LifeWatch

The E-Biodiversity Research Institute Proposal for Italy’s Contribution to LifeWatch

eScienceandTechnologyInfrastructureforBiodiversityandEcosystemResearch

u1ps

OuO1Ops

«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

OuO1Ops

5 the e-biodiversity research institute

Preamble«

»

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

Ou O1 Op s


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.

«

OuO1Ops


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

u1

u


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

OuO1Ops


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.

10 thee-biodiversityresearchinstitute

OuO1Ops


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


OuO1Ops

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;


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.

w


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;

OuO1Ops


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.

q


uO1ps

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


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

k


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

OuO1Ops


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;

k


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.

OuO1Ops


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.


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

k


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-

OuO1Ops


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

k


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.


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

OuO1Ops


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,

k


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’.

OuO1Ops


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

k


controlonthebioticdatatotheCollectionsLab,asregardsspeciestaxonomy,andtotheInteractionsLab,asregardsspeciesinteractionsandtrophiclinks.


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.

OuO1Ops

p


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


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)


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)


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


.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


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.

OuO1Ops


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


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


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;


• 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


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.


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


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


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:

LifeWatch

Technology

Transcript of LifeWatch