lifewatch
TRANSCRIPT
The E-Biodiversity Research Institute Proposal for Italy’s Contribution to LifeWatch
eScienceandTechnologyInfrastructureforBiodiversityandEcosystemResearch
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«Preamble / 5
12.Service Centre / 11 2.1 Access to the infrastructure / 11 2.2 The Service Centre implementation / 122.3 Management of the Service Centre / 122.3.1 Management,co-ordinationandcontracts–backoffice/122.3.2 Coordinationofdistributedservices/122.3.3 Businessdevelopmentandmarketing/132.3.4 Fundraising/132.4 Interfacewithusers/132.4.1 Helpdesk/132.4.2 Multimedia/132.5 Networking and liaisons / 142.5.1 Userplatforms/142.5.2 Publicrelationsandcommunication/142.6 Training activities / 142.6.1 TheLifeWatche-Learningprogramme/152.6.2 LifeWatchChallengeFellowshipprogramme/152.6.3 LifeWatchCentralTrainingActivities/152.6.4 DistributedTrainingActivities/15
s4. Start-up Plan / 294.1 Networking the scientific community / 294.2 Coordinating with the Start-up of LifeWatch-ERIC / 294.3 Temporary start-up organization / 304.4 Organising the Central Service Centre / 314.5 Organising the Biological Research Department / 314.5.1 Establishthestart-upnodesfortheVirtualLabs/314.5.2 Developtheinter-operabilitywithinVirtualLab/314.6 Develop a model Showcase / 314.7 Financial plan for the start-up / 32
Annex 1 / 34ProtocolofintentformalisingtheJointResearchUnitdefinedas:LifeWatch-ITAannex 2 / 39FinancialPlanforthe5yearscommitment
p3. Virtual Laboratories / 163.1 Virtual Lab ‘Biomolecular’ / 163.1.1 Rationale/163.1.2 Structure/163.1.3 ProductsandTools/193.1.4 ApplicationsandImpact/193.2 Virtual Lab ‘Collections’ / 203.2.1 Rationale/203.2.2. Structure/203.2.3. ProductsandTools/213.2.4.ApplicationsandImpacts/223.3 Virtual Lab ‘Interactions’ / 223.3.1 Rationale/223.3.2 Structure/233.3.3 ProductsandTools/243.3.4 ApplicationsandImpacts/243.4 Virtual Lab ‘Mediterraneo’ / 253.4.1 Rationale/253.4.2 Structure/263.4.3 ProductsandTools/283.4.4ApplicationsandImpacts/28
u1. Structure of the E-Biodiversity Research Institute / 7
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Preamble«
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Whatmakesourplanetdifferentfromallothersislife.Gaiaisalivingplanet(Lovelock,1979;Gaia, a new look of Life on Earth).Tosomeextent,andwithinthecontextoftheabioticdrivers,lifeisself-organisedintospatialandfunctionalunits,whichwecallecosy-stems,nestedwithintheBiosphere,thelargestEarthecosystem.
IfthecomplexityoflifecanbesummarisedbytheconceptofBiodiversity,comprisingalsoourselvesandouractivities,thenBiodiversityisself-organisedwithintheBiosphereandthesmallernestedecosy-stems,determiningallthoseecosystemfunctionsandservicesthatoursocietiesperceiveasimportantbenefits.
Biodiversityisinthehighestpriorityinthepoliticalagendaatalllevelsbecausewearestartingtorealisethesocietalbenefitsthatweget,ascleanairandwater,unpollutedfoods,stableclimate,naturalme-dicinesandgloballysafeenvironments,allofwhichdependontheself-organizationofBiodiversity,whichoccursathighlevelofspatialandfunctionalhierar-chy(i.e.,ecosystems,landscapes,eco-regionsandbios-phere).Biodiversityisstillnotcompletelyunderstoodanddescribed.Inordertofillinthegapsofknowled-ge,scientificresearchonbiodiversityhasbeendeve-lopedintoahugenumberofdisciplinesandfieldsthatarecontinuouslyproducinggreatachievementsinsomeparticularfieldbutalsoanincreasinglyhighfragmentationofknowledge.ThereisaclearneedforanintegrativescienceonBiodiversitythatmergesalltheexpertiseandknowledgerequiredtoaddresswithascience-basedknowledgetheproblemsrelatedtothesocietalandpoliticalneedtomaintainanden-hance,whenpossible,theecosystemfunctioningandservicesresultingfromtheself-organizationofLife.
Onascientificground,ecologyandevolutionarybio-logyarethesciencesthatmightmergealldisciplinarysciencesandapproachestobiodiversityorganization,frommoleculartoeconomicandsocialsciences,intoanintegrativeframework;the‘EcosystemApproach’
isanexampleofthisintegrativescienceappliedtosocietalneeds.Fromthetechnologicalpointofview,therecentdevelopmentsofInternetfacilitiesandofICTtoolscansupplytheelementsforaninfrastructu-rethatcanstronglysupportthedevelopmentoftherequiredintegrativescienceonbiodiversity.AnICTinfrastructurereducesthedistanceamongscientificinstitutionsandamongscientists,facilitatesthenet-workingofscientists,supportscollaborativeresearch,reducesthefragmentationofdataandenhancestheefficientuseoftheachievedknowledge,decreasesthecostofscientificresearch,increasessignificantlytheefficiencyintheuseofresearchfunds,speedsupthedetectionofgapsofknowledgeandcaninspireawisepolicyoffundingscientificresearch.
Italyisabiodiversityhotspot.Theissueofbiodiversityisahighpriorityinthepoliticalagendaatthenatio-nallevelsincewehaverealisedthatourqualityoflifedependsonbiodiversityandtherelatedecosystemservicesandalsobecausetourismisanimportantcomponentoftheeconomicbalanceinmanyItalianregions,duetotheirbeautifulnaturallandscapes.However,scientificresearchonbiodiversitysuffersfromalltheflawshighlightedinthepreviouspara-graphs:fragmentationofsciences,ofresearchinstitu-tionsandamongscientists,fragmentationofknow-ledgeandlackofactualavailabilityofexistingdata,fragmentationofresearchfundingandlowefficiencyiftheuseofavailableeconomicresources.
ThecommitmentofItalytoLifeWatch,theEuropeanResearchInfrastructureonBiodiversity,createstheconditionsforthedevelopmentinItalyofanE-Biodi-versityResearchInstitute.TheE-BiodiversityResearchInstitutewillalsoserveasthedistributedItalianLife-WatchCentreandwilldevelopinadditiontheServiceCentrepartoftheLifeWatch-EuropeCommonFaci-litiestobeplacedinthecentralEuropeanLifeWatchorganization.TheICTPlatformoftheInstitutewillsupporttheinfrastructuretoreducethefragmen-tationinthescientificcommunity,topromotetheintegrationoftheexistingdataandtoenhancetheir
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availabilitytothescientificcommunityitselfandtothewholestakeholdercommunity.ResearchandHigherEducationInstitutions,scientificsocietiesandfederations,associations,NGOsandprivateenterpri-seswillcontributetothedevelopmentofanintegra-tivescienceonbiodiversitywiththeirhumancapital,theestablishedknowledgeandthebackgroundofscientificinformationanddata.AttheNationallevel,theE-BiodiversityResearchInstituteisaimedatsup-portingthescientificresearchinorderto:» Strengthentheknowledgeonbiodiversity;» Deepencurrentunderstandingonbiodiversity anditsrelationshipswithecosystemservices andsocietalbenefits;» Optimisetheuseofpublicresearchfunding andincreasethecompetitivenessofItaly intheacquisitionofEUandotherinternational researchfunds;» IdentifyknowledgegapsinthecurrentIT platformsonbiodiversity,implementingthem withtheknowledgestemmingfromfocused researchprogrammes;» Supportbiodiversityandecosystemhealth managementwithscience-basedplans,strategies andrealisticproblem-solvingapproaches;» Supportdifferentcrucialsectorsofthenational economyandsocialsecuritysystem,suchas agricultureandfisheryindustries,tourism industryandthehumanhealthsector;» Increasetheawarenessoftheimportance ofpreservingbiodiversity,evenwhenthescale ofbiodiversityorganizationrequiresinvestments outsidethenationalterritory[i.e.,migratorybirds; largepelagicfishes(tunafishorswordfish); sharedecosystems];» Supportenvironmentalpolicyforbothlegislative andgovernanceaspects;» Supportthepoliticalandinstitutionallevel todevelopnationalstrategiestocopewithclimate changeissues,theenergeticproblem,andwaste management.AnationalE-BiodiversityInstitutebasedonthemostadvancedICTswillbringbenefitstoalltheseaspectsthroughthedevelopmentofanintegrativescienceonbiodiversity.AttheEUlevel,theE-BiodiversityResearchwilldevelopcommonfacilitieswithLifeWatchandwillattractanimportantcomponentofEULifeWatchfunds,withasubstantialrewardtothenationalinvestment,aswellasfundsfromtheFP7andFP8programsaimingatreinforcingtheestablishedEULargeResearchInfrastructures.
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1Structure of the E-Biodiversity Research Institute
TheInstituteisconceivedasadistributedresearchinfrastructure,partoftheLifeWatch-EU,hostingtheCentralServiceCentre.
Ingeneralterms,themissionoftheE-BiodiversityResearchInstitute,whichisanICTinfrastructure,issimilartothatofmoreconventionalphysicalinfra-structures:providingaccesstotheinfrastructurefa-cilities/capabilities,reinforcingscientificresearchandeducation,withaparticularfocusonyoungscientistsintheearlystageoftheircareerandonthehighereducationprogrammesfornewscientistsonbiodiver-sity,andconnectingthemostadvancedsciencewithsocietalrequirements,supportingknowledge-basedmanagementandgovernancedecisionsattheadmi-nistrative,economicandpoliticallevels.Specifically,themissionoftheE-BiodiversityResearchInstitu-teistoreinforcescientificintegrativeresearchonbiodiversity.Themainfocusisonscientificresearchonspecies,withtheirgeneticandphenotypictraits,includingbehaviouralones,theirnichesandtheirinteractions.However,toolsandservicesproducedbytheE-BiodiversityResearchInstitutedeterminesocie-talbenefitsinmanyfieldsofapplication,includingamongothers(Figure 1.1):
Adaptation toClimate change
Genes &Evolution
Species&Selection
Niches &Adaptation
Environmentalsecurity
Foodsecurity
increase knowledge and deepen understanding
Scientifc issues
support governance & policy
Policy issues
Figure 1.1
Integration of scientific and supporting policy issues
of the E-Biodiversity Research Institute
Environmental Security,istherelativepublicsafetyfromenvironmentaldangerscausedbynaturalorhumanprocessesduetoignorance,accident,mis-managementordesignandoriginatingwithinoracrossnationalborders(MillenniumProject;www.millennium-project.org).Allspeciesreact,eithernegativelyorpositively,toactualenvironmentaldanger.Wemaysaythatthereisnopollutionunlessbiologyisharmedatsomelevel.Sincemostspe-ciesaresmallerthanweare,theyarelikelytobeonaveragemuchmoresensitivethanus,andreactatmuchlowerlevelsofimpactthanthoseaffectingourhealth.Speciescanbeverysensitiveandspeciestraitscanbeverysensitivetoo;biodiversitychangescantellusalotaboutthestateoftheenvironmentandhelpustomaintainasafeenvironment.Thefocusofenvironmentallegislationisshiftinginallcountriesfromtheintroductionofchemicalsintheecosystemandontheirconcentrationtothespeciesandecosy-stemresponsestopotentialdangersdeterminedbytheintroductionofsubstancesorbythealterationofecosystempropertiesduetohumanactivities.Know-ledgeonbiodiversityandonitsorganizationisincre-asinglysupportiveinidentifyingecologicalindicatorsofstress,respondingtotherequirementsonmanydifferentEU-Directives.Deepeningourunderstandingofbiodiversityresponsestoanthropogenicstresseswillgreatlycontributetosetsaferlimitsofacceptableconcentrationofpotentialpollutantsintheair,waterandsoil,basedonbio-availabilityandactualtoxicity,ratherthanonun-specifiedconcentrations.Ecologicalriskassessmentbasedonspeciesresponsesisbeco-mingapowerfultoolinenvironmentallegislation.
Food security,whichreferstotheavailabilityoffoodandtheaccesstoit.Thisissueislinkedtofoodprovisionanddealswithagricultureandfisheries.Biodiversityresearchhasstrongpositiveimplicationsforthedevelopmentofbiologicalagricultureandforpracticesofnaturalselectionofplantvarietiesthatfitwithdifferentlocalabioticconditions.Conservationofplantvarietieswithinbotanicalgardens,seedandgenebanks,isaninsuranceforthefutureofgreen
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agriculture.Anationalstrategyfortheconservationofbiodiversityofagriculturalinterest,producedbytheMinistryforProductiveActivities,acknowledgestheimportanceofbiodiversityresearchforasustai-nableagricultureinthefuture.Theplanfocusesonthenaturalvarieties,theirtraits,potentialnicheandoptimalnicheconditions,andonthegeneticre-sources,ofbothplantandanimalresourcesincludingmicroorganisms.TheE-BiodiversityResearchInstitutecangreatlycontributetosupporttheneedofsustai-nableagriculturebyorganisingandmakingavailabletheexistingdataonplantandanimalvarietiesandsupplyingonlineservicestoanalysethevocationofdifferentvarietiestocopewithnaturallocalcondi-tionsthroughprocessesofnichecompatibilityanaly-sis.Similarly,provisionalinformationonthenurseryareasandtheinteractionwebsrepresentvaluableservicesthattheE-BiodiversityResearchInstitutewillmakeavailabletosupportthefisheryindustry,includingaquaculture,withadvancedknowledgeonsustainableexploitation.
Adaptation to climate change.Climatechangeischangingtheenvironmentalcontextwithinwhichspeciesplaytheirroles.Whilemodel-drawingscena-riosofchangefortemperature,precipitation,wateravailabilityandsealevelriseareincreasinglymoreaccurateandspatiallydefined,weknowverylittleaboutthepotentialforspeciesadaptationandtheexpectedchangesinspeciesdistribution,overallbio-diversityanditsorganization.Weareawarethattheservicesprovidedbyecosystemsandtherelatedsocialbenefitsaregoingtochangeaccordingly,butwedonotknowenoughaboutthedirectionandtheextentofthesechanges.IncreasingthecurrentknowledgeontheactualbiodiversityoftheBiosphere,atthegenetic,taxonomicandlandscapelevels,anddee-peningcurrentunderstandingonspeciesplasticityandadaptationsandbiodiversityorganizationareamongtheresearchprioritiesthattheE-BiodiversityResearchInstitutecanaddresssupportingnationalandinternationalpoliciesofadaptationtoglobalchange.ForparticularecosystemtypesandregionalareasrealisticstrategiesofmitigationoftheglobalchangeimpactsareamongtheservicesforeseenbytheE-Institute.
TheE-BiodiversityResearchInstituteisorganisedintoDepartments(figure 1.2),whicharefunctionallycluste-redintotwomajorcomponents:aCentralService,asacentralcommoncomponentoperatingintheLife-Watch-EUandhostedbytheE-BiodiversityInstitute,andaResearchUnitconstitutedbydistributedVirtualLaboratories,asnationalcontributiontoLifeWatchEU.ThebasicstructureoftheE-BiodiversityResearchInstitutewithinthelargerLifeWatch-EUstructureisshowninfigure 1.3.
e-biodiversity institute
Functions
General coordinationFinancial and staff ManagementLegal issuesFund raising
Web portal developmentWeb interfaceInteroperability and GRId functionsE-learning platform
Phd programmmesMobility of young scientistsResearch fellowship programmes
LW research planningVirtual organizationdata managementModeling and Tool development
NetworkingPress office organizationInformation products production
departments
Management and coordination
it services
e-training & mobility
biological research
outreach and communication
Figure 1.2
Structural organization of the E-Biodiversity
Research Institute.
eric general asseMbly
board of directors
LifeWatch Central Facilities
Board of Chief Officers
Service Centre
Formal agreement
(Independent)LifeWatch Centres
Operational relation
E-BIOdIVERSITyRESEaRCh INSTITuTE
community
countries
individuals
Figura 1.3
The E-Biodiversity Research Institute
within the LifeWatch Eu Infrastructure
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sentialcomponentsofeachVirtualLaboratory.
Theattractivenessofthedataand‘e-experimentalsets’storedintheVirtualLaboratoriesforthescienti-ficcommunityisensuredbythedataelaborationandtheprocessoffillinginthegapofknowledgeexistingintheoriginaldatasets,e.g.bydescribingfunctionaltraitsandlimitingnichedimensionsforeveryspecies(seesectionsp3 .2.2andp3 . 3.2fortheprocessesoftraitandnichedimensionselection),whichwillbetheinternalactivityperformedwithintheVirtualLabora-tories.Theinformationcontentofthedatasetsmadeavailable,willbemuchwiderthantheinformationcontentofthedatasetsoriginallyincludedintheVirtualLaboratories,astheywillbecomplementedthroughnewdatacollectionaimedatfillingintheexistinggaps.
Atleastothertwokindsofmajorgapsinthedataor-ganisedintotheVirtualLaboratoryICTinfrastructurecallfornewdatacollection:
i1Collecting new data in order to complete a collection;thisactivityisgoingtobebasedontheinformationalreadyexistingintheE-BiodiversityInstitutedataplatformandwillbedrivenbythemostinnovativedevelopmentofthescienceofbiodiversity,aswellasbytherequirementsofimplementationofthenatio-nallegislationandEU-Directives,includingtherequi-rementsofoptimisationofthenationalmonitoringprogrammesondifferentcategoriesofecosystems;
Figure 1.4
Organization of the Biological Research department
into a Virtual Laboratory structure. The inter-connections
among laboratories and with LifeWatch-ERIC Service Centre,
hosted by the Institute, are shown.
ThestructuralcomponentsoftheCentralServiceCenteraretheDepartmentsforManagementandCoordination,E-TrainingandMobility,OutreachandCommunication,andITServices.TheCentre,whoseorganizationandfunctioningisdescribedindetailinsections12 .1.4,isdevotedtorunallactivitiesofmanagementandcoordinationoftheE-BiodiversityResearchInstitute,ofe-trainingande-learning,net-workingwiththedataprovidersanddatauserscom-munities.TheCenterwillalsosupplycommunication,organizationandITservicesforthewholeLifeWatchInfrastructure.
TheDepartmentofBiologicalResearchisthecorestructureforthedevelopmentofnationalresearchactivitiesonbiodiversity.ItisorganisedintofourVirtualLaboratories(biomolecular,collections,interac-tions,mediterranean),whichfocusontheprovisionofinformationandtoolsthatareessentialfordeepeningtheknowledgeonthespecies,theirinternalvariability,theirtraitsandtheirinteractionswiththeabioticandbioticcomponentsoftheenvironmentsinwhichtheylive.Therationale,structure,productsandimpactsoftheVirtualLaboratoriesaredescribedinsectionp3 .ThecoreactivityoftheBiologicalResearchDepart-mentwillbethedevelopmentandimplementationofanationalcadastreofSPECIES&SPECIESFUNCTIONS.Alllaboratoriesarefullyinterconnected,eventhoughtwoofthem,i.e.COLLECTIONSandINTERACTIONS,arethebuildingblocksofTHECADASTREOFSPECIES&SPECIESFUNCTIONS.
Virtuallaboratorieswillbeimplementedfirstofallwithexistingdata,throughfacilitiesofdatainter-operabilitythatwillbedevelopedintheServiceCen-treDepartment‘ITInterfaces’.Dataselection,standar-disationandqualitycontrolareessentialcomponentsofthedataimplementationprocesswithineachVirtualLaboratory.Asafirstpriority,databasesresul-tingfromrobustexperimentaldesignsandtestingclearandoriginalhypotheseswillbeselectedandenteredas‘collections’.Theselectionprocessisaimedatintegratingandmakingaccessiblethosedatabasesthatareofthehighestinterestforthescientificcom-munity,whichwilltakeadvantageoftheavailableinformationanddatatointegratethemintolargerexperimentaltestsofinnovativeandinterdisciplinaryhypotheses.Datastandardisationandqualitycontrol,bothforthetaxonomicidentificationanddescriptionandfortheabioticsupportingdata,areessentialcomponentsofallICTdataplatformsandwillbees-
u
e-biodiversity institute
virtual labs
Biomolecular
Collectionsspecies and traits
Interactionsniches and food webs
Mediterraneanfunctional nodes/show cases
stakeholdercommunitydata Providersdata users
service centreuInterface with users
uTraining and capacity
building
uNetworking and
liaison
uCoordination
management
and fund raising
Species FunctionsCadastre
i2Collecting new data in order to cope with changing environments;itiscleartoeveryonethatenviron-mentalconditionsarecontinuouslychanginginmostoftheBiosphere.Climatechangesareamaindriver,affectingeveryecosystemnestedintheBiosphere.Humanactivitiesareasecondmajordriver,generallybutnotnecessarilymorelocalised.Humanactivitiesmayresultinathreatfortheecosystemaswellasamitigationandrecoveryaction.ThechangesintheagriculturalpracticesthathaveoccurredinEuropeinthelast50yearshaveremarkablyreducedthesurfaceusedforagriculture,stronglyimpactingtheusedareasbutalsoallowingforaslowrecoveryofallthesurfacesthatwereabandoned.Relevantinforma-tionneedstobeupdatedinordertoprovideusefulinformationandproducethoseservicesthatmeettherequirementsoftheLifeWatchStakeholdercommu-nity.
TheScientificCommitteeandtheAdvisoryBoardoftheE-BiodiversityResearchInstitutewillhighlighttheprioritiesfornewdatacollection,takingintoaccountboththeneedofdeepeningthescientificknowledgeandcurrentunderstandingandtheneedtosupportscience-basedknowledgefortheadministrativeandpoliticalstakeholdersofLifeWatch.Thestakeholdercommunityneedsthatinformationandknowledgeinordertoensuretheoptimalgovernanceofnatu-ralresources(includingbiodiversityandecosystemservices)anddefinethepolicyallowingtoachievethewin-winsolutionofahigherqualityoflifeinabetterenvironment.TheCommitteeisinchargeofadvisingthefundingagenciesontheprioritiesandeventuallypreparinganopencall,tothewholenationalscien-tificcommunityandtotheinternationalLifeWatchCommunityatlarge.Partofthefinancialcommit-mentofItalyisdirectedatincreasingthebudgetforthenewdatacollectionsrequiredtoenhancethequalityofdataintheLifeWatchICTinfrastructure,throughthedistributednodeconstitutedbytheE-BiodiversityInstitute.
TheStakeholderCommunityoftheproductsandservicesoftheE-Institute,andofLifeWatchisconsti-tutedbyusersatdifferentlevels,includingNationalandInternationalInstitutions,AdministrationandProtectionAgencies,ResearchandAcademicInstitu-tions,privateenterprisesandNGOs,students,citizensandlocalcommunities.
ThestaffoftheE-Instituteisrepresented,firstofall,bythescientists,whowillcooperatetothedevelop-mentoftheBiologicalResearchDepartment;anum-berofInstitutionshavealreadysignedacooperationagreementtoconstituteaLifeWatchItaly(LW-ITA)JointResearchUnitandhavedesignedtheirresourceallocationincompliancewiththeircommitmenttothedevelopmentoftheJRUactivities(Annex 1).Theinvolvementofamuchlargerscientificcommunitywiththesupportofthescientificsocieties,federationsofsocieties,thematicresearchconsortiaandobserva-torieswillenlargethiscomponentoftheE-Institutestaffandreinforceitseffectiveness.Asecondcom-ponentoftheE-InstituteisconstitutedbytheCen-tralServiceCentre,hiredwiththefinancialsupportcomingfromLifeWatch-EUasincashcontribution.ThelattercontributionincludestheItalianbasicin-cashcontributionwithanadditionalsitepremium,requiredfortheinternationalagreementthatItalywillhosttheLifeWatchCommonFacilities.InthefullconstructionphasethefinancialsupporttotheimplementationoftheCentralServiceCentre,includingstaff,isplannedtobecloseto5millioneuroperyear.ItmightbelessifintheinitialstagenotallEUcountrieswillcommittoLifeWatch,determiningareductionofthecashflowandadelayintheLife-Watchconstructiontime-plan.AthirdcomponentoftheE-BiodiversityResearchInstitutestaff,includingboththeServiceCentreandResearchDepartments,willbeconstitutedbyperson-nelhiredonthebudgetofthenationalcommitmentinordertocompletethestaffrequiredtoruntheactivitiesplanned.
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ThemainpurposeofLifeWatchistoservethebiodi-versityandecosystemresearchcommunityinitsworktosupporttheunderstandingandrationalmanage-mentofourecosystemsbypolicymakers,resourcemanagers,theprivatesectorandthegeneralpublic.
TheServiceCentre,asacorecomponentoftheE-BiodiversityResearchInstitute,willdealwiththeprovisionofservicestotheusercommunitysoastofacilitatetheuseoftheinfrastructure,provideinformationandsupportwithaparticularfocustoyoungscientists,fostertheuserengagementintheservices’development,drawnewcommunitiesofinteresttotheinfrastructure.Theinterfacewithusersisthe‘FrontOffice’componentoftheServiceCentre;managementandcoordinationoftheactivitiesandcoordinationofthedistributedcentersarethe‘BackOffice’component(Figure 2.1).
TheServiceCentrestaffwillbeselectedtomeetdiffe-rentkindoftasks,whichwillbedescribedindetailinthesectionsbelow.
12 Service Centre
12 .1Accesstotheinfrastructure
Therationaleforestablishingresearchinfra-structuresistopromoteinnovationandabettercompetitivepositionbyofferingnewcapabilitiesforresearchers.Inthisregard,itiscrucialfortheESFRIandtheECtopromoteexcellencebyena-blingaccesstotheinfrastructuresforthebestresearchersbyvariousmeans.TheEUregulationforestablishingresearchinfrastructures(ERIC)requiresinfrastructurestomeettheconditionofopenaccessandprovide(independent)selectionproceduresandcriteria.
ManyresearchinfrastructuressuchasLifeWatchareofferingtheircapabilitiesmostlythroughtheInternet.TheLifeWatchServicePlanindicatesthatusersmayalsowanttoworkwithLifeWatchstaffondevelopingspecificcapabilities(i.e.modellingalgorithms)fortheirproject.Capacityforsuchser-vicesisalwaysbudgetlimitedbutforLifeWatchitisveryimportanttopromotesuchaccesssincethisisaverystrongdriverforinnovationandimprove-mentofLifeWatchcapabilities.
Figure 2.1
Structure
and organization
of the Central
Service Centre
wCENTRAL SERVICE CENTRE STRUCTURE
Strategic development
of LifeWatch Services
LSC Management,
Coordination & Contract
development
and Management
Coordination
of distributed
Services
Partnership
and Networking
Services
user Platform
and Interface
Expert
Consultation
helpdesk Funding
Opportunities
Multimedia
Support
Training
and Capacity
Building
distributed Services
back office
Front office
portal interface
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DefiningtheLifeWatchaccesspolicy,includinguserregistrationaspects,isapriorityfortheearlycon-structionphase.Asfundingcountriesincreaseandastheaddedvalueofcollaborationismoreevident,ac-cesspolicieswillbereviewedonthebasisofscience,IT,LifeWatchdevelopmentsandusers’requirements.
12 .2TheServiceCentreimplementation
Thefirstactivitiesofthestartupphasewillbefocu-sedontheestablishmentofthemanagementofficeoftheCentralServiceCentreandonthecoordinationbetweenlocalandcentralservices,crucialtocon-structanefficientnetworkofservicecentres.Afterthis,itwillbeimportanttostartacommunicationcampaignand,inparallel,monitortheusers’responseandengagementlevelthroughtheuserplatform.
Followingthestart-upoftheinfrastructurecapabili-tiesconstruction,theservicecentrewillfacilitatetheaccesstoservicesthroughtheestablishmentofahel-pdesk,andcoordinatethedevelopmentandavailabi-lityofe-learningcapabilitytosupportinitialservices.
Firstservices,whichwillbeprioritiesfortheactivationintheconstructionphase,arethosefoundmoreap-pealingfortheusercommunityduringtheLifeWatchpreparatoryphase,accordingtotheresultsofaquestionnaireontheusersneedswidelydistributed:i.e.,fundingopportunities,e-learning,legalsupportetc.Onthebasisoftheresultsobtainedwiththefirstreleaseofservices,theservicecentrewilldecidehowtoproceedwiththeestablishmentoftheremainingservices(trainingandfellowshipactivities,engage-mentofexpertsetc).
Thecriticalactivitieswillbethosedirectedatmoni-toringthedegreeofusers’satisfactionandarationalmanagementofthecentralanddistributedservicesthatshoulddefinewhichserviceshavetobedelive-redfirst,bywhom(centraland/ordistributedservicecentres)andgapstobefilledbynewservices.
12 .3ManagementoftheServiceCentre
AteamofOfficerswillmanagetheServiceCentre.Theyareresponsibleforthemanagementandco-ordinationofCentralServiceCentrestaffandtheiractivities,forthecoordinationofdistributedservices,fundraisingactivities,businessdevelopmentandmarketing.The
backofficewillbethepointofcontactwiththecoordi-natingstructureoftheItalianE-BiodiversityResearchInstitute,aswellaswiththeLifeWatchexecutiveofficeandStatutorySeatthatwillhaveoverallresponsibilityforcoordinatingallLifeWatchactivities.
12 .3.1Management,co-ordinationandcontracts–backoffice
Theofficewillberesponsible,amongothers,forthefollowingtasks:officemanagementandcoordination,periodicresultassessment,riskmanagement,qualitymanagement,recordsmanagement,assetmanage-ment,equipmentmaintenance,liaisonwithhostsandcontractmanagement.
Theofficewillbeintouchwithanyserviceprovidertocoordinatetheactivitiesandtochecktheefficiency.
12 .3.2Coordinationofdistributedservices
Asmentionedabove,theLifeWatchCentralServiceisresponsibleformanagingandcoordinatingtheser-vicesprovidedbythedistributedcentersandserviceproviders.
Thefacilitiesofferedbythedistributedservicecenterscouldbeflexibleandmanifold.Thedistributedservicecenterswouldbegenerallyclassifiedintwotypologies:1 Distributedservicecentres(DSC)providinggeneral usersupportservices;and1 Distributedserviceunits(DSU)providing specialisedservicescoveringathematicarea (e.g.afieldofbiodiversityresearch)oraLifeWatch relatedservicearea(e.g.training,ITdevelopment).
Theofficewillberesponsibleofthefollowingtasksdefiningthedetailsonacase-by-casebasis:1 Selectionandagreementofstandardsofservice provision;1 NegotiationsbetweenLifeWatchandthe distributedservicecenters;1 Guidancefortherationaldistributionofservices onageographicalorthematicscale;1 Capacitybuilding:helpcreatingnationalfacilities tofillgapsinservicingofuserneeds;1 InternalcoordinationwithintheLifeWatch componente.g.,technicalconstruction,scientific networkcommunityengagementetc;1 Helpfordistributedservicecenterstobecome operative;
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1 Managementofcentralbudgetforeseento financedistributedservices;1 Coordinationoftasksamongalldistributedservice centers;1 Encouragementofcooperationandpartnerships amongdistributedservicecenters;1 Co-ordinationoftrainingforprovidersofservices.
Theofficewillmanagetheprovisionofallthecentralanddistributedservicesfollowingtheprinciplesofrationaldistributionofresources,aswellastheop-portunitiestotakeintoaccountdifferentrealitiesandneeds,theidentificationoftheservicestargetalsoonamarket-basedorientationandtheopportunitiesoffinancingofLifeWatchactivitiesbyMemberStatesorotherparties.
12 .3.3Businessdevelopmentandmarketing
ThebusinessdevelopmentunitensuresthatthevalueoftheLifeWatchinfrastructureisunderstoodatnationalandEuropeanlevelsanddevelopsoppor-tunitiesandprogrammesthatcouldfundLifeWatchresearchanddevelopmentactivities.Inparticular,thisunitwillberesponsibleofthedevelopmentofaBusinessOrientedMarketingPlan.ThisunitwillworkinstrictcooperationwiththeBackoffice(tocheckthequalityofproductsdeliveredbyallthecentralanddistributedunitsoftheinfrastructu-re),withthePRandCommunicationunit(todevelopmarketingactivitiesforservicesandfacilitiespro-videdbytheinfrastructure),andalsowiththeFundraisingoffice(toattracton-goingsupport).
12 .3.4Fundraising
TheFundraisingofficewillsupporttheInfrastructureinallthetasksrelatedtothefinancingmechanisms:acquisitionandmanagementofcommercialandpubliccontracts,involvementinEUproposalsandtendersandotherfinancialopportunities,supportforusersonpotentialfinancialinstrumentsandmecha-nismsatglobal,Europeanandnationallevel.
12 .4Interfacewithusers
12 .4.1Helpdesk
Thehelpdeskwillberesponsibleforon-lineandoff-line(bytelephoneandemail)assistancetousercommunityprovidingallthenecessaryinformation
ontheuseoftheinfrastructure,theservicesandfaci-litiesoffered,activitiesandcollaborationopportuni-ties.Itwillactasafirstinterfaceoftheinfrastructurewithalltheneedsandrequirementscomingfromtheusers.
ThehelpdeskwillbeincontactwithalltheotherunitstofurnishupdatedinformationofservicesandfunctionsofLifeWatch(includinginformationonITaspects,accesstodataanddatause)butalsotopro-videsupportonfundingopportunities,contactwithexperts,contactwithservicesprovidersetc.
Inordertosupportitsfront-lineservices,thehelpdeskisresponsiblefor:1 Preparingprotocolsforfurnishingassistance andansweringtorequestsandquestions;1 Preparingandmanagingstandardanswers;1 Updatingthehelpdeskservices;1 PreparingandupdatingtheFAQs;1 Planningandmanagingperiodicalmeetings withhelpdeskpersonnelinthede-centralised ServiceCentres;1 Escalationofrequests/questionsthatcannot bedealtwithbythehelpdeskdirectly.Foritscrucialimportance,thehelpdeskhasbeenincludedinthefirstreleaseofservices/facilitiestobeprovidedduringtheconstructionphaseoftheLife-WatchResearchInfrastructure.
12 .4.2Multimedia
Themultimediaservicewilltakecareoftheidentifi-cation,implementation,managementandinnovationofmultimediaservices.MultimediatoolswillbeusedbytheServiceCentretooffertheusercommunitymanyadditionaltypesofinformationonbiodiversityoutsidetheusualconceptsofdigitaldata.Thesewillinclude:1 Imagesandphotosonhabitatsandspecies;1 Videosonhabitatsandspecies;1 Amateurimagesandvideos;1 Soundrecordings(e.g.birdsandinsects);1 Cartographies,e-maps;and1 Adviceondigitisationofspecimendatafrom naturalhistorycollections.
Themultimediatoolswillalsobeusedtopromotegeneraleducationactivitiesdesignedtoimprovetheunderstandingofbiodiversityofthenon-scientificaudiences.
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12 .5Networkingandliaisons
12 .5.1Userplatforms
TheUsersPlatformisthemeansbywhichLifeWatchcommunicateswithitsuserbase,andviceversa.Engagementwithstakeholdersisthereforecrucialtodefinethescopeoftheserviceprovided,itsmethodofdelivery,aswellasthenatureofsupportfromtheServiceCentre.Itcantakemultipleforms:face-to-faceforum,emaillists,electronicforumsuchasbulletinboard,newsfeed,threadedconversationsandsharedorcollaborativeelectronicspace.
TheLifeWatchinfrastructureisprimarilyaresearchinfrastructurebutitisplannedtomeetarangeofotheruserneeds.TheServiceCentrewillestablishandmanagemethodsandproceduresforinteractingwithkeystakeholdergroups.Itwilldothisthroughacom-binationoftop-downandbottom-upapproaches.
1 Top-down:willbethroughtheestablishment ofaformaluser-platformrepresentingkey Europeanstakeholders,inparticularfromthe worldofscience.UserPlatformswillbe establishedtoensurethatnationaland internationalusersoftheLifeWatchresearch infrastructure,especiallyfromtheEuropean researchcommunity,haveeffectiveaccesstoall infrastructurefacilities.Theywillalsoprovide advicetomanagementontheprioritisation, developmentandresourcingoftechnical ornon-technicalservices.1 Bottom-up:willbethroughthedevelopment ofarangeofsocialnetworkingandparticipatory approachesenablingusergroupstocome togethertoaddressspecificissuesandneeds. Thesegroupsmaybeshortorlonglasting accordingtoneeds.
TheLifeWatchUserPlatformannualeventwillbeaconference,runalongsimilarlinestothewell-regardedEGEEUserConference.TheAnnualConfe-renceisgoingtobepreparedbyaseriesofperiodicworkshops,developedduringtheyearonspecificthematicareasandtargetedtospecialiststakeholdercommunities.
12 .5.2Publicrelationsandcommunication
ThesuccessofLifeWatchclearlydependsonitsabilitytoengagewithboththeprovidersandusersofLifeWatchservicesandtodevelopeffectivecom-municationchannelsappropriatetodifferenttargetaudiences.Thecommunicationstrategy(Sier,2009)outlinesastrategyforthecommunicationandgeneralmarke-tingoftheLifeWatch‘brand’.Fourhigh-levelcommu-nicationobjectivesareidentified.Theycanbesum-marisedas:1 RaiseawarenessofLifeWatchservicesand resources;1 Encouragepotentialuserstobecomeactualusers;1 EnableLifeWatch,managersandproviderstolearn fromusersandimprovetheprovisionofservices andresources;and1 EnsurethegrowthoftheLifeWatchsupportbase.
ThePRunitwillberesponsibleforcollectionandpresentationofqualitativeandquantitativeinforma-tiontodemonstratethevitalroleofLifeWatchanditsaddedvalueusingalltheavailablecommunicationchannels(thewebsite,E-mail/e-newsservice/RSSfeeds/blogservices,leafletsandflyers,talksandpo-stersateventsetc).LifeWatchshouldalsomakemaxi-mumuseofthecommunicationchannelsprovidedbyotherrelatednetworks,initiativesandorganizations.
Thepublicrelationsandcommunicationsunitwillberesponsiblefordeveloping,updatingandimplemen-tingtheLifeWatchexternalcommunicationstrategy,thestrategicdirectionofcommunications(includingdirectcommunicationwithfunders),thepromotionandmarketingofLifeWatch(branding,website,othere-communications,marketingmaterials,pressrelationsandcentralevents),theengagementwithEuropeanandgloballevelstakeholdersandthema-nagementofcertaincontentonthewebsite(e.g.userforum,etc.)
.12 .6Trainingactivities
ThepurposesoftheTrainingandCapacityBuildingProgrammeare:1 FamiliarizeusercommunitieswiththeLifeWatch servicesandcapabilities,enablingthemto performstate-of-the-artresearchusingLifeWatch services;
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1 ProvideLifeWatchspecifictrainingtospecificuser communities;1 Attractwiderusercommunitieswhichmaybring intotheinfrastructurenewcontributionsfrom differentresearchthemesorothersectors;1 Engageusersinthedevelopmentofservices,data andapplications;1 Stimulateandfosterbrightyoungresearchersto exploreoriginalwaysofperformingresearchvia theinfrastructure’sfacilities.
12 .6.1TheLifeWatche-Learningprogramme
ThisprogrammeconcentratesonpreparingandcollectingLifeWatchtrainingmaterialintheformofmultimediacontents(hypermediasuchashypertext,audio,video,etc.).Materialwillbetargetedatspecificusergroupstoprovide:1 BasicICTtraininggivinganintroductiontotheICT technologiesbeingusedintheLifeWatchsystem;1 Conceptualleveltrainingtoexplainthepurpose oftheLifeWatchservices,applicationsandtools andwhythesewouldbeusefultothem;1 Hands-ontutorialswithstep-by-stepguideson howtousethesystemandutiliseitsdifferent features;1 Basicintroductionstobiodiversityandecosystem science;and1 State-of-the-artexamplesofbestpracticeto stimulateactivitiespushedbynewscientific researchandpolicyfrontierswithinthescope oftheLifeWatch.
12 .6.2LifeWatchChallengeFellowshipprogramme
TheobjectiveoftheLifeWatchChallengeFellowshipprogrammeistoenabletheusercommunitytoconductresearchintheframeworkoftheLifeWatchinfrastructureprovidingfellowshipsintheformofsabbaticalsandPhDscholarships.
Thefellowshipscanbetargetedtointerdisciplinaryresearchoncurrentandemergingissues(relatedtobiodiversity,relatedsectorsandalsoICTissues),usingoftheinfrastructurecapabilitiesandalsocontribu-tingtoitsdevelopment.Thefellowshipprogrammewillbeorganisedincol-laborationwithvarioushostacademicandresearchorganizations(e.g.researchorganizations,Pan-Euro-peanUniversities,etc).TheScientificCommitteeandtheAdvisoryBoardof
theE-BiodiversityResearchInstitutewilloverseetheproceduresandwillalsoberesponsibleforselectingresearchproposals.
12 .6.3LifeWatchCentralTrainingActivities
TheCentraltrainingactivitieswillsupportmoretradi-tionalmethodsbyprovidingfacetofacetrainingvia,forexample:summerschools,workshops(conductedon-demandinordertodeliverspecific/customisedcourses)andconferences(toprovideopportunityforthebiodiversityandICTcommunitiestoengageonthecurrentandnewstate-of-the-artresearchfrontiers).ThiselementenablestheLifeWatchcommunitytogetfamiliarwiththeLifeWatchservicesandunderpin-ningbiodiversityresearchissues.
12 .6.4DistributedTrainingActivities
Distributedtrainingactivitieswillbeaimedatunder-andpost-graduatelevelsinuniversitiesacrossEuropetofacilitateunderstandingofthebiodiversityissuesandencouragebroaderuseofLifeWatch.Trainingwillbedeliveredbylocaleducationalfacili-tiesusingacurriculumormaterialthatisdevelopedincollaborationwiththeLifeWatchServiceCentre.
TodeliverthesedistributedtraininginitiativestheLifeWatchServiceCentrewill:1 EnterintopartnershipswithselectedMember Statestrainingfacilitiesofferingfranchise agreementswherebytheuniversityinstitutions canofferLifeWatchaccreditedtraining programmes,andtherebybenefitfrom theLifeWatchbrandandassociatedinvestments;1 Engagewithe-IRG(e-InfrastructureReflection Group)andinvestigateandsupporttheinitiative fortrainingandeducationinPan-European Universities;1 IdentifysuitableeLearningmaterial,whichcould beincludedincoursesatundergraduateand/or postgraduatetraininglevels;and1 LinktrainingtoopportunitiesforLifeWatch fellowships.
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3p3 Virtual Laboratories
p3 .1VirtualLab‘Biomolecular’
p 3 .1.1Rationale
Asformostbranchesofbiology,biodiversityscienceisincreasinglyrelyingonmolecularapproaches.DNAsequenceshavebecomeaprimarysourceofinforma-tioninbiodiversityanalysisalongwithmorphologi-cal,biochemical,physiologicalandecologicaldata.Molecularmethodsmaypossiblyovercomesomeofthedrawbacksandlimitationsof‘classical’methods,suchasspatialheterogeneity,lackoftaxonomicknowledge,taxonomicambiguityand,especiallyformicroorganismsandprotists,theinabilitytogrowtheminculture.
DNAprovidesrelevantinformationaboutthehistoryoftheindividualsthatcomposecommunities,andontheirorganizationintohierarchicallyrelatedgroups,frompopulationstohigherlevelsofthesystematicclassification.Crossingthisinformationwithgeogra-phicaldataallowstoreconstructhowcommunitiesexchangeindividualsandhowcommunitiescameabout;byintegratinggeneticwithgeologicalinfor-mationitispossibletoinferhowpastenvironmen-talchangesmodifiedcommunities,andbycrossinggenotypeswithphenotypesitispossibletoidentifyatwhatlevelofhierarchicalorganizationspecieslie.ThesecondkindofinformationthatcanbederivedfromDNAsequencingisaboutorganismfunctions,fromthegene/proteinleveltobiochemicalpathwaysandtheirinterconnectionsinindividuals(SystemsBio-logy)uptothepopulationlevel,givingimportanthintsonhoworganismswithincommunitiesinteractandhowcommunitiesrespondtoenvironmentalchanges(populationsystemsbiology).Inaddition,functionalinformationcanalsobeobtainedbydirectanalysisofgeneproductsinisolatedspeciesorstrainsandenvi-ronmentalsamples(transcriptomicsandproteomics).
Ideally,toallowtheiruseinbiodiversitystudies,mo-lecularsequencedatasetsshouldbeattachedtomor-
phological,physiological,geographicalandecologicalinformation.Thesubsequentintegratedanalysisofsequencedataischallengingandalsorequiresappropriatescalingupofstateoftheartalgorithmsandsoftwareformanagingandanalyzinghugeamountsofdata.Furthermore,asmoleculardataareoftenproducedbylaboratorieswithoutthenecessaryexpertiseinlargescalebioinformaticsanalysis,thetoolsforthedatamanagementandanalysisshouldbeeasilyaccessibleanduser-friendlythussettingthestageforanewwaveofbiodiversityappliedbioinfor-matics.
Existinglargemoleculardatasetsaregenerallyatthespecieslevelandhardlycoverthelargeinter-populationandintra-populationvariationonwhichevolutionaryprocessesandself-organizationmecha-nismsofbiodiversityarebased.TheVirtualMolecularLaboratorywillfocusspecificallyontheseaspects,whichfundamentallydealwithindividualplasticityandspeciesandpopulationadaptationstoenviron-mentalchangesandallowinvestigatingthedegreeofconnectivityofintra-specificpopulationsaswellasoftheecosystemswherethepopulationslive.TheLabITCinfrastructurewillorganisemoleculardataatthespecieslevel,mainlycomingfrommajordataprovidersbutwillfocusondatasetsthatcompareinter-populationandintra-populationdataforselec-tedspecies.Fillingingapsofparticularimportancedealingwiththeseaspectscanbeselectedaspriori-tiesoftheoverallBiologicalResearchDepartmentfornewdatacollectionprogrammes.AbriefdescriptionoftheinLabfacilitiestohandlenewdatacollectiontakingprofitfromtheexpertisedevelopedinItalyisalsoreportedbelow.
p 3 .1.2Structure
TheBioMolecularVirtualLabwillintegrateknow-howandtrainedinfrastructuresformolecularanalysisandbioinformaticsinordertoprovidethebiodiver-sitycommunitywithintheLWprojectwithexpertiseandtoolstoproduce,manageandanalyzegenetic
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data.Itcomprisestwohighlyintegratedbuildingblocks,amolecularlaboratoryinfrastructureandabioinformaticsinfrastructure.
Lab services.In-labservicesareaimedatsettingcompleteworkflowsforbiodiversityappliedmole-cularanalysis,fromsamplepreparationtosequenceproduction,functionalanalysisandphyl-geneticinference.Anumberofapproacheshavebeendevelopedtostudydiversityatmolecularlevel,suchasPCRbasedDNAfingerprintingmethods(DGGE/TGGE,RFLP,RAPD,AFLP,SSCP,RISA/ARISAandT-RFLP)aswellasPCRindependentmethods(G+Ccontent,DNAmicroarrays,SNPsandDNAre-associationanalysis).Theexpansionofsequenceinformationfromgenestogenomeshasalsoinfluencedbiosystematics,allowingphylogeno-micanalysesthatinvolvetheuseofwholegenomesequencestostudyevolutionaryrelationships.Morerecently,DNAbarcodes,shortstandardizedspecies-specificgenomicsequences,arebeingusedasaglobalstandardforspeciesidentificationandbiodiversitystudies.
Athigherlevelofsystematicclassification,aclearcon-sensusexistsforeachmacrogroups(seethedifferentTreeofLifeprojects).Forthespecieslevel,consensusexistsforbacteriaandforlargemacrogroupsinEukarya,thankstotheBarcodeinitiatives(CBOL&IBOL).DNAbarcodingaimsatdevelopingmethodsforspeciesidentificationbylimitingtheanalysistosmallfragmentsofgenomes.Afragmentofamitochondrialgene,cytochromecoxidase1(cox1)hasbeenproposedastheDNAbarcodetoachievespecies-levelresolutioninanimals,whereas2-3differentfragmentsmightbeneededinothergroups.Asameasureofconnectivityamongpopulations,speciesspecificSTR(SingleTan-demRepeat)andSNPs(SingleNucleotidePolymor-phism)markersareavailable,andveryrecentlyNextGenerationSequencing(NGS)basedapproachtocollectnonspecies-specificSNPsdataappeared.
Theuseofmolecularmethodshasbeenofenormousimportanceintheidentificationanddiscoveryofmicroorganisms(bacteria,archea,viruses,fungiandprotists),inparticularwiththehelpofphylogeneticanalysesofubiquitousgenes(oftentheSmallSubunitrRNAgenesequences).Amongmicroorganisms,bac-teriacontributesubstantiallytothetotalbiomassonEarthandpopulateeveryterrestrialandmarineenvi-ronment,aswellashumansandanimals(e.g.gut);
yet,thenumberofknownspeciesisrelativelylimited,andevenlessarethosecultivable,whiletaxonomicdefinitionsareoftenambiguous.Similarproblemsaffectalsotheknowledgeofprotists,whichconstitutethelargemajorityofautotrophicandheterotrophicorganismsintheaquaticenvironments.Theinnova-tivemetagenomicapproachmighthelpovercometheproblemofmicroorganismcultivation,allowingdirectisolationoftotalDNA(metagenome)fromenvironmentalsamples.Theapplicationofamplicon-basedorshotgunmetagenomicsapproachesbyusinghigh-throughputsequencingplatformscannowpro-videextraordinaryandunprecedentedpossibilitiesforthetaxonomiccharacterizationofenvironmentalsamples,aswellastoinvestigatetheirpopulationdynamics.Therefore,sequence-basedanalysisofthemetagenomecouldvirtuallyrevealalltheresidentspecies,includingtheuncultivableones,aswellasstrainsatsubspecieslevel,whichisofgreatimpor-tance,forinstance,todiscriminatebetweenvirulentversusnonpathogenicstrains.Moreover,metatran-scriptomicapproachesallowtouncoverthefunctio-nalpotentialwhichisactuallyexpressedinspecificenvironmentalconditionswithouttheneedofspeciesorstrainisolation.
InthelasttwentyyearstheBiomolecularcommu-nityhasorganizedaninformaticsinfrastructureformoleculardatasharingtheInternationalNucleotideSequenceDatabaseCollaboration,thatencompassesthethreelargestdatabases:GenBank,EMBL(nowENA)andDDBJ.TheseDatabases(DBs)arerecognizedasprimaryDBbecausetheystorejointlythetotalityofpublicinformationonbiosequence,theirrawex-perimentaldata(i.e.trace),andfewsequencerelatedannotation.Thenecessarylimitonthetypeofannotationavaila-bleanddifficultiesinmaintainingupdatecareinsogeneralistDBs,pushedfirstthegenomiccommunitytodevelopsecondaryDBsthatreferredtotheprimaryonesbutstoredamoreupdatedandmorethematicannotation(i.e.flybase,wormbase,etc).Atfirst,partofthebiodiversitycommunitysetupanagreementwithNCBIin2005(www.barcoding.si.edu/pdf/dwg_data_standards-final.pdf)inordertoidentifyasubsetofdatawithamoredetailedandpreciseannotationontheidentificationofthebiosequencesourceorga-nismandamorestandardizedinformationontheex-perimentthatproducedthemwouldbeavailable.ThedocumentwaslateramendedrecognizingCatalogueofLifeasanauthorityalthoughnotmandatoryfor
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taxonomy.SimilarlywiththeappearanceofthematicDBsinthegenomiccommunity,theneedforupdatedannotations(especiallyonthespeciesidentificationfield)andforamoreefficientintegrationofgeneticdatawithothertypesofdataasoutlinedinourpro-posalofspeciescadastre,isfosteringtheappearanceofspecialisedDB.ProjectsasBOLDorMarineGenomi-csofferexamplesofthematicintegrationofgeneticdatawithinabiodiversitycontext.ToovercomethenarrowfocusofspecializedDBsbutrecognizingthedispersednatureofcompetenceforcorrectannotation,webelievethatthebestDBinfrastructurewouldbeadistributedoneinwhichlocalexpertsofagivensubsetofannotationwouldbeentrustedtomanageandeditspecificsectionsoftheDB.Furthermoreusersshouldbeallowedtoflagandcommentdubiousannotationsinordertomaintainadirectanddiffusecontrolofdataquality.TheBiocaseandtheMBLABprojectspartiallyimplementedthisviewoftheworld,theformerlimitedtotaxonomicin-formationandthelatterlimitedtoasmallsetofDBs.
In silico services. Theinsilicoservicesarethoughtasacollectionofmodularservicesthatcouldbeusedasbuildingblocksfortheanalysisworkflow.Atfirst,serviceswillbeexposedonlyaswebapplications.Inasecondstagetheywillbeexposedaswebservi-cesandcouldbeusedbyout-of-the-shelfworkflowengine(i.e.Taverna)orbytheworkflowengineoftheLifeWatchResearchInfrastructure.Theseservices,oncebuiltaswebservices,needtobeadvertisedandexposedinpubliccatalogueinitiative(i.e.http://www.biocatalogue.org/)andlinkwithsocialnetwor-ks(i.e.http://www.myexperiment.org/),whichexposetheproposedworkflowofanalysisbasedontheseservices.Itisfundamentalthattheentirecommuni-tykeepsgoodpracticeontheuseoftheservicesuptodate.Forinstance,maintaininghighstandardforgoodpracticesintheuseofphylogenetictoolsisacomplextaskgiventhedifferentfieldsofapplication.
Theselectionofservicesfortheinsilicocomponentta-kesintoconsiderationthefollowingtypesofanalysis:p Phylogeography;p Speciesidentificationinenvironmentalsamples;p Functionalcharacterizationofenvironmental
samples.Incommontothethreepaths,weidentifiedservicesofBlastandDBqueries.Tobefunctionaltobiodiver-sitycommunities,theblastserviceneedstobeabletoworkwithuserdefinedreferencesequencesand
allowforjobcomposedofhundredofthousandofqueries.ThisispossiblepoweringtheserviceswiththedistributedEGIcomputinggrid,asitwasdoneintheLIBIproject(http://www.libi.it/).QueriestogathergeneticdataforbiodiversitystudiesneedtobeperformedintegratinginformationacrossgeneticDB(GenBank/EMBL)andcollectionrepositories(GBIF,butalsoNational/localcollectionsystemwithmoredetailedinformation),aswaspartiallydonewithintheMBLABproject(http://www.mblabproject.it).
Typicalofthephylogeographicanalysispatharetheservicesofalignment,phylogeneticandphylogeo-graphicinference.Weselectedthoseservicesbecau-sephylogeneticandphylogeographicapproachesarestillnotfullyintegratedinmodernbiodiversityresearch.Thisisespeciallyduetodifficultiestohandlelargedatasetsandruncomplexanalysesthatrequiredesigningandselectingdetailedmodelsofevolution.Sincetheemergenceofhighthroughputsequencingmethods,sampleselection,alignment,downstreamanalysis,andaccesstocomputingpowerforphylo-geneticinferencehavebecomecentralproblemsinphylogeneticsastheseproceduresoftenrequireindividualandcomputationalintensesolutions.Inadditiontothecomplexitiesresidinginthetreeshapeitself,agreatdealofcomplexityisaddedbythemodelofthecharacterevolutionthatisappliedinthetree,i.e.largerphylogeniesemployadifferentsubsti-tutionmodelwitheachindividualpartitionsinthedataset.
Thephylogeneticservicededicatemakeparticularattentiontoofferthesameapplicationforphyloge-neticservicespoweredusingdifferentcomputingstrategies.Infact,thecomputationalproblemscouldbesolvedbyGRIDandPRACEservices,e.g.dodistribu-tingcomputing(i.e.HTC)asavailableinGRIDforsta-tisticalreplicationofentireanalysisinMLbootstrapreplicates,coalescentsimulationasinABC,orbiolo-gicalreplicatesinphylogenomic,meta-genomicandbiogeography.Forexplorationoftheparameterspace(e.g.duringtreesearches)withlargedatamatrices(bothascharacterandtaxa)computing,highlevelsofparallelizationandlargeamountofRAMareneces-sary,availableinHPC(HighPerformanceComputing)facilitiesasPRACE.Finally,GPUcomputing,thatwillbesoonavailableindifferentserviceprovider(i.e.JST)willallowtoimplementanduseinreasonablytimecomplexevolutionarymodelsthatrequirelargesubstitutionmatrices,likeaminoacidmodelwith
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variablesubstitutionandstationaryparametersorcodonmodel(Suchardetal.2009).NewdistributionsthatuseGPUforwell-knownapplicationsforphylo-geneticinference(BEAST,MrBayes,etc),basedontheGPUlibraryBeagle(bothforCODAandOpenGLGPU),areonthewaytobedistributed.
Theservicededicatedtospeciesidentificationwilloffereitherafastanddeterministicoption(asthoseproposedintheCBOLwebsite)oraslow,probabilisticandphylogeneticbasedoptionasthoseimplementedwithintheMBLABproject.ThespecificMeta-genomicserviceswillincludealign-ment-basedmethodsandgeneannotationtoolsthatwouldallowtoextractfromenvironmentalcollectionofsequencesinformationnecessaryforassessmentsofecosystemtaxonomiccomplexityandfunctionalityandforthemanagementofnaturallyharvested-andinvasivespecies,aswellasfortracingtheoriginofpathogens.Well-definedworkflowsallowforthegenerationofreproducible,standardizedandqualitycontrolledmetagenomicprofiles,i.e.,thecataloguingofthediversityofspeciesandfunctionalgenesinaspecificenvironment.Theseprofilesgiveinformationontheconditionandwealthofthehabitatbyasses-singthetaxonomicandfunctionalcompositionoftheresidentcommunity.Theseassessmentscandiscloseprocesseslikelossofbiodiversity,changesincommuni-tycomposition,discoveryofinvadingspecies,andanyanomaliesinmetabolicactivitiesofthecommunity.Moreover,theycangiveinformationaboutpotentialcausesforalterationsofthecommunitystructure.
p 3 .1.3ProductsandTools
Whilenucleicacidsextractionfromahighnumberofsourcesisawell-establishedprocedureinmostlabora-toriesinterestedinbiodiversity,thereisnoclearconsen-susontheapproach,orgooddiffusionofstandardizedtechniquesforeffectiveenvironmentalsampleextrac-tionandprocessing,whichareimportantpotentialbottlenecksinbiodiversitystudies.Inaddition,meta-transcriptomicsandhighthroughputtechnologiesfortranscript,proteinandprotein-proteininteraction,aswellasmetaboliteanalysisarestillintheirinfancy.
Thein-labserviceswillsetupefficienttoolsandpro-ceduresfor:p Extraction,processingandanalysisofnucleicacids fromisolatedspeciesandstrainsand
environmentalsamples;
p DNAbarcoding,includingamplification,setupofNGSlibrariesanduseofofficialmarkersfromtheCBOLconsortium;
p Prokaryotestrainidentificationandphylogeneticanalysis;
p Developmentofapproachesthatfacilitatehigh-throughputanalysis;
p Developmentofhighthroughputornovelscreeningmethodsfortheidentificationofproductsofcommercialinterest;
p Metagenomicsandmetatranscriptomics;p Databasesystemtoarchive,annotateand
integratedatacomingfromtheothervirtuallabs.
Theinsilicoserviceswillinclude:p NCBIBlastpoweredbydistributedcomputingunits;p Alignmentstools(i.e.Muscle,PROMALS)and
alignmentsqualitycontrolsoftware(i.eGblocks)poweredbydistributedcomputingunits;
p MotifandPatternsearch(e.g.PatSearch)poweredbydistributedcomputingunits;
p Phylogeneticinferencesoftwarewithflexiblemodelspecification(i.e.MrBayesandRaxML)ondistributed,parallelunits,someofwhichpoweredwithGPUsystem;
p PhylogeographicsoftwareABC-based(i.e.Simcoal)poweredbydistributedcomputingunits;
p Geneannotationsoftwareandpredefinedpipelineofsoftwareforgeneannotationpoweredbydedicatedcomputingfarm;
p Speciesassignmentwithfastanddeterministicmethod(i.e.logicprogramming)orslowandprobabilistic(phylogeneticapproach).
p 3 .1.4ApplicationsandImpact
Thecombinationofthelabandinsilicoserviceswouldallowtotacklethefollowingquestionsinmolecularbiodiversity,functionaltoamorecompletecomprehensionofthebiodiversityasawholetarge-tingthescientificcommunityasstakeholderandusercommunity:p Understandinghowmolecularvariationis relatedtofunctionalandphysiologicaldiversity, includingevolutionarymechanismsofgenome
organisationandgenomevariation;p Evolutionandgenerationofdiversityin
thegenomesoforganellesandotherextra-chromosomalgenomes;
p Roleofgenome-environmentinteractionsandtheirrelationshipswithageing,nutritionandstress;
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p Understandingthegeneticbasisofquantitativevariations;
p Improvingtheunderstandingofkeypathwaysindifferentorganisms,includingpathogens(viruses,bacteria,parasites);
p Identificationofnovelmetabolicandphysiologicalpathways;
p Identificationofpotentiallyexploitablenaturalproducts.
Theassessmentofindividualplasticityandspeciesadaptation,intraspecificconnectivityamongpopu-lationslivingindifferentecosystemsandconnecti-vityamongtheecosystemsthemselvesaregoingtohaveapplicationsandimpactsattheconservation,management,governanceandpolicylevels,whichhavethenaturalresourcemanagers,administratorsandpolicymakersastargetcommunities.Possibleapplicationsconcerntheformulationofconservationandmanagementplansatdifferentspatiallevels,todesignprotectedandmanagedareas,todrawrealisticmitigationplansbasedonexpectedclimatechangeimpactsandadaptationstrategies.ImpactsareexpectedontheimplementationofEU-Directivesandnationalstrategies.TheformerincludestheNa-ture2000directive,whichrequiresthedevelopmentofthemanagementplansforalltheSCIsandSPZsattheEUlevelwithin2012.Theassessmentofpopula-tioninter-connectivityandecosystemconnectivityisessentialtodrawrealisticmanagementplansandallowtheproperimplementationoftheEU-Directiveavoidingtherisksofproceduresofinfractionsandstrongbiasesinthemanagementplansresultinginalowperformanceoftheconservationprocedures.Thelatterincludesthenationalstrategytoclimatechangeadaptation,whichgreatlybenefitsfromtheassessmentofthepotentialofspeciesadaptation,particularlyinsensitivegroupsandfragileecosy-stems,suchascoastallagoons.
.p3 .2VirtualLab‘Collections’
p 3 .2.1Rationale
BiodiversitydataareavailableinItaly,buttheyaredispersedinmanystructuressuchas:NaturalHisto-ryMuseums(atUniversitiesorMunicipal,Regional,Provincial),ResearchInstitutes,Herbaria,BotanicalGardens,NationalParks,Archives,Libraries,andpriva-tecollections.Thedispersionoftheinformation,coupledwiththe
lowpercentageofdatainelectronicformatandthescarceavailabilityofon-lineinformation,donotfacilitatetheavaiabilityandexplotationofdataforresearchersandotherend-users.Toenhancethisgreatheritage,thevirtuallaboratory‘Collections’aimsat:p Makingthealreadyavailabledigitaliseddata-
basesinteroperableandavailableonline,withaninterconnectionwiththedataofthe‘Ambiente2010’portal,whichisunderconstructionatMATTM,avoidingduplicationofdataandservices;
p Increasingthedigitalization(andtheensuingonlineavailability)ofbiodiversitydatainthecollectionsofMuseums,e-ResearchInstitutes,herbaria,BotanicalGardens,NationalParks,PhotographicArchivesandprivatecollections,alsowiththeaimoffillingthegapcreatedbytheabsenceofItalyfromGBIF(GlobalBiodiversityInformationFacility),whichisthelargestdatabankforbiodiversitydataintheworld;
p Integratingtaxonomicgeo-referenceddataofsinglesamplesofthevariousspecieswithinformationabouttheirdistribution,genetics(e.g.DNAbarcode),biologyandecology,mainidentificationfeatures(e.g.identificationkeys),withthemainreferencepublications(originaldescriptions,revisions,phylogeneticandbiogeographicalstudies,etc.);
p Highlightingandemphasizingtheimportanceoftaxonomy(asthebasisofecologicalanalysesandofascriptionofbio-moleculardata)givingitanewthrustwiththetrainingofyoungtaxonomists(integratingclassicalandmoleculartaxonomies),e.g.byestablishinganationallydistributedschool(similartoEDIT-EuropeanDistributedInstituteofTaxonomy)throughcourses,seminars,masters,graduateschools.
TheCOLLECTIONSLABORATORYwillinteractwiththeBIOMOLECULARLABORATORY,forallaspectsregardingthosetopics,andwiththeINTERACTIONSLABORATO-RY,forallaspectsregardingspeciesniches.
p 3 .2.2Structure
TheVirtualLaboratoryCollectionsaimsatdevelo-pingproceduresfortheapplicationofinformaticstotaxonomy,includingmethodsandtoolsforthedigitizationofthecollections,thecomputerizationofcataloguesandthediffusionofsocialnetworksandinformaticsplatformstosupporttaxonomicandnomenclaturalwork.
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TheVirtualLaboratorywillmainlybeanITinfra-structure,whereseveraldifferentkindsofdatawillconvergeonbiodiversityandcorrespondingtraitsofindividualspecies:taxonomy,morphology,lifecycles,genetics,habitat,andhistoricaldistribution.Thisinformation,togetherwiththoseregardingthedescriptionofthespeciesnichealongthemostrele-vantdimensionsandanumberofstronginterspecificinteractions,asprey-predator,competitor-competitor,host-parasite,aregoingtobeorganisedintheSPE-CIESANDSPECIESFUNCTIONSCADASTRE,whichisthemaindeliverableoftheE-BiodiversityResearchInstitute.AninternalScientificCommitteeandanexternalAdvisoryBoardwillrecommendprioritiesinthetraitselectionanddescriptioninordertoma-ximisethecontentofinformationoftheCADASTREwhileensuringthecompletenessofthedata-basefortheselectedtraits.Theselectionoftraitshasobviouscomplementaritieswiththenichedimensionselec-tion,developedintheVirtualLaboratoryInteractionsandwiththemaindriversofeachecosystemtype.
Protocolswillbeidentifiedforthedigitizationofpublicandprivatecollections,livingorganismcollec-tionsinnationalparksandprotectedareas,SCIs/SPZsinthenetworkNature2000,ecosystemsandecosy-stemtypes.Thankstothecomputerizationofthesedata,itwillbepossibletoapplymodelstoassessbiodiversitychangesovertime.
ItisessentialthatLW-ITA,amongitspriorities,aimesattheestablishmentofanItaliannetworkontaxo-nomy,i.e.aninfrastructurewhichfollowstheprinci-plesoftheEUNetworkofExcellence(NOE)EDITandoffersnewtoolstoresearchers,includingtaxono-mists,ecologists,geneticists,etc.,withthefinalgoalofdevelopingthestudyandtheprotectionofbiodiversi-ty.Inthisway,LW-ITAcouldalsocontributetooverco-metheverycomplexsituationofmuseumcollectionsinItaly.DifferentlyfromotherEuropeancountries,inItalythereisnoNationalNaturalHistoryMuseum,althoughthereareseveralstructuresofvariablesizedistributedacrosstheterritoryandoftenbelongingtodistinctadministrations.ThankstotheroleplayedbytheNaturalHistoryMuseumoftheUniversityofFlorence,whichisthemainnaturalisticmuseuminItalyandmemberoftheCETAF(EuropeanConsortiumincludingthemainNaturalHistoryMuseums),LW-ITAwillpromotethedigitizationofthelargestpartofavailableinformationonItalianbiodiversitycollec-tions,makingthemeasilyandreadilyaccessible.
p 3 .2.3ProductsandTools
a.Interoperabledatabasesgatheringdatafrommu-seumcollections,privatecollections,andcollectionsoflivingorganismsinnaturalprotectedareas,livingecosystemandecosystemtypes.
Thefirststepisarecognitionandintegrationoftheexistingdatabases.Tothisend,itisparticularlyim-portanttocreatealinktothe‘SistemaAmbiente2010’fundedandunder-constructionattheMATTM,whichincludestheclassificationandtheintegrationofthedifferentsourcesandarchivesofdataonobservationsandcollectionsonbiodiversity.Forthedigitizationofnewdata,prioritywillbegiventoselectedareasorspeciesgroups,accordingtothecriteriareportedabove.ThedatabaseselectedforenteringtheCollec-tionsLabcoversawiderangeofdatacollections;theyincludee-experimentsonkeytopic,accessibletothescientificcommunityinordertotestinnovativeandintegrativetheories,andmodelstudycases,supplyingapplicationstoaddressissuesrelevanttotheconser-vation,recoveryorimprovementofsocietalbenefits,aswellasthetomeettherequirementsofnationalandEUlegislationorenvironmentalstrategies.Exam-plesofdatabasesfillingintherequirementsofbothstakeholdercategoriesarethefollowing:p ExistingLongtermEcologicalResearch(LTER)
biodiversitydatabases;p Databasesfromprotectedareasandpublic
institutions(Nationalandregionalparks,monitoringprogrammes,SCIs/SPZsoftheNature2000etc);
p Integrationandnewdigitizationofdatacollectedwithinselectedresearchprojects.
b.Onlinecatalogueofthescientificliteratureonindividualspeciesandtheirtraitsbasedonbothalreadyexistingelectronicdocumentsandexnovodigitizationofselectedtexts.Withinthecatalogue,theinformationretrievalwillbeperformedthroughsoftware(OCRtype)adequatetotheidentificationoftheselectedkeywords.Alinkshouldbeactivatedtointernationalprojectsofonlinelibraries,suchasBHL,BHL-EuropeandEuropeana.
c.Identificationofcasestudies,e.g.selectedgeogra-phicalareasorgroupsofspeciesonwhichthisVLwillfocusasastart.Theseareaswillincludekeyterrestrialormarineregionsand/orspeciesgroupsforwhichmoreorlesscompletedatabasesalreadyexist,suchas
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protectedareas,longtermobservatories,partiallyortotallydigitizeddatacollectionsetc.
d.Trainingofyoungtaxonomists,allowingmobilityamongstructureswherethestudymaterialislocated,andpromotingtheirworkthroughtheestablishmentofITplatformstailoredontaxonomyandnomencla-turework.Averycriticalaspectthatstronglyconstrainsthestu-dyofbiodiversityisthefastdisappearanceoftaxono-mists,whichislikelytolimitalsothefullexploitationofthehugeamountofbio-moleculardatathatwillpredictablybeavailableinthenextyears.TheVirtualLaboratoryCollectionsaimsatcoveringapivotalroleasareferencepointforthetrainingofnewprofessio-nalcareersof‘moderntaxonomists’,whowillbuildupexpertiseonclassicmorphologicalanalysescoupledwithadvancedmolecular,microscopyandbio-infor-maticstechniques.
p 3 .2.4.ApplicationsandImpacts
TheapplicationsofthisVLwillnecessarilyberelatedwiththoseoftheotherVirtualLaboratoriesinLW-ITA.
Theplannedbio-informaticsplatformwhichwillgatheralldataonindividualspeciesandtheirtraitswillallowstakeholderstoperformcomplexsearchesandrelatebiologicaldatatoabioticfactors(e.g.ge-ographicandclimatic)inordertostudythechangesoccurringoverthetimeandformulatehypothesesonfuturescenarios,basedonexpectedorhypothesizedchangesandtrends.
Thecareforthetrainingofanewgenerationtaxo-nomiststhroughtheestablishmentofataxonomyschooldistributedovertheterritory(amongMu-seums,universities,researchinstitutionsandparks)isparticularlyimportantinthisVirtualLaboratory.ThislearningstructurewillbeintegratedbyspecificSum-merschoolsforinterestedstudents(similartothoseorganizedbyEDIT),whichwillcoupleclasses,activefieldresearchanddataanalysis.
Ahighermobilityofyoungundergraduate,graduate,post-docstudentsandresearcherswillalsohaveanimportantimpactontheirtrainingandonthestan-dardizationofmethodsanddiffusionofknowledgeamonglaboratories.AnexamplealongtheselinesisprovidedbytheEUprojectSynthesis,whichfundsthetravelandsubsistencecostsatdifferentmuseums
andlaboratoriesinrelationwithtaxonomyprojects,whichareselectedbyaspecificevaluationpanel.
.p3 .3VirtualLab‘Interactions’
p 3 .3.1Rationale
Speciesdonotliveinisolation;theiroccurrenceinspaceandtimewithinecosystemsistheresultofanetworkofinteractionswiththeabioticandbioticecosystemcomponents;interactionscanbeclassifiedashorizontal,i.e.thoseofspecieswiththeabioticcomponentsandwiththespeciesoccurringandcommonlycompetingatthesametrophiclevel,andvertical,i.e.thoseofspecieswithotherspecies,whichmaybepreysorpredators.SpeciesnicheandfoodwebtopologyaretheavailableanalyticaltoolstodescribepotentialandactualInteractions.
Biodiversityisorganisedthroughtheseinteractions,whichdeterminespeciesperformanceunderdifferentclimatesandphysical/chemicalconditionsaswellasspeciesfitnesswithineveryparticularguildandcommunity,accordingtotherelativeperformanceofeverysinglespeciescomparedtotheperformancesofallothercoexistingspecies.Theformerinteractionscanbedescribedasafilteringprocess,wherepoten-tialcolonisersareselectedfororagainstaccordingtothedegreeofcompatibilitybetweentheirrequi-rementsforenvironmentalconditionsandthelocalvaluesforclimateandphysical/chemicalparameters(hereafter,reportedas‘environmentalniche’);thelat-tercanbedescribedasaprocessofintegrationofcon-flictingrequirementsinthecontextofinter-specificcoexistence,whereadaptationandco-evolutionplaykeyroles.Everychangeintheabioticcontext,resul-tingdirectlyorindirectlyfromanthropogenicactivi-ties,islikelytoaffectthewholeinteractionnetworksupportingbiodiversity,witheffectsonbiodiversitythatmightbedifficulttounderstand.Thesechangesincludeecosystemdegradationduetoanthropogenicpressuresbutalsoecosystemrecoveryduetotheposi-tiveimpactsoftheincreasinglyeffectivenationalandinternationalenvironmentallegislations;theyincludelandusechanges,naturalresourceexploitation,andclimatechanges.
Understandinghowbiodiversityisorganisedatthedifferentlevelsofspatialscalefromthelocalscaleofsingleecosystemstotheeco-regionalandcontinen-
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talscalesisofparamountimportancetodefinethemostadequateinternationalandnationalpolicies,governancestructuresandmanagementactivitiestoprotectbiodiversityandthoseecosystemservicesandsocietalbenefitsthatinmostcasesarestrictlyrelatedtobiodiversity.Actually,mostbiodiversityconserva-tionissuesdependontheavailableknowledgeontheinteractionnetworkandontheactualunderstandingofthemechanismsofinter-specificcoexistenceinthedifferenttypesofecosystems.
Lotsofinformationonspeciesniches,resultingfromlargenationalmonitoringprogrammesandinterna-tionalprojectscollectingdataonbothspeciescom-positionandkeyparametersoftheenvironmentalniche,arepotentiallyavailablebuttheyarenotyetorganisedwithaspeciesnichebasedapproach;muchpoorerinformationareavailableonthetrophiclinksamongspecies,eventhoughthetechnicalinnova-tionsrecentlyintroducedinthefieldisstimulatingagrowingexperimentalattentionandmassesofnewdataarebecomingavailable.
ThegoaloftheVirtualLabInteractionsistoorga-niseandmakeavailabletheexistinginformationofspeciesnichesandtrophiclinksandtopromotebasicresearchinthefieldinordertocoverthehugegapsofinformationonspeciesnichesanddetailedtrophicstructureofecosystems.TheLabaimstobuildasystemwherespeciesnichesandtrophiclinks,thelatterwithin‘foodwebbasednodes’,canbestoredandmadeavailabletothefullrangeofanalysisofthepotentialinteractionnetwork;theLabalsoaimstoprovideaccesstotoolstosyntheticallydescribeandintegrateinteractionsandaddressapplicationofthebasicknowledgeindifferentfields.
Theintensemonitoringofthecoastalmarineenvi-ronmentperformedinthelastfifteenyears,whenItalywassupplyingalmost50%ofdataonthemarineenvironmenttotheEuropeanStateoftheEnviron-ment,thedevelopmentofCartadellaNaturaonmorethanonetenthoftheItalianterritoryandthefundingofhugeresearchprojectsontargetecosystemsandprocessesfromtheplacesItalianMinistryofEdu-cation,putItalyinpolepositiontobuildupwithinLifeWatchaVirtualLabInteractions,thatfullyinte-grateswiththeotherLifeWatchVirtualLabs.ThesepotentiallyavailabledatarepresentafirstbuildingblockofinformationthatplacesItalyintheconditiontoplayakeyroleinthedevelopmentofthisinfra-
structureonspeciesnichesandtrophiclinks,gene-ratingcataloguesofpotentialinteractionnetworksofparamountimportancetofuelbasicandappliedresearchonbiodiversityorganizationandconserva-tion,ecosystemfunctioningandhealthassessment.TheimplementationoftheVirtualLab‘Interactions’intheLifeWatchconstructionphasewillallowexten-dingthenichecataloguetoabroaderarrayofspeciesandecosystemtypesandtofillinadensercatalogueoffoodwebbasedtrophiclinksforalargenumberofecosystemtypes.
p 3 .3.2Structure
Asthespeciesnicheisann-dimensionalspace,theconstructionofaninteractivecatalogueofspecies(orpopulationorindividual)nicheshasnochanceofsuccessunlessnichedimensionsareproperlyselected.Selecteddimensionsneedtoencompassalldimensionscriticalforthespeciesperformanceandfitnessstillkeepingthenumbersmallenoughtobetractable.
Asimilarprocessisrequiredtodefinetrophiclinks,sincemostspeciesmayingestalmosteverythingthathasabodysize(orparticlesize)compatiblewiththetrophicapparatusofitsindividuals.Itiswellknown,forexample,thatfreshwaterbenthicinvertebratesingestdiatoms,whichmostlydonotdigest,anddigestdifferenttypesoforganicmatterbecauseoftheenzymesthatsomeoftheirpreysproduce.Eveninthiscaseaselectionprocessoftrophiclinksaswellasanevaluationoftheassociateuncertaintyisrequired.
ThestructureoftheVirtualLab‘Interactions’hasthreebuildingblocks:anecologicalinfrastructure,anITin-frastructure,andaQualityControloperationalservice.
Theecologicalinfrastructureisdefinedbytheconcep-tualstructure,use-inspired,ofthespeciesnicheandtrophiclinkoveralldataplatform.Itinvolves:p Theselectionprocessofnichedimensions,based
onaguildandecosystemtypeclassification;p Theselectionprocessoftrophiclinks;p Theplanningofthedegreeofdataaggregation
requiredinordertobuildupe-studycasesofparticularrelevancetobeusedastestmaterialforthemostupdatetheoreticaladvancesinthefield;
p Theplanningofthedegreeofdataaggregationrequiredinordertoupe-studycasesofparticularrelevancetobeusedastestcasesforthe
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applicationofbio-monitoringtools,conservationactions,recoveryactionsorotherappliednichebasedbiodiversitymanagementissues.
AScientificCommitteeandanAdvisoryBoardareinchargetobuildupandboosttheecologicalinfra-structureoftheLabandtodefineallQCproceduresthatneedtobeperformedondataandmetadataeligibletoentertheplatform.
TheITinfrastructurehastwoparallelcomponents:theSpeciesNicheInteractiveCatalogueandtheTro-phicLinkInteractiveCatalogue.Theformerisspecies-oriented,beingstrictlyrelatedtotheotherLabs,withabi-directionalrelationshipwiththeLab‘Collections’;thelatterisfoodweb-oriented,beingstrictlyrelatedtotheotherLabs.TheITinfrastructureisadistributedinfrastructure,whichinvolves:p Informationmanagementprocedures,including
datastandardisationprocedures;p Informationprocessingprocedures;p Inter-operabilityproceduresoftheexistingand
distributeddatabasesanddataportals.
AScientificCommitteeandaTechnicalTeamareinchargetoconstructandkeepworkingtheITInfra-structure.
TheQualityControloperationalserviceisakeycom-ponentoftheLab,whichwillberunbythetechnicalTeam.QualitycontrolchecksinvolvethefulfilmentofcriteriafortheinclusionofdataintheLabITinfrastruc-ture,thecontrolofmetadataspecification,thedefini-tionandevaluationofthedatauncertaintyprotocols.
p 3 .3.3ProductsandTools
Inachangingenvironment,asweareexperiencingbecauseofthegrowingmanageableandun-mana-geablepressuresonthedifferentecosystemoftheBiosphere,speciesperformancesatlocalsitesandspeciesdistributiononalargerscaleareexpectedtooccur.Wheneverchangesaredirectional,asinthecaseofclimatechange,targetspeciesareexpectedtobeseverelythreatenedandbiodiversityisgloballyex-pectedtodecrease,eventhoughatthehighlatitudeslocalincreasesareverylikelytooccur.Ecosystemfun-ctioningandresultingservicesandsocietalbenefitsarealsoalreadychangingatallscales.
Despitethefactthatinter-specificcoexistencehavebeenfordecades,andstillare,amainissueofeco-
logy,whyaretheresomanyspeciesintheBiosphereandhowbiodiversitycanincreaselocallyevenwhenlimitingconditionsarewellascertainedarequestionsnotyetcompletelyanswered,orun-answered.Ontheotherhand,mostoftheknowledgeoninter-specificcoexistencehasbeenbuiltbyaddressingverysmallsubsetsofguildsandcommunities,focusingonpair-wisespeciesinteractionsoronareducednumberofspeciesniches,loosingthefullpicture.
TheVirtualLab‘Interactions’issupplyingorganisedinformationonpotentialandrealisedinteractionnetworks,whicharenotavailablesofar.Theyoffergroundfortestingecologicaltheoryonbiodiversityorganizationatdifferenttypeofecosystemsandfordifferentspeciesguilds.Theyallowawiderangeofstakeholderstoperformpowerfulanalysisofnichere-lationshipsandtoaddressexpectednicheresponsesandbiodiversitychangesalongdirectionalgradientsofchangesintheenvironmentalniche.Aschangingenvironmentalnichesisacriticalissue,thespeciesnicheorganiseddata-setsande-experimentsaregoingtobeproductsofparamountimportanceforscientists,whomayplane-experiments,testtheori-esandperformapplicationstolocalstudycases,foradministrators,whomayusetheavailableknowledgetobuildchangingscenariosatthelocallevel,planmi-tigationorrecoverystrategiesandtestthestrategiesonmodelstudycases,forprivatecompaniesexploi-tingnaturalresources,whocanacquireinformationontargetspeciesnicheandimprovethenaturalresourcemanagement.
Theinteractivecataloguesandthee-studycasesarethemainproductsthattheLabismakingavailabletotheStakeholdercommunity.
WhentheconstructionphasewillbecompletedandtheLabisoperational,itwillalsomakeavailablenotonlynichemodellingtoolsspecificallyfocusingonspeciescoexistencebutalsoonthebiodiversityecosystemfunctionin,onecosystemservicesandthebiodiversityorganizationindicatorsoftheecologicalstatusofecosystems.
p 3 .3.4ApplicationsandImpacts
Nichemodelsaddressawiderangeofbiodiversityconservationissuesandecosystemconservationandrecoveryissuesbothinterrestrialandaquaticeco-systems.Nichederivedmodelsarealreadyapplied
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toassessecologicalstatus(RIVPACS)andtheimpactofdams(MWF)ininlandaquaticecosystems;theyarewidelyusedasenvironmentalevaluationmodels(EEM)forbiodiversityconservationprogrammes,speciesre-introductionandecosystemrecoveryplans.Morerecently,theyareusedforfocusedrecoveryofspecifictargetgroupsinaquaticecosystemsoftheEUlevel,inordertofulfiltherequirementsoftheWaterFrameworkDirectivetoachieveagoodstatusforallbiologicalrelevantcomponents(theWFDBiologicalQualityElements,BQEs)withinthe2015.
Nichemodelsrepresentthemostaffordabletoolstoaddressexpectedbiodiversitychangeswithrelatedchangesintheenvironmentalniche.Theyareakeytooltoincorporatespeciesresponsesandbiodi-versityresponsesinthemodelsofclimatechangesproducingbiodiversitychangescenarios;similarly,theyarekeytoolstoaddressspeciesresponsesandbiodiversityresponsestoland-usechanges.Atthelocallevel,nichemodellingcanbeappliedtoevaluatetheperformanceofbiodiversitymanagementplansaswellasofecosystemrecoveryplanandecosystemre-construction.
TheseapplicationsofproductsandtoolsoftheVirtualLab‘Interactions’isgoingtohaverelevantpo-sitiveimpactsontheimplementationofinternatio-nalandnationalpolicies,governancestructuresandmanagementactivitiesinordertoprotectbiodiversi-tyandthoseecosystemservicesandsocietalbenefitsthatinmostcasesarestrictlyrelatedtobiodiversity.
.p3 .4VirtualLab‘Mediterraneo’
p 3 .4.1Rationale
TheMediterraneanarea,withitspeculiarandcom-plexgeographicalfeatures,representsauniqueenvironment.Itisconsideredahotspotofbiodiversity,mainlybecauseofamongseasonsandamonghabi-tats,landscapesandecoregionsdifferences,whichresultinhighandbiodiversity.
Ahighdiversityofhabitatsandarichnessofendemi-smcharacterizetheterrestrialandfreshwaterbiota;endemismisespeciallyrelatedwithplants,amphi-bian,reptilesandfreshwaterfishes(http://www.bio-diversityhotspots.org/xp/hotspots/mediterranean/Pages/biodiversity.aspx).
TransitionalandcoastalMediterraneanwatersarealsobiodiversityhotspotsandtheyhavecontinuouslysuppliedvaluableecosystemservicesandsocietalbenefitstotheMediterraneansocietiesatleastacrossthelast5,000years.Thedeep-seabiodiversityoftheMediterraneanisincreasinglyshownasrichandoriginal.Thegeographicalpositionandthephysio-graphicalcharacteristicsoftheMediterraneanEco-Regioncontributetothehigh-realizedbiodiversity.Infact,theMediterraneanEco-Regionisahugefunctio-nalecotonebetweenclimaticareas,biogeographicalregionsofspeciesevolution,terrestrialfreshwaterandmarineecosystems.Asanecotone,theMediterra-neanareaisaparticularlyopenecosystem,highlyex-posedtospeciesinvasionandcolonization,whicharepresentlyinteractingwithecosystemfunctioning,ser-vicesandthesocietalbenefitsthathadamajorroleinthedevelopmentofboththeMediterraneancultureandscientificthinking.Understandingbiodiversity,itsorganizationandrelationshipwithecosystemfunctioningandderivingbenefitsorenvironmentalproblemsforthesocio-economicalcomponentsishighinthepoliticalagendaofNationalStatesandInternationalInstitutionsandOrganizations.IndeedithasclearlybeenrealizedthattheMediterraneanisafunctionalEcosystemunit,withintheframeworkoftheEcosystemApproach,thatcannotbehandledatanationalorlowerlevelgeographical,administrativeorpoliticalscale.
LifeWatchisthelargestbiodiversityresearchinfrastruc-tureinEuropematchingthestrengtheningofecologi-calresearchonbiodiversitywithsocietalrequirements.ThedevelopmentofaMediterraneanVirtualInstituteinLifeWatch,asNationally-basedtransnationalLab,isneededtoallowforanapplicationofthescientificknowledgetosupportthesustainabilityofthequalityoflifeatallspatialandadministrativelevels.
ItalyisthebestcandidateforbuildinganddevelopingaVirtualResearchLaboratoryontheMediterranean.Geographically,ItalyhasastrategicpositionintheMediterraneanarea,asitcoversanextendedlatitu-dinalrange,andencompassesalargeamountofgeo-morphologicvariations.ThecomplexorographicandenvironmentalcharacteristicinItalyresultinrapidtransitionsatsmallspatialscales.TheseasurroundingtheItalianpeninsulaandthemajorislands(Adriatic,Ionian,Tyrrhenian,LigurianSeas,andSicilyChannel)arealsodifferentintermsofhydrographyandincludeavarietyofdifferentlyimpactedcoastalenvironments,
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frompristinetoeutrophic,withsteepinshore-offshoregradientsandopenoceanwatersrelativelyclosetoland.Themarkedseasonalitycontributestotheenvi-ronmentalvariability,whichisatthebaseofthehighbiodiversityofthewholearea.Historically,theZoolo-gicalStationofNapleshasbeenthefirstlargeBio-diversityResearchInfrastructureintheworld,beingfoundedfewyearsafterthepublicationofDarwin's‘Theoriginofthespecies’andbeingdeeplyinspiredbytheecologicalandevolutionarythinkingofErnstHa-eckel,whoonlyafewyearsbeforeopenedthefieldtothescienceofecologybyintroducingthenewwordinthescientificcommunity.SincethenbiodiversityintheGulfofNapleshasbeenstudied,makingthatmarineecosystemoneofthedensestnodesofbiodiversityknowledgeintheworld;yethugegapsstillexistinthespeciesnumberandrangesoverwideareas,especiallyinthesouthernandeasternregionsoftheMediter-raneansea.Inaddition,thediversityofmicroorgani-sms,protistsandmanyinvertebratesremainspoorlystudieddespitetheirpivotalroleintheproductiveprocessesandtrophicwebsinthesea.
ItalyhasboththeskillofthescientificcommunityandtheITinfrastructuretobuildanddevelopaVirtualResearchLaboratory‘Mediterraneo’.Overtheyears,theItalianresearchcommunityhasbeeninvolvedinseveralnationalandinternationalprojectsaddres-singbiodiversityinItalyaswellasoverthewholeMediterraneanarea.Speciesdistributiondatahavebeengatheredalongwithabioticandbioticparame-ters.Forexample,overthelastyearsrelevantinforma-tionhasbeengatheredwithinthenationalprojectsSIDIMAR,MIURPrisma,Prisma2,SINAPSIandVECTORandintheinternationaleffortsALTERNET,MARINEGENOMICS,MARBEF,POEM,PROSOPE,SESAME,BOOMetc.ItalyhasamajorroleintheERANETCIRCLE-MED,hasbuiltaninfrastructuretomergeallabioticandbiodiversitydata,mainlyfortheterrestrialenviron-ment,intheappliedframeworkofCartadellaNa-tura.Moreover,ItalyhasfundedaNationalResearchCenterdevotedtothestudyofclimatechangeintheEuroMediterraneneco-Region(CMCC),whichisoneoftheEuropeannodesforabioticandclimatedataorganizationandmanagementaswellasforregionalscenario-building.Inaddition,thenetworkLTER-Italyandotherthematicnetworkshaveallowedtodrawtogetheravarietyofterrestrial,freshwaterandmari-nesiteswherebiodiversityisobservedonthelong-termscale.Finally,Italyisalsotheleadingcountryintheprepara-
toryphaseoftheESFRIEMBRC,whichwilllinkmarinelaboratoriesacrossEuropeforamoreeffectiveuseofmarineresources.
Theavailablebioticandabioticdatasets,alongwiththeexistinglevelofnetworkingwithinthescientificcommunityandwiththeinstitutionsandadmini-strationsatnationalandinternationallevels,offerauniqueopportunitytorelatebiodiversitytoenviron-mentalfeaturesandtousethedatainmodelsandprojectionofbiogeographicalranges(realizedniche,envelopmodelsetc.)aswellasinthedevelopmentofmodelapplicationandscenariobuildingthataddresssocietaldemandsofknowledge-basedmanagementandgovernanceofecosystemsandtheirservices.Examplesofapplicationofthebiodiversityknowled-gethatcanbedevelopedinthe‘Mediterraneo’Labincludethedevelopmentofmodelapplicationandscenariobuildingfor:p Biodiversityresponsestoclimatechange;p Cascadingimpactsofclimatechangeon
ecosystemfunctioningandsocietalbenefits;p Land-usechangeimpactsonbiodiversityand
cascadingecosystemfunctioning;p Performanceevaluationofthemitigationand
recoveryactionsrequiredintheimplementationoftheEU-Directives(e.g.WFDrecoveryofgoodecologicalstatus;MSPDrecoveryofgoodenvironmentalstatus;NitrateDirective);
p Optimizationofprotectionmeasuresandconservationstrategiesofbiodiversityatthedifferentlevelofgeographical,administrativeandpoliticalscalesintheMediterranean.
Adetaileddescriptionofthebenefitsresultingfromapplicationsthatcanbedevelopedbythe‘Mediterra-neo’Labandtherelatedimpactsaredescribedinthefollowingsection12 .4.4
p 3 .4.2Structure
TheMediterraneanVirtualLaboratoryistheecosy-stemlevelLaboftheE-BiodiversityResearchInstitute.Itismergingspatiallydefined‘Collections’ofbiodi-versitydataattheecosystemlevelwithabioticdataandpressuredataatthesamespatialandfunctionalscale,constitutingfunctionalnodesofdataaggre-gation;thesefunctionalnodesrepresentthehighestlevelofdataaggregationoftheE-BiodiversityVirtualInstitute,beingorganisedintheframeworkofthe‘EcosystemApproach’.
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Atthenationallevel,theInstitutefortheEnviron-mentalResearch(ISPRA)hasorganisedthedataontheanthropogenicpressuresalongallItaliancoastandpressuresdataonallWaterDistrictsarebeingorganisedintheimplementationoftheWaterFra-meworkDirective.Thenationalprojectslistedintheprevioussectionshadwelldevelopeddatastorage,organizationandmanagementsystemforthehugecollectionsofabioticdata.Nationalandregionalmo-nitoringplansarealsoamajorsourceofabioticdataforawiderangeofItalianecosystems.
TheMediterraneanVirtualLaboratoryhasareticulatestructureconnectingthefunctionalnodes,aroundwhichbasicandcross-cuttingquestionsonbiodi-versityandbiodiversitycascadingimplicationsattheecosystemlevelcanbeaddressedbyavarietyofstakeholders,usingtheavailabledata,thesuitablestatisticandmodellingtoolsproduced.
ThestructuresofMediterraneanVirtualLaboratoryfunctionalnodesaresimilartothoseoftheotherVirtualLabs,havinganecologicalinfrastructure,anITinfrastructureandaQualityControloperationalserviceasbuildingblock,andinteractbi-directionallywithotherLabs,mainlywiththeCollectionsandInte-ractionsLabs.
Theecologicalinfrastructureisdefinedbythecon-ceptual,problem-orientedstructure,ofthe‘Ecosy-stemApproach’.Itisbasedonacollectionofspeciesdataintegratedwithacollectionofabioticdataandanthropogenicpressuresdataatthesamespatialscale.Tothisend,theMediterraneanVirtualLabora-toryinteractswiththeCollectionsLab,byexchangingbi-directionallycollectionsofspeciesandreceivingcollectionsofspeciesandspeciesfunctionaltraits;theMediterraneanVirtualLaboratoryalsointeractswiththeInteractionsLabbydeliveringspeciescollectionsandecosystemabioticparametersandreceivingspeciesnichedescriptionsandmetrics.TheMediter-raneanVirtualLaboratoryisanintegrativeLab,which,beingproblem-oriented,involvesaselectionprocessoftheenvironmentalcomponents,includingpressu-res,closelydesignedonthefunctionalnodeproper-tiesandtheavailablescenariooftheirevolution.
AScientificCommitteeandanAdvisoryBoardareinchargetosupervisetheselectionofthefunctionalnodes,amongthoseproposedfortheinclusionintheMediterraneanVirtualLaboratoryinfrastructure,as
wellasoftheessentialabioticcomponentsrequired,withtheprincipleofparsimony.Theseprocessesinclude:p EvaluationofthekeyMediterraneanissues
dealingwithbiodiversityandsuggestionforafocusonspecifictopicsintheecologicalinfrastructure;
p Callsforideasandproposalsofpossiblefunctionalnodes;
p Evaluationandselectionoffunctionalnodesproposed,basedonamount,qualityandaccessibilityofdata;
p Selectionoftheenvironmentalparameterstobeintegratedintheinfrastructure;
p Identification,analysisandproposalofappropriatebiodiversityindicators(singlespecies,structuringspecies,non-taxonomicandtaxonomicindexes)tobeproduced;
p Identification,analysisandproposaloftheproblem-orientedtoolstobeimplementedandmadeaccessible;
p ProposalofshowcasesdirectlydevelopedintheMediterraneanVirtualLaboratory,asdevelopedexampleandtrainingmaterialsforthewidestakeholdercommunity.
TheITinfrastructurehastwoparallelcomponents:thefunctionalnodesBioticDBandthefunctionalno-desAbioticDB.Theformerisspecies-oriented,beingcommontoallfunctionalnodesandstrictlyrelatedtotheotherLabs,withabi-directionalrelationshipwiththeLab‘Collections’;thelatterisproblem-orientedwithfunctionalnodespecificity,beingstrictlyrelatedtotheotherLabs,withabi-directionalrelationshipwiththeLab‘Interactions’.TheITinfrastructureisadistributedinfrastructure,whichinvolves:p Informationmanagementprocedures,including
datastandardisationprocedures;p Informationprocessingprocedures;p Inter-operabilityproceduresoftheexistingand
distributeddatabasesanddataportals.
TheQualityControloperationalserviceisakeycom-ponentoftheLab,whichwillberunbythetechnicalTeam.QualitycontrolchecksinvolvethefulfilmentofcriteriafortheinclusionofdataintheLabITinfra-structure,thecontrolofmetadataspecification,thedefinitionandevaluationofthedatauncertaintyprotocols.IntheMediterraneanVirtualLaboratory,qualitycontrolwillfocusspecificallyonthedataen-teringthefunctionalnodeAbioticDB,leavingquality
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controlonthebioticdatatotheCollectionsLab,asregardsspeciestaxonomy,andtotheInteractionsLab,asregardsspeciesinteractionsandtrophiclinks.
p 3 .4.3ProductsandTools
Environmentalissues,determinedbytheincreasingdensityandextentofanthropogenic-basedresourceexploitation,areallmediatedbytheinteractionofbio-diversitywiththeabioticecosystemcomponents.Intheecosystemapproachperspective,allenvironmen-talissuesarebiologicallybased,yetourknowledgemainlyreliesontheabioticcomponentandonthatpartofthebioticcomponentdescribinganthropoge-nicpressures,i.e.,ourimpactontheabioticcompo-nent.Thebiodiversityroleonmitigating,compensa-tingoremphasisingenvironmentalissuesismuchlessknown.Understandingthebiodiversityroleneedsintegrationofbiodiversityandecosystemabioticdataoveralargenumberofstudycasesinordertoanalysethepatternsofvariationandsearchforcommonpat-ternshighlightingcausaldeterministicmechanisms.
TheMediterraneanVirtualLaboratoryisactuallyinte-gratingthetwosetsofdataonanEco-Regionalscaleandthefunctionalnodeapproachgeneratesstudyca-ses,whicharethemainproductsoftheMVL.Thereti-culatestructureoffunctionalnodesistheintegrativeproductoftheMVL,offeringresearchopportunitiestothescientificcommunityandaconsistentbasisofinformationtobuildknowledge-basedconservationplansofbiodiversityandecosystemmanagementandgovernanceplans.
TheMediterraneanVirtualLaboratoryisstructuredinordertodeveloptoolsandtestprocedureswherebiodiversitydataareusedinanecologicalcontext.Toolsincludeawidesuiteofmodelsandstatisticalproceduresinordertoimplementtheproblem-orientedapproachofthisVirtualLab.Atoolkitfortheinterpretationofbiodiversitychangesoverspatialandtemporalgradientsacrossdifferentenvironmen-taltypologiescanbeimplemented.Inthiscontext,indicationscanbeobtainedonfundamentalbiodiver-sityissuesintheMediterraneanareaincluding:p biodiversityloss,p alienspecies,p impactofclimatechangeandacidification,p harmfulspecies,p fisheriesdecline,p effectsofanthropicactivities.
Attheendoftheconstructionphase,whentheLabwillbefullyoperational,itwillalsoprovideecosystemmodellingtoolsspecificallyapplicabletodescribingtherelationshipsbetweenbiodiversityandecosystemfunctioningandservicesunderdifferentenvironmen-talconditions.TothisaimtheMediterraneanVirtualLaboratorytakesadvantageoftheproductsandtoolsofallotherlaboratoriesfromtheE-BiodiversityRese-archInstitute.
p 3 .4.4ApplicationsandImpacts
TheMediterraneanVirtualLaboratoryisconceivedasacollectionofshowcases.Therefore,itrepresentstheLaboratorythatismostdirectlylinkedwiththewholeStakeholdercommunityofLifeWatch.
Thestudycases,whicharefullye-developedwithintheMediterraneanVirtualLaboratory,includeanum-berofe-experimentsaddressingkeyinterdisciplinaryissuesandshowcasesofbiodiversityresponsestoawiderangeofanthropogenicandnaturalpressuresintheMediterraneanEcoRegion(s).Theapplicationsoftheshowcasesaredevelopedinordertohaveim-pactsontheimplementationoftheEU-DirectivesandtheItalianenvironmentallegislation,aswellasontheimplementationofnewpoliticaleffortstoprotectandmanagebiodiversityandtherelatedecosystemservicesandsocietalbenefits.ThepositiveimpactsoftheactivitiesdevelopedinsidetheE-BiodiversityResearchInstituteontheissuesofenvironmentalandfoodsecurityandglobalchangeadaptationaregoingtoberealisedmainlythroughtheMediterraneanVirtualLaboratory.
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s4 Start-up Plan
.s4 .1Networkingthescientificcommunity
Therelevanceandoverallimpactofaninfrastructureismeasuredbythevaluethattheusersassigntoit,bythedensityofrequestsofuseandbythewillin-gnessofuserstopay.Therefore,thefirstpriorityfortheE-BiodiversityResearchInstituteistonetworkthescientificcommunitywithinLifeWatch.Tothisaim,earlyinthestart-upphasethefollowingactionswillbeperformed:s ToprovideinformationonLifeWatch,itspast,
presentandfuturedevelopments,tothescientificsocieties,theEuropeanFederationsandAssociations,theResearchConsortiaandtheDataProviderPlatformsthathavethestudyofbiodiversityintheirmissions;
s ToinvitethesescientificorganizationstodevelopformallinkswithLifeWatchandtodelegateamembertoentertheScientificCommittee;
s ToorganisetheparticipationoftheLifeWatchCommunitytotheConferenceofthesescientificorganizations.
Aspartofthe‘UserPlatform’interfaceoftheServiceCentre,networkingthescientificcommunityisnotimportantonlyinitselfbutinitscapacitytoactuallylinktheinfrastructuretoitsUsercommunities,de-signingtogetherthecontentoftheinfrastructureinordertobemosteffectiveinsupportingtheUsers’ac-tivities.Theresearchcommunityneedstobeeffective-lyinvolvedtocontributeraisingtheattentiononthemostpromisingandinnovativetheoriesandhypothe-sis.Inordertoachievetheobjective,theserviceCentrewillprioritise:s ThedevelopmentoftheUserPlatformsinterfaces
intheLifeWatchportal;s Theorganizationofe-Dahlemtypeworkshops;s ThedevelopmentofDahlemtypeworkshopswith
thematicgroupsofdelegatesofthescientificorganizationsthathavebeendevelopedformallinkswithLifeWatch.
Inthestart-upplanwegiveahighprioritytothedevelopmentofarangeofsocialnetworkingandparticipatoryapproachesenablingusergroupstocometogethertoaddressspecificissuesandneedsanddetermine:s Whichservicesthebiodiversitymanagers,the
localadministratorsandthepolicymakersareexpectingtofindintheLifeWatchServiceCentre;
s Whichinformationthecitizenswanttohaveaboutbiodiversityanditsimpactonthequality
oflife;s WhichsupporttheeducationsysteminEurope isexpectingfromalargeITresearchinfrastructure
onbiodiversity.
.s4 .2CoordinatingwiththeStart-upofLifeWatch-ERIC
LifeWatchisstartingtheconstructionphaseinatran-sitionperiodwitharestrictednumberofFoundingFathers,threeofwhich,aregoingtotaketherespon-sibilitytohosttheCentralCommonFacilities.ThesecountriesareItaly,NetherlandsandSpain.
s SpainishostingtheStatutorySeatanditisleadingtheICTcore,whichisincorporatedintheStatutorySeat;
s TheNetherlandsishostingtheLifeWatchITResearchandInnovationCentreleadingtheVirtualLabandInnovationLabdevelopmenttosecureaphasedapplicationintegration;
s ItalyishostingtheServiceCentreleadingalltheactivitiesconnectedtodevelopingservicesandsupportingend-users.
ThethreecountrieshostingtheLifeWatchCommonFacilitiesagreedthatthestart-upactivitiestoesta-blishtheLifeWatchCommonFacilitiesarebasedonacollaborativeinternationalspirit.ThefinalstepsfortheestablishmentofthelegalLifeWatchERICwillbepursued,togetherwiththeothercountrymembersintheStakeholdersBoard.TheLifeWatchstaffwillbe
s
30 the e-biodiversity research institute
es account manager Organisation and Core Technology
Staff and services
nl account manager Virtual and Innovation Labs
Staff and services
it account managerService Centre and data Resources
Staff and services
appointedafteranopenrecruitmentprocess.
Accordingly,thethreecountrieshaveagreedanallo-cationofactivityandresponsibilitiesonthebasisoftheplandraftedbythesteeringgroupoftheprepara-toryphaseandreportedbelow.
Thestart-upactivitiesare(forthepurposeofthisdocument)organizedinthreedomains:(A)Generalmanagementandadministrativeactivities,(B)Exter-nalrelationsandserviceactivities,and(C)Technicalconstruction.Itisproposedthateachleadingcountryrespondstothisdocumentwithconcreteproposalsformanagingitspartofthestart-upactivitiesinthe-sethreedomainsbasedonthetaskdivisionamongstthecountriesassuggestedinthenextpages.
Thestart-uporganizationshouldactasasinglebodyandwithaclearcommoninterim-management.Assuchitisproposedthateachcountrynominatesaninterimmanagerforoneofthreestart-updomains,andthatthethreeinvolvedmembersoftheStakehol-dersBoardagreeonwhomofthethreewillactasin-terimdirector.Theinterimdirectorisresponsibleforthestart-uporganizationanditsoutputs,andreportstothe3involvedmembersoftheStakeholdersBoard.
.s4 .3Temporarystart-uporganization
ThefollowinginterimorganizationfollowstheJiraconstructionprojectSTARTUP.Thisconstructionprojectdescribestherequiredinitialactivitiestostartconstructionandtopopulateaconstructionteamwithinoneyear.
country expressed interests start-up tasks outputs (deliverables/month)
IT s Central Service Centre
s External network
coordination
NL s LifeWatch Exchange,
connecting data
and tools
s Innovation Lab
ES s Core ICT Infrastructure
s Facilitating central
organization, including
legal affairs -
1. Interaction with national and network stakeholders
2. directing, planning and coordination of the service organization
(central + coordination distributed service tasks/centers) (SERV)
3. Negotiating Service Level agreements
4. Formal establishment of data Resources Platform (SCSuPP)
5. Preparation of Mous with data resources + related protocol
development (daTaGEN)
6. Establishment of related organization structure, annual planning,
job descriptions and recruitment (together with NL and ES)
7. directing, planning and coordination of e-Science workflow strategy
8. development start-up activities (ICTSERV, RESTaSKS, related TECh)
9. Interaction with distributed ICTSERV & RESTaSKS construction
10. design of Innovation Lab + grant proposal preparations
(incl. BTCN start-up strategy)
11. Establishment of related organization structure, annual planning,
job descriptions and recruitment (together with IT and ES)
12. Establishment of Contracts office
13. Supervising the Jira database as management tool
14. Facilitating and managing central organization (ORG)
15. Managing internal and external (paper and web-based) communication
16. directing and finalizing legal arrangements, agreements and contracts
17. directing, planning and coordination of core technical construction (TECh)
18. Establishment of related organization structure, annual planning,
job descriptions and recruitment (together with IT and NL)
1. Meeting schedule/structure, agreements with
networks/countries
2. Construction team, division of tasks in SERV, distributed
service centers identified
3. Service Level agreements for distributed service centers
4. data Resources Platform
5. Mou, protocols and agreements for daTaGEN projects
6. Local hRM support for start-up phase
7. E-science / virtual labs implementation plan
8. E-Science Technical team in place
9. distributed ICTSERV & RESTaSKS projects identified
with action plans
10. INNOLaB designed and BTCN plan
11. Local hRM support for start-up phase
12. Staff and facilities for contracts office
13. Transfer of JIRa to technical experts + regular updates
14. Organizational and staffing scheme
15. Communication officer part time serving LW
16. Legal team, arrangements with external advisors
17. Core technical management organization in place
18. Interim management in place, including integrated
hRM unit
uO1ps
stakeholders board executive board (chair to be agreed) a. Basset B. Sanchez P. Tienderen
strategic managements acting director & Executive secretary (W. Los)s Systems architect (a. hardisty)s Community liaison officer (O. Spinelli)
operational management
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.s4 .4OrganisingtheCentralServiceCentre
TheCentralServiceCentreisgoingtobeorganisedinthestart-upphasebasedonacollaborativeinter-nationalspirit.ComponentsoftheServiceCentre,dealingwiththestrategicselectionanddevelopmentofservices,thelegalaffairsandcontracts,thecoordi-nationofthedistributedservicesaregoingtobeco-ordinatedwiththeotherLifeWatchCentralCentres:i.e.,theStatutorySeatandtheITresearchandInnova-tionCentre.
TheorganizationoftheCentralServiceCentrewasdesignedduringthepreparatoryprojectandisnowgoingtobedevelopedandfine-tunedinthestart-upphase.
Definitionoftheservicesrequiredbythedifferenttypologyofstakeholders,organizationoftheworkingteam,staffingandaccomplishmentoftheagree-mentsamongpartnersrepresentthefirstpriorities.
Ontheoperationallevel,theHelpdeskwillbethefirstinterfaceoftheServiceCentrethatwillbecomeavai-lableassoonasthenewLifewatchportalisdevelopedbytheICTstaff.
.s4 .5OrganisingtheBiologicalResearchDepartment
.s4 .5.1Establishingthestart-upnodesfortheVirtualLabs
ThefirstoperationalnodesoftheVirtualLaboratoriesintheE-BiodiversityResearchInstitutearegoingtobemadeupbytheJRUpartnerinstitutionsandtheconnectedlaboratories,initiativesandnetworks.
TheconnectednodesincludetheUniversitiesofBari,Florence,Rome‘TorVergata’andSalento,theNationalResearchCouncil,withtheLifeScienceandEarth&EnvironmentDepartments,TheZoologicalStationofNaples,theMediterraneanAgronomicInstituteofBari,theEnvironmentalAgencyofPugliaandComu-nitàAmbiente.Moreover,theLTER-Italy(LongTermEcologicalResearch)nodes,anumberofSItE(ItalianEcologicalSociety)nodesandoftheCoNISMa(Natio-nalConsortiumfortheMarineSciences)areincludedthroughsomeoftheJRUpartners.
.s4 .5.2Developingtheinter-operabilitywithinVirtualLab
InteroperabilityoftheVirtualLaboratoriesisgoingtobedevelopedundertheresponsibilityofTheNether-lands,leadingtheITresearchandInnovationCen-tre.TheinteroperabilitydevelopmentwilltakeintoaccounttheITCcoretechnology,thatisgoingtobedevelopedbySpainwithinthecontextoftheStatuto-rySeat.
TheinteroperabilityoftheE-BiodiversityInstitutevirtuallabswillbecoordinatedwithacollaborativeinternationalspirit.Atthenationallevel,interopera-bilityisgoingtobedevelopedwiththeinternationalstandardsofLifeWatchinordertomakepossibletherealisationofthetwoShow-Cases.Acheckofdataavailabilityanddatastandardsisgoingtobeaddres-sedfirstofallwithintheJRUpartnership.
.s4 .6DevelopamodelShowcase
VirtualLabsaredesignedinordertofacilitatethedevelopmentofintegrativeresearchesonkeyscien-tificissuesbyusingalreadyexistingevidences,whichareorganised,reinforcedwithadditionalinformationandmadeaccessible.SinceLifeWatchisaResearchInfrastructureaimedatproducingknowledgeanddeepeningunderstandingonbiodiversityinordertosupportthedevelopmentofactions,includinglegisla-tiveactions,toprotect,recoveryormanagebiodiversi-tyandtherelatedecosystemservices,scientificissueshavetobelinkedtoenvironmentalpolicyissues.
Alienspecies,particularlywheninvasive,representamajorissuewhendealingwithbiodiversity.Anthro-pogenicactivitieshavehighlyfacilitatedthealienspeciescolonisationofalmostallcategoriesofeco-systems.Theyhavearolebothasvectorsofinvasionforalienspeciesandas‘mutualists’,byperturbingcommunitiesandecosystemscreatingemptynichesoralteringthecompetitiveequilibria.Alienspecieswereuntilveryrecentlyconsideredamajorthreattobiodiversityandcommunityorganization,beingpo-tentiallyabletodisrupttheinter-specificequilibriumandtocauseshort-terminstabilityandnativespeciesextinctionandbiodiversityloss,inthelong-term.Ho-wever,recentevidencesandtheexpectedoutcomeofclimatechangearegivingadifferentpicturetoalienspeciesinvasionandrequireadeepenedunderstan-
s
32 the e-biodiversity research institute
dingoflong-termimpactofalienspeciesonbiodiver-sity,ecosystemfunctioningandserviceprovisioning.
Abetterknowledgeoncharacteristicsofbothalienspeciesandecosystemsusceptibilitytoinvasionarerequired.Theconstructionofalargeresearchinfra-structure,whichorganisedata-setsfromdifferentsources,coveringawidespectraoftaxonomicgroupsandecosystemcategories,opensupthepossibilitytoimproveourcurrentknowledgeandmapthefragilityofecosystemstoalienspeciesinvasion.
Ecosystemsusceptibilitytoinvasionandthetaxo-nomicoriginofinvadersarethemainsubjectsofamodelstudycasedevelopedintheE-BiodiversityResearchInstitute.Thestudycaseisentitled:‘Ecosy-stemfragilitytoalienandinvasivespecies:mappingecosystemvulnerabilityandthreatstobiodiversityandserviceprovisioninginItaly’.
Thestudycaseisdevelopedthroughaninter-operabi-lityexerciseonasetofdatabasescoveringcollectionsofspeciesalongaidealtransectrangingfromthedeepregionsoftheSouthernAdriatic-IonianSeatothehighaltitudewoodlandsinCentralandNorthernItaly.Coastalmarineecosystems,lagoons,lakesandrivers,prairies,woodlandsandcavesareecosystemcategoriesavailableinthedistributeddatabases.Plantsandanimals,plankton,benthosandnektonaresomeoftheconsideredguilds.
Asimplifieddatasetisrequiredforeverycollection,reportingonlythetaxonomiclistofspecieswithasinglespeciestrait,alienornative,expressedinabi-naryway.Optionaltraitsareaverageindividualbodymassandthespeciesrole(expressedinabinaryway)intheecosystemservices.
Ecosystemfragilitywillbeevaluatedfromthepropor-tionofnativeandalienspecies;similarlythevulnera-bilityoftaxonomicorfunctionalgroupswillbeeva-luatedfromtheproportionofnativeandalienspecieswithineverygroup.TheaccessibilityofdatastoredindistributeddatabaseswillallowmappingecosystemvulnerabilityonthelayerofecosystemtypesinItaly.Bio-moleculardataonselectedspeciesandspeciesgroupswillprovideserviceswiththeobservationofindividualsandpopulations.
Byusingthesimpletraitsselectedfortheanalysis,estimatesofthescenarioofchangeforecosystem
servicesinthedifferenttypesofecosystemswillbeperformed.
ThestudycaseiseasilyexpansibletoecosystemsinotherEUcountries,coveringawiderrangeofeco-systemtypesandtaxonomicgroups.TheextensionofthestudycasetocountriesonNorth-SouthandWest-Eastgradientsisparticularlyrelevantinordertosearchforgeographicalpatternsofecosystemfragilityandtopreferentialpathwaysforalienspeciesinvasions.
.s4 .7Financialplanforthestart-upphase
TheLifeWatch-ITApreliminaryfinancialplanforthefirst5yearcommitmentperiodisreportedasAnnextothisdocument(Annex 2).Thestart-upperiodofLifeWatchimpliesacommit-mentofthenationalnodesattwodifferentlevels.AtthenationallevelthegeneralorganizationofthenationalLifeWatchorganizationhastobedeveloped;attheEU-level,thesetupoftheCommonLifeWatchCentreshastobedefinedandcoordinatedamongthecountriesthatsharetheresponsibilities.SinceItalyisoneofthesecountries,bothlinesofactivitieshavetobedevelopedandfundedduringthestart-upphase.
Activitiesareorganisedintofourmaingroups:Mana-gement&Coordination,ServiceCentre,VirtualLabo-ratoriesandShowCases(table 4.1).Theoverallbudgetrequiredforthestart-upperiodis750.000,00euro,onethirdofwhichisgrantedbytheJRUpartnership,asinkindcontribution.Management&Coordination,accountingalsofortheoverheads,requires22,0%oftheoverallbudget,thestart-upoftheServiceCentrerequires32,0%,theinteroperabilityandorganizationoftheVirtualLabs20,0%and26%isdevotedtotherealisationoftwoShowCasesagreedinthegroupoffoundersofLifeWatch.
Mostofthebudgetisduetopersonnelexpenses,ac-countingforthe61,6%oftheoverallbudget;howevermorethan50%ofthecostofpersonneliscoveredbytheJRUpartnersas‘inkind’contributiontothedeve-lopmentofthestart-upphase.TheCommonCentreactivities,involvingallServiceCentreactivitiesandtheShow-Cases,arebasedonacollaborativeinternationalspirit.
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Table 4.1
Financial plan for the start-up phase. The required budget is allocated per activity and voices of costs. 1 Consultancy: brochures, posters and publications; 2 Other costs: Software/hardware; 3 Consultancy: groups of taxonomists,which may be external to the JRu; 4 Consultancy: groups of experts, collection of new data.
s
VoICES oF CoST PERSoNNEL TRAVEL MEETINgS ANd CoNSULTANCy oThER CoNTINgENCy ToTAL
ACTIVITIES CoNFERENCE
Management & Coordination
General Coordination 86000 10000 10000 40000 146000
Service Centre Coordination 10000 10000
Virtual Laboratory Coordination 10000 10000
Service Centre
Networking/meetings 1 20000 3000 50000 20000 93000
Executive planning of services 27000 27000
distributed Centers & agreements 20000 3000 5000 28000
data resource Platform 45000 3000 15000 63000
MOu, protocols agreements 20000 10000 30000
Virtual Laboratories
Setup Interoperability 2 50000 20000 25000 95000
VL setup 3 24000 2000 20000 10000 56000
Show Cases
alien species 4 104000 3000 10000 10000 15000 142000
Wetlands 46000 4000 50000
ToTAL 462000 28000 80000 70000 70000 40000 750000
34 the e-biodiversity research institute
Cooperation agreement to develop researchactivities in the field of Biodiversityinfrastructures Through a joint research unit (JRU) defined as LW-ITA (Lifewatch Italia)
Withthefollowingagreementamongtheunderlistedparties:Consiglio Nazionale delle Ricerche (CNR)representedbythePresidentandlegalrepresentative,Prof. Luciano Maiani, Università degli Studi di Bari ‘Aldo Moro’representedbytheRectorandlegalrepresentative,Prof. Corrado Petrocelli,Università degli Studi di Firenze representedbytheRectorandlegalrepresentative,Prof. Alberto Tesi, Università degli Studi di Roma ‘Tor Vergata’representedbytheRectorandlegalrepresentative,Prof. Renato Lauro,Università del SalentorepresentedbytheRectorandlegal,representativeProf. Ing. Domenico Laforgia, Stazione Zoologica Anton Dohrn NapolirepresentedbythePresidentandlegalrepresentative,Prof. Roberto di Lauro, Istituto Agronomico Mediterraneo di Bari (IAMB)representedbytheDirectorandlegalrepresentative,Dott. Cosimo Lacirignola, Agenzia Regionale per l’Ambiente in PugliarepresentedbytheGeneralDirectorandlegalrepre-sentative,Prof. Giorgio Assennato,Comunità AmbienterepresentedbytheManagerandlegalrepresentative,Oliviero Spinelli.
Premise
Whereas
TheEuropeanstrategyforResearchforeseesthecon-structionofaninfrastructurededicatedtothestudyofbiodiversity,andcalledLifeWatchconsistingin:• Anetworkofobservatories,institutions,research
groupsonbiodiversity;• Innovativetoolsforgeneratingandprocessing
dataonbiodiversity,aswellastheirintegration,interoperabilityandaccessibility;
• Adistributedsystemofvirtuallaboratorieswhich,amongtheissuesofinteresttobiodiversityresarch,willdevelophighlyinnovativeinterdisciplinaryresearchandwillmakeavailableorganizeddata,newmethodsandprocedures,advancedtoolsfornumericalanalysisandmodeling;
• Aservicecenterthatprovidesaccesstodata,applicationsandcomputingsystemsandorganizeadvancedtrainingcourses;
OnJanuary31,2011thepreparatoryplanningphaseoftheLifeWatchinfrastructure,basedonEuropeanCommissionfunding,willbeconcludedand,atthesametime,atransitionphasewillbeactivatedinordertocreateforeseen–inaccordancewithRegula-tion(EC)No723/2009oftheEuropeanCouncilontheCommunitylegalframeworkapplicabletoaEuropeanResearchInfrastructureConsortium(ERIC)–thelegalentitythatwillhandletheconstructionandoperationoftheinfrastructure,onthebasisofthecontributionsandguidanceofthememberstateswhichwilljointheinitiative;
ItalyexpresseditssupporttoLifeWatchthroughtheparticipationofnumerouspublicandprivateinsti-tutionstotheinfrastructure’spreparatoryphaseandthroughtheincreasedinvolvementofnationalscientificcommunity,aswellasthroughthesigningofofficialdocumentsofaccessionbytheMinistryofEducationwhichinclude,on5August2010,aMemo-randumofIntent“prodromaltointergovernmentalagreementsofERICandthesimultaneousassign-mentofanationalrepresentativesinthe”Stakehol-derBoard,thebodyresponsibleforcoordinatingthetransitionfromplanningtothestartoftheconstruc-tionoftheinfrastructure;
Annex 1ProtocolofintentformalisingtheJointResearchUnitdefinedas:LifeWatch-ITA
35 the e-biodiversity research institute
Partieshavecompetencesconsistentwiththeobjec-tivesofEuropeanresearchinfrastructureLifeWatchandhavedevelopedsignificantinterdisciplinaryrese-archonbiodiversitycharacterisedbyastronginterna-tionalcharacter.ThepartieshavecooperatedwiththeEuropeanconsortiumthatmanagedthepreparatoryphaseofLifeWatchandjoinedaseriesofactivitiesorganizedincollaborationwiththeDepartmentofLifeSciencesoftheCNR,whohasplayedtheroleofcoordination;
TheParties,recognizingthehighscientific,socialandeconomicvalueofresearchonbiodiversityanditsroleintheinternationalpoliticalagenda,expresstheirinterestinthestrengtheningofscientificresearchinthisinterdisciplinarytopic.
ThePartieshavecollectionsanddatabasesonbiodi-versity,andperformactivitiesofvariouskinds,whichmaybepartofthenationalcontributiontothecon-structionandoperationofLifeWatch;
Theconventionschemeforgrantsofthe7thFra-meworkProgrammeforResearchandInnovation(FP7)foreseestheJRU(JointResearchUnit)asapartnershipamongdifferentlegalentities-generallyofthesamenationality-basedonaspecialagreementwhichnotcreateanindependentlegalentity;
AJRUcannotjoincontractswiththeEuropeanUnionbut,underClause23oftheconventionsschemeofFP7,amemberoftheJRUmaybecontractingandrepor-tingtheworkdonebyothermembersoftheJRUandtransfertheircontributionsonthebasisoftheJRU.
It is agreed as follows
Art. 1 Premises 1.1 Thepremisesareanintegralandsubstantialpartofthisdocument,andtheyrepresentaprerequisiteandinseparablesection.Art. 2 Subject 2.1 Inthetransitionphase-thatgoesfromthepre-paratoryphaseofLifeWatchtotheconstructionoftheintergovernmentalconsortiumthatwillmanagetheconstructionandoperationphasesoftheinfrastruc-tureLifeWatch(hereafterLW-ERIC)-thepartiesshallestablishaformalcollaborationthroughtheestabli-shmentofaJointResearchUnitLW-calledITA.2.2 LW-ITAaimstopromoteandfacilitatethepar-ticipationofItalytothecontructionoftheLifeWatchinfrastructure,encouragingabroadparticipationofthescientificcommunity,andoptimalreturnsoninvestmentsinourcountry;2.3 LW-ITAwillrealizethecoordinationofactivitiesandsupporttheorganizationoftheItaliancontribu-tiontotheintergovernmentalconsortiumLW-ERICthroughtherecognitionandsystematizationofre-sourcesofmembersoftheJRUpotentiallyaccounta-bleasacontribution‘inkind’totheLW-ERICwhichthepartiesundertaketoidentifywithinthirtydaysfromtheaccessiontoLW-ITA;2.4 LW-ITAwillworktoachievespecificagreements,subsequentlydefinedbetweenthepartiesandanyothers,aimedattheItalianparticipationintheinter-governmentalconsortiumLW-ERICand,whererequi-red,toimplementthemeasuresreferredtoinarticle3.2.5 LW-ITAwillalsoperformactivitiesrelatingtotheconstructionofinfrastructure,definedinspecificplansjointlydefined,and,inparticular,willbeabletoparticipateinFP7Europeanprojectsincludingactivitiesaimedattheconstructionoftheresearchinfrastructureoratitsuse;
Art. 3 ActivitiesandobligationsoftheParties3.1 TheactivitiesunderthisAgreementwillbethesubjectoffurtherspecificandperiodicworkplansoftheJointResearchUnit,agreedbetweentheParties;3.2 Activitiesthatmaybecarriedoutaspartofthisagreementareaimedat:• Pursueabetterappreciationofthesharedskills,databasesandcomputingresourcesofeachparty• CoordinatethenationalactivitiesinthetransitionphaseandprovidesupporttotheMIURandotherMi-nistriesintheorganizationoftheItalianmembershipinLW-ERIC;
36 the e-biodiversity research institute
• UndertakeactionsaimedatstrengtheningtheoverallcontributionoftheLW-ItalianinERIC;• PromoteasystematicactionfortheintegrationoftheItalianscientificresearch,encouragingnewaccessiontoLW-ITAwiththeprocedureslaiddowninart.3.2;• StrengthentheItalianscientificresearchinthefieldofbiodiversityandpromoteeducation• Promotetechnologytransferandperformactivi-tiesofscientificdisseminationandcommunicationinthefieldofbiodiversity;• PlanningandorganizingpilotdemonstrationoftheoperationofLW-ERIC,highlightingthepeculiari-tiesofanItaliancontribution;• PromoteregionalnodesLW-ITAandcoordinatetheirintegrationintothenationalcomponent;• Consolidate,strengthenandexpandtheItaliancontributiontotheEuropeanresearchinfrastructureonbiodiversityLifeWatchparticipatinginthecallsoftheSeventhFrameworkProgrammeandinothercallsdedicatedtoinfrastructuresattrans-national,nationalorregionallevel;• AnyotheractionrelatedtowhatisreferredtoinArticle2.3.3 ThePartieshavetherighttoterminatethisagreement,statingthereasons.3.4 Otherpublicinstitutionsorconsortiaofrese-arch-dominatedpublicorprivatebodiesactiveinresearchanddevelopmentinthefieldofbiodiversityandoftheoverallpurposeoftheJRU,canadheretotheJointResearchUnitLW-ITAwithseparateacts,subjecttoacceptanceofallPartiestothisAgreementandwiththeapprovalofamajorityoftwothirdsoftherepresentativesofthepartiesintheGeneralAssembly,underArticle6.Art. 4 Management of the activities 4.1 TocarryouttheactivitiesreferredtoinArticle3bytheJointResearchUnit,thePartiesagreetousetheworkofthefollowingoffices:• CoordinationCommittee;• GeneralAssembly;• ManagementCommittee.Art. 5 Coordination Committee 5.1 ThePartiesdelegatethecoordinationoftheactivitiesoftheJRULW-ITAtotheCNR;5.2 TheCoordinatingCommitteeisthebodyisinchargeofcoordinatingallactivitiesoftheJRULW-ITA;5.3 TheCoordinatingCommitteeismadeupof5members:• TheCoordinator;• TheJointResearchUnitManager;
• TheCoordinatoroftheadministrativeandac-countingactivities;• TwomembersappointedbytheGeneralAssembly.5.4TheCoordinatorisappointedbytheCNR;5.5TheCoordinator:5.5.1 RepresentstheJRUtothirdpartiesunlessspeci-fiedinArticle6.5.5;5.5.2 ChairstheGeneralAssembly;5.5.3 Designates,withtheagreementoftheparties,theJointResearchManagerandtheCoordinatoroftheadministrativeandaccountingactivities;5.5.4 DesignatesthreeadditionalmembersoftheGeneralAssembly,withtheagreementoftheLifeSciencesandEarthandEnvironmentDepartmentsoftheCNR;5.6 TheJointResearchUnitManager:5.6.1 ChairstheManagementCommittee;5.6.2 RepresentstheJRUinoperationalactivities;5.6.3 ParticipatestotheGeneralAssembly,withoutvotingrightsunlesswheretherighttovoteshallnotbeconferredbytherepresentationofaParty;5.7 TheCoordinatoroftheadministrativeandac-countingactivities5.7.1 Willtakecare,inconsultationwiththeManagerJRU,ofthedraftingofaadministrativeandac-countingregulationoftheJRUtobeapprovedbytheGeneralAssembly;5.7.2 WillcoordinatetheadministrativeactivitiesandreportingofanyfundingreceivedbytheJRUtocarryouttheactivitiesreferredtoinArt.3;5.7.3 WillcollaboratewithaunitofadministrativepersonnelappointedbyeachPartyinaccordancewiththetermsoftheplandefinedbythePartiesrefferrigtotheirownresourcesengagedintheactivitiesoftheJRUandreportedinAnnex1tothisAgreement;5.7.4 ParticipatestotheGeneralAssemblywithoutvoting;5.8 TheJRUManagerandtheCoordinatoroftheadministrativeandaccountingactivities,ifemployeesofoneoftheadministrationsthatcontributetotheformationoftheJRU,willperformaspartoftheiremploymentcontract.Art. 6 The General Assembly 6.1 TheGeneralAssemblyisthehighestgoverningbodyoftheJRULW-ITA;6.2 TheGeneralAssemblyiscomposedbyonemem-ber,withvotingrights,appointedbyeachparty,evenwhenitjoinedaftertheestablishmentoftheJRUinaccordancewithArticle3.4above,withtheexceptionoftheNationalResearchCouncilwhich,accordingtoitinArt.5.4.4,isgiventheopportunitytonominate
37 the e-biodiversity research institute
uptothreemembersinrelationtothenationaldi-mensionoftheAuthorityanditsfunctionalorganiza-tioninDepartments;membersmayparticipatetotheGeneralAssemblywithoutvotingrights,asdefinedinArt.5.5.3and5.6.4oraccordingtospecificrequestsoftheGeneralAssemblyitself;6.3 PartiesarefreetodeterminethedurationofthemandateofitsrepresentationthatcanberevokedandreplacedatanytimebyregisteredlettersenttotheCoordinatoroftheJRUbythelegalrepresentativeoftheinstitutionthathadmadetheappointment;6.4 ThePartiesshallidentifytheirrepresentativesintheGeneralAssemblytogetherwiththeiraccessiontotheconstitutionoftheJRU.ThecompositionoftheGeneralAssemblyatthetimeofformationoftheJRUisthenannexed(Annex2);6.5 TheGeneralAssemblymay:6.5.1 ProposetomembersagreementsandMemoran-dumofUnderstandingwithotherJRU,organizationsorpublicandprivateentitiesthathaveapositiveandsignificantimpactontheaimsandactivitiesoftheJRUdefinedinpreviousarticles;6.5.2 Approverequestsfornewmembership.TheGeneralAssemblyvoteseffectivelywithamajorityoftwothirdsofitsmembers,intheeventofatievote,thevoteoftheCoordinatorprevails;6.5.3 AdoptregulationsandguidelinesandtakethenecessarydecisionstoensuretheeffectivenessoftheJRUinpursuingitsobjectives;6.5.4ElecttheMembersoftheManagementCommit-teefromamongitsMembers;6.5.5 ApprovetheparticipationoftheJRUtocallsforsubmissionofprojectproposals,identifyingtheleadingbodyamongtheconstituentpartsoftheJRUaccordingtotheskillsrequiredinthenotices,asdefi-nedinthenextart.8.2;6.5.6ApproveperiodicallyaJRUprogramofactivities;6.5.7 Approvebyconsensustheplanandfinancialreportingperformed;6.5.8VoteonallmattersbroughttotheattentionoftheAssemblybytheManagementCommitteeorbyarepresentativeofatleast30%oftheParties;6.5.9Prepareandapprovetheminutesofmeetings;6.5.10 ApprovetheJRUannualactivityreportsub-mittedbytheJRUManager;Art. 7 The Management Committee7.1 Theoperatingorganizationandimplementa-tionofactivitiesunderthisAgreementisguaranteedbytheManagementCommittee;7.2 TheCommitteeactsasdelegateoftheGeneralAssembly;
7.3 TheManagementCommitteeiscomposedofeightmemberselectedbytheGeneralAssemblyandtheJointResearchUnitManager,appointedinaccor-dancewithart.5.4.2;7.4 TheCommittee’staskistoidentifyanddefinetheactivitiesreferredtoinArticle3andtoensureacorrectandcoordinatedcoursesolvingeveryproblemthatmightariseandoverseeingalltechnicalandoperationalaspects;7.5 TheCommitteeischairedbyJRUManagerandvoteonallmattersconcerningtheactivitiesoftheJRUwithasimplemajorityofitsmembers;7.6 TheCommitteemaycomprisefunctionalgroupsofwork,whichmayincludetheparticipationofex-ternalexpertstotheCommittee,andidentifyitsownrulesofoperation.Art. 8 Financial resources 8.1 TheJRU,forthefinancingoftheactivitiesmayuse:• revenuesfromtheprojectproposalsmadedirectlybyJRU;• revenuesfromtheprojectproposalsmadebyunitsoftheJRU;• fundsprovidedbyeachoftheinstitutionsinvolvedintheJRU;8.2 Therelationshipbetweenthepartiesrelatingtoanyrequestforcontributionswillbegovernedbyspe-cificagreementssignedandapprovedbytheGeneralAssemblywhichinturnwillidentifyaProjectLeaderforthepurposesofplanningforwhichcontributionisrequested;8.3 Tooptimizetheperformanceofactivities,theJRUcanpromote,throughtheinstitutionsinvolved,post-graduateandpost-docfellowships.Art. 9 Knowledge, equipment and intellectual property rights 9.1 EachPartyremainstheownerofthepriorknow-ledgethataremadeavailabletoothersfortheacti-vitiesdevelopment.TheexpertisedevelopedjointlyconstitutethecommonpropertyofthePartieswhichmayusethemtotheirinstitutionalobjectives.9.2 EachPartyownsthepropertiespurchasedwiththecontributionswhichtheJRUmayprovideinprojectactivities;itisunderstoodthatthegoodsthusacquiredwillbeavailabletotheprojectanditsfuturedevelopments.9.3 EachPartyisalsotheownerofanyrightofexploitation,includingthatonetopatent,arisingfromactivitiescarriedoutindividually,inthecaseofactivitiescarriedoutjointlybytheJointResearchUnitLW-ITAanyrightsofexploitation,includingthatonetopatent,pertainjointlytothepartiesinvolved.
38 the e-biodiversity research institute
Art. 10 Miscellany10.1 Thepartnership,theappointmentofthePartnerLeader,theestablishmentofaJointResearchUnitandanythingelsedonebythePartiesortheleadersubjectdoesnotleadtotheestablishmentofanyassociation,company,consortiumorsimilarrelationamongtheParties,eachofwhichmaintainsitsownlegalandeconomicautonomyforthepurposesofmanage-ment,tax,socialsecuritycontributions.10.2 ThePartiesmayalsospecifywithfurtheragre-ementstherulesprovidedinthisAgreement.AnychangesoradditionstothisAgreementwillnotbeenforceableunlessmadeinwritingandwiththeuna-nimousconsentofallParties;forthispurposebythisActtherepresentativesofeachpartyintheGeneralAssemblyaredelegatestothesignatureoffurtheragreements,changesoradditionstothisAgreement.Art. 11 Jurisdiction 11.1 Foranydisputeconcerningtheinterpretation,applicationandenforcementofthisAct,thepartiesstatetheexclusivejurisdictionoftheCourtofRome.Art.12 Validity of this act12.1 ThisActshallenterintoforceuponitssigningandshallceaseanyeffectfouryearsaftertheconclusion.12.2 ThisactwillremainvaliduntilthecompletionofactivitiesforeseenbyanyprojectsacquiredbyJRULW-ITAandnotyetbeencompletedpriortotheexpi-rationofthisact.
Consiglio Nazionale delle Ricerche (CNR)Prof.LucianoMaianiUniversità degli Studi di Bari ‘Aldo Moro’Prof.CorradoPetrocelliUniversità degli Studi di Firenze, Prof.AlbertoTesiUniversità degli Studi di Roma ‘Tor Vergata’Prof.RenatoLauroUniversità del Salento, Prof.Ing.DomenicoLaforgiaStazione Zoologica Anton Dohrn Napoli, Prof.RobertoDiLauroIstituto Agronomico Mediterraneo di Bari (IAMB), Dott.CosimoLacirignolaAgenzia Regionale per l’Ambiente in Puglia, Prof.GiorgioAssennatoComunità Ambiente, OlivieroSpinelli
39 the e-biodiversity research institute
Annex 2FinancialPlanforthe5yearscommitment
Management & Coordination E- Institute
General Coordination 146.000,00 146.000,00 146.000,00 146.000,00 146.000,00 730.000,00
Service Centre Coordination 100.000,00 100.000,00 100.000,00 100.000,00 100.000,00 500.000,00
Virtual Laboratory Coordination 100.000,00 100.000,00 100.000,00 100.000,00 100.000,00 500.000,00
Service Centre
Management
Management 425.500,00 410.500,00 460.500,00 598.500,00 733.500,00 2.628.500,00
Networking/meetings 93.000,00 100.000,00 100.000,00 100.000,00 110.000,00 503.000,00
Executive planning of services 27.000,00 30.000,00 30.000,00 32.000,00 35.000,00 154.000,00
distributed Centers & agreements 28.000,00 30.000,00 30.000,00 32.000,00 35.000,00 155.000,00
data resource Platform 63.000,00 63.000,00 63.000,00 63.000,00 63.000,00 315.000,00
MOu, protocols agreements 30.000,00 30.000,00 30.000,00 30.000,00 30.000,00 150.000,00
Services provision
Support services 972.000,00 1.208.000,00 1.555.000,00 1.911.000,00 2.115.000,00 7.761.000,00
Training and Capacity building 2.330.600,00 2.568.200,00 2.935.200,00 2.945.200,00 2.706.000,00 13.485.200,00
PR/ Communication 115.000,00 105.000,00 105.000,00 165.000,00 206.000,00 696.000,00
distributed services 800.000,00 1.050.000,00 1.333.333,00 2.683.333,00 3.933.333,00 9.799.999,00
Virtual Laboratories
Setup Interoperability 95.000,00 250.000,00 350.000,00 100.000,00 100.000,00 895.000,00
VL setup 56.000,00 250.000,00 250.000,00 250.000,00 250.000,00 1.056.000,00
Show Cases*
alien species 142.000,00 142.000,00 142.000,00 142.000,00 142.000,00 710.000,00
Wetlands 50.000,00 500.000,00 750.000,00 750.000,00 750.000,00 2.800.000,00
5.573.100,00 7.082.700,00 8.480.033,00 10.148.033,00 11.554.833,00
42.838.699,00
*Titles refer only to the first year of activities; different showcases will be launched from year 2 to 5 and an increasing budget
is allocated to showcases along the line two. Line one refers to showcases of LW-ITa and we may expect a showcase per year
TheItaliancontributiontoLifeWatchwillbetwofold.ThemajorpartoftheeffortwillbededicatedtotheconstructionandmanagementoftheLifeWatchServiceCentreandthefollowingprovisionofsupportservices.MoreoverItalywillcontributetoLifeWatchalsoengagingmanynationalscientificbodies(Uni-versities,researchcentersetc)intothedevelopmentofshowcasesandvirtuallaboratories.Theshowcaseswillbeindividuatedonthebasisofscientificprioritiesandcooperationamongmemberstates.Therefore,onafinancialpointofview,themajorper-centageofthebudgetwillbeinvestedtotheconstruc-tionandmanagementoftheServiceCentreandtotheprovisionofservices:onatotalof42.838.699mil,36.147.699milwillbededicatedtotheServiceCentreascommonoperationsand6.691.000miltothedevelop-
mentofshowcasesandvirtuallaboratories.Thebudgetwillbedistributedasfollows:
Costs Total
National priorities
General coordination 730.000,00
Virtual laboratory coordination 500.000,00
Virtual laboratories 1,951.000,00
Show cases 3.510.000,00
6.691.000,00
Common operations
Service centre coordination 500.000,00
Service centre management 3.905.500,00
Services provision 31.742.199,00
Total 42.838.699,00
40 the e-biodiversity research institute
Thenationalcontributionwillfinancethedevelop-mentofshowcasesandvirtuallaboratoriesandone/thirdofthecostsrelatedtotheServiceCentre.
CoNTRIbUTIoNS
National
National priorities 6.691.000,00
Common operations (Ita) 12.049.233,00
Site premium 4.098.466,00
Total 22.838.699,00
LW Europe 20.000.000,00
Total 42.838.699,00
SoURCES
National contribution 22.838.699,00
National committment 12.740.233,00
Other programs 3.000.000,00
LW Ita partners 3.000.000,00
Site premium 4.098.466,00
LW Europe 20.000.000,00
LW Europe income 20.000.000,00
Total 42.838.699,00
Thefinancingsourceshavebeenidentifiedasfollows: