheUniversityofKansasin
collaborationwithUSGSBiologicalResources,theUniversityofNewMexico,theUniversityofCaliforniaBerkeley,California
AcademyofSciences,theUniversityofMassachusettsBoston,andtheReferenceCenterforEnvironmentalInformation
(CRIA),SaoPaulo,Brazil.

References

Stockwell,D.R.B.andD.Peters1999.TheGARPModelingSystem:problemsandsolutionstoautomatedspatialprediction.
InternationalJournalofGeographicalInformationScience13:2143158.

Stockwell,D.R.B.andA.T.Peterson2002.Effectsofsamplesizeonaccuracyofspeciesdistributionmodels.EcologicalModeling
148:113.

Vieglais,D.A.,D.R.B.Stockwell,C.M.Cundari,J.H.Beach,A.T.Peterson,andL.Krishtalka1998.Thespeciesanalyst:Tools
enablingacomprehensivedistributedbiodiversitynetwork.Biodiversity,Biotechnology&Biobusiness,2ndAsiaPacific
ConferenceonBiotechnology,2327November,Perth,WesternAustralia.

AuthorInformation

JamesH.Beach,AssistantDirectorforInformatics,BiodiversityResearchCenterandNaturalHistoryMuseum,Universityof
Kansas,1345JayhawkBlvd.,Lawrence,KS66045,beach@ku.edu

AimeeM.Stewart,SoftwareDeveloper,BiodiversityResearchCenterandNaturalHistoryMuseum,UniversityofKansas,1345
JayhawkBlvd.,Lawrence,KS66045,astewart@ku.edu

GregoryY.Vorontsov,SoftwareDeveloper,BiodiversityResearchCenterandNaturalHistoryMuseum,UniversityofKansas,
1345JayhawkBlvd.,Lawrence,KS66045,voron999@ku.edu

RicardoScachettiPereira,ResearchManager/SystemsAnalyst,CentrodeRefernciaemInformaoAmbiental,CRIA,Av.
RomeuTrtima,388,BaroGeraldo,13084520CampinasSPBrazil,ricardo@cria.org.br

DavidR.B.Stockwell,AssistantResearchScientist,SanDiegoSuperComputerCenter,UniversityofCalifornia,SanDiego,
9500GilmanDrive,LaJolla,CA,920930505,davids@sdsc.edu

DavidA.Vieglais,SeniorScientist,BiodiversityResearchCenterandNaturalHistoryMuseum,UniversityofKansas,1345
JayhawkBlvd.,Lawrence,KS66045,vieglais@ku.edu

ScottR.Downie,WebProgrammer,BiodiversityResearchCenterandNaturalHistoryMuseum,UniversityofKansas,1345
JayhawkBlvd.,Lawrence,KS66045,sdownie@ku.edu

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