biodiversity observation and biosensor data Francisco Hernandez Joram Declerck Klaas Deneudt Lifewatch EGI engage M ay 2015 Outline Lifewatch EGI ENGAGE Collaborative scientific ID: 1026056
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1. Collaborative scientific platforms for accessing, processing and validation of biodiversity observation and biosensor data. Francisco Hernandez, Joram Declerck, Klaas DeneudtLifewatch - EGI engage May 2015
2. OutlineLifewatchEGI - ENGAGECollaborative scientific platformBiosensorsChallengesStatusVirtual labs and research environmentsProgress
3. Lifewatch infrastructureEuropean research infrastructure, ESFRI roadmapStudy of biodiversity and ecosystemsAccess to realtime dataBiosensor networksBIG data, inline data processingMore info : http://www.lifewatch.eu Example VRE : http://marine.lifewatch.eu/Belgian contribution: http://www.lifewatch.be
4. BiosensorsBiological sensors that enable observations at space and time scales relevant to organisms behavior, physiology and life historyOptics, Acoustics, Genetics, GPSDiscrete => continuousDelayed mode => real-time
5. http://www.lifewatch.be/en/sensors
6. ZooscanHigh resolution flatbed scanner for water samplesDigital storage and processing of zooplankton samples -> taxonomic composition and abundanceImage acquisition: 2400-4800 dpiData generation: +/- 4 GB/sample; 432 Gb/yearAnalysis: pattern recognition software (Plankton Identifier [Tanagra], ZooImage [R], …)
7. Video Plankton Recorder (VPR)Real-time underwater digital camera system + strobeRapid quantification of plankton taxonomic composition and abundanceImage acquisition: 30 frames/second of 7.2 ml image volumeData generation: +/- 10GB/h (at 150kb/image) , 1.5M files / hAnalysis: pattern recognition software (Visual Plankton software [Matlab])
8. Flow cytometerLaser based instrument for particle detection and characterisation in fluidsCounting and characterisation of phytoplankton particles -> taxonomic composition and abundanceImage acquisition: particle scattering + fluorescenceData generation: +/- 200 MB/sample; 1Tb/yearAnalysis: clustering software (Easyclus [Matlab], FCM [R], …)
9. Acoustic fish telemetryAcoustic fish tag trackingStudying distribution, migration and habitat use Data generation: 25 MB/monthAnalysis: GIS mapping & visualization (CartoDB), behaviour analysis (Matlab, Python)
10. Multibeam echosounderAcoustic high resolution depth sounding sonarBathymetry and sediment typologyData generation: sediment 10Gb; water column 100Gb/dayAnalysis: data cleaning and validation, chart creation, deriving sediment typology (CARIS, Fledermaus)
11. Sediment profiler imagingDigital Sediment Profiling CameraVertical cross section of the sediment/water interfaceImage acquisition: 24.1 Mpixel images of 320 cm2 of sedimentData generation: 1Gb/image; 130 Gb/yearAnalysis: Image pattern recogition software, relating to benthic communities
12. Acoustic bat recorderUltrasound detection and recordingSound acquisition: 500 kHz with 16 Bit amplitude resolutionData generation: 1 MB/per second of sound recording; 0.5 Gb/nightAnalysis: Call detection and recogition software
13. Bird tracking with GPSTracking of large birds with GPS tags developed by UvA-BiTSStudying migration and habitat useGPS position every 10min, 70 birds, soon > 100Data generation: 3G/year (Flemish LifeWatch), multiple GB/year (UvA-BiTS)Analysis: GIS mapping & visualization, behaviour analysis (Matlab,Python,R)
14. ChallengesBiosensor buy and install equipment: sensors, winches, antennastechnical calibration, raw signal processing, vendor softw.ITreal-time data transfer, storage, processingBiologysensor output -> biodiversity parametersaggregating, combine data, models & predictions, visualization, sharing, validation,…
15. InfrastructureStatusBird GPS tracking network + web cams3 base stations installed and operational70 birds with GPSFlow CytometerInstalled on RV Simon Stevin and operationalMulti beamInstalled on RV Simon Stevin and operationalAcoustic bat detectorsTest installation installed. Offshore installation in preparation ZooScanInstalled in MSO lab and operationalVideo Plankton RecorderTo be installed July 2014Sediment Profile ImagingInstalled on RV Simon Stevin and operationalAcoustic fish telemetry40 fishes tagged, 51 receivers installed, data for >2 yearsEnvironmental DNASeveral species of fish and jellyfish under investigation
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17. Doctoral studies on sensor use and application4 PhD’s at Ghent UniversityStarted October 2014Work on :Standard operation proceduresAlgorithms for translation of sensor output to biodiversity parameters on abundance and distribution of taxaRecommendations on optimization and upgrade of the infrastructureApplications of the infrastructure in biodiversity and ecosystem studies
18. Collaborative platform for sensor data processing and analysisFlowcytometerSensor network Fish tagsBird tracksSensor dataArchive?R, Java, Python, Rstudio, RshinyScripts, workflows, algorithmsScientific dataRsyncCalibration dataProcessing network Species identifications, field observations, crowd sourcingScience community VPRBird RadarBenthic imgFish sonarRemote sensingIn situ habitat obs.Bird videoHydrophoneseDNAPostgis, GeoserverLW ICT coreFedCloud?
19. ProgressOngoing testing with ICT Core facilities: IFCA, EGI ENGAGECreate virtual servers on fedcloudR, R studio server, Rshiny : donePostGIS, geoserver : startedmanage virtual serversSet up data transfer from ship & stations to IFCA : daily Rsync operationalfrom VLIZ geoserver to IFCAmanage storage capacitySet up user interfaces for scientistsVLIZ users : startedexternal usersmanage resources: user data, algorithms, scripts, models, …
20. Lifewatch virtual labs to ICT coreMeeting in AmsterdamCollect and present existing virtual labs Lifewatch Marine Virtual Research Environment (VRE) : doneVRE for terrestrial & other thems: startedUpscale virtual lab components using LW ICT coreEnvironmental layers, Species occurence dataBIOVEL portal , Biodiversity catalogueTaxonomic, Biostatical & Modelling webserviceshttp://marine.lifewatch.eu/
21. More infoLifewatch website http://www.lifewatch.eu Marine VRE : http://marine.lifewatch.eu/Belgian contribution: http://www.lifewatch.beFlanders Marine Institute : http://www.vliz.be