10/24/09

Oceanographic Data Sources, Data Management, 1) Oceanographic Data Sources And Software Tools • In-situ • Remotely-sensed For Marine Mammal Modeling • • Models • Static

2) Data Management • Metadata • Data Formats

3) Software Mark Baumgartner • Processing • Plotting/Visualization Woods Hole Oceanographic Institution • Analysis/Statistics

1) Oceanographic Data Sources • Along-track • In-situ • Remotely-sensed • Profiled • Climatologies • Tow-yo’ed • Ocean Models • Moored • Static

2) Data Management • Metadata • Data Formats

3) Software • Processing • Plotting/Visualization • Analysis/Statistics

• Along-track • Along-track • Profiled Primary Measurements • Profiled • Tow-yo’ed Water Depth • Tow-yo’ed • Moored • Moored Currents Thermosalinograph Scientific Echosounder Fluorescence Zooplankton Acoustic Backscatter

Acoustic Doppler Current Profiler

1 10/24/09

• Along-track • Along-track • Profiled • Profiled • Tow-yo’ed • Tow-yo’ed • Moored • Moored Fluorometer BIOMAPER CTD Seasoar Scanfish

Optical Video Plankton Conductivity Plankton Counter Temperature Acoustic Recorder Depth Instrument Doppler Current Acrobat (CTD) Profiler

• Along-track 3 m NDBC discus buoy Resources • Profiled • Instrumentation • Tow-yo’ed → Oceanographers • Moored → Instrument Manufacturers

• Data Archives → National Oceanographic Data Center (www.nodc.noaa.gov) → National Data Buoy Center (www.ndbc.noaa.gov)

You are here (San Diego)

AVHRR 1) Oceanographic Data Sources • Passive • In-situ • Remotely-sensed → surface • Climatologies temperature SeaWiFS • Ocean Models (AVHRR) QuikSCAT • Static → 2) Data Management (SeaWiFS) • Metadata • Data Formats • Active 3) Software → Sea surface height • Processing (TOPEX/Poseidon) • Plotting/Visualization • Analysis/Statistics → Winds (QuikSCAT) TOPEX/Poseidon

2 10/24/09

Resources

• → JPL Data Archive (poet.jpl..gov; podaac- www.jpl.nasa.gov/sst) → NOAA Coastwatch (coastwatch.noaa.gov)

• Ocean Color → NASA SeaWiFS (reason.gsfc.nasa.gov/OPS/Giovanni/ ocean.seawifs.shtml) Coverage: Local Coverage: Global • Sea Surface Height Resolution: 1 km Resolution: 18 km → JPL Data Archive (poet.jpl.nasa.gov) Available: ~twice daily Available: Weekly → Aviso (www.aviso.oceanobs.com)

1) Oceanographic Data Sources : Long-term average conditions • In-situ Anomaly: Deviation from the long-term average conditions • Remotely-sensed • Climatologies • Ocean Models • Static

2) Data Management • Metadata • Data Formats

3) Software • Processing • Plotting/Visualization • Analysis/Statistics

Salinity at 1000 m Climatology from World Ocean Atlas

Surface Salinity Climatology from World Ocean Atlas

3 10/24/09

Surface Temperature Front Climatology Resources

• Global Climatology → World Ocean Database and World Ocean Atlas (www.nodc.noaa.gov/OC5/indprod.html)

• Regional or Local Climatology → Find in the literature and request data from authors

Ullman, D.S. and P.C. Cornillon. 1999. derived sea surface temperature fronts on the off the northeast U.S. coast. Journal of Geophysical Research 104:23459-23478.

1) Oceanographic Data Sources • In-situ Back in the day… • Remotely-sensed • Climatologies • Ocean Models • Static 2) Data Management ? • Metadata • Data Formats

3) Software • Processing • Plotting/Visualization • Analysis/Statistics

Today… Resources • Global Models → U.S. Navy Models (www7320.nrlssc.navy.mil/ global_nlom)

• Regional Models → U.S. East Coast Regional Ocean Forecast Model (polar.ncep.noaa.gov/cofs)

• Local Models Model Surface Currents → Find local modelers and build collaborations in the Northwest Atlantic from the NOAA Regional Ocean Forecast System

4 10/24/09

1) Oceanographic Data Sources • • In-situ • Remotely-sensed • Coastlines • Climatologies • Ocean Models • Static

2) Data Management • Metadata • Data Formats

3) Software • Processing • Plotting/Visualization • Analysis/Statistics

Resources 1) Oceanographic Data Sources • In-situ • Remotely-sensed • High-resolution bathymetry (ETOPO5, ETOPO2, • Climatologies SRTM30_PLUS) • Ocean Models → Scripps Institution of (topex.ucsd.edu/ • Static WWW_html/mar_topo.html) → U.S. National Geophysical Data Center 2) Data Management (www.ngdc.noaa.gov/mgg/global/global.html) • Metadata • Data Formats • Coastlines → U.S. National Geophysical Data Center 3) Software (www.ngdc.noaa.gov/mgg/shorelines/shorelines.html) • Processing • Plotting/Visualization • Analysis/Statistics

Metadata: “Data about data” Metadata: “Data about data”

Why collect data about your data?

5 10/24/09

Metadata: “Data about data” Kinds of things to include in your metadata… • Project name Why collect data about your data? • Geographic area • Because you’ll forget!!! • Species of interest • Facilitates data sharing – your collaborators will • Platform thank you • Who collected the data (e.g., name, organization) • Kind of data (e.g., salinity) • Type of instrument (what it is, model, serial number) • What kind of processing has been done to the raw data

Resources 1) Oceanographic Data Sources • In-situ • Remotely-sensed • Metadata standards • Climatologies → Federal Geographic Data Committee Metadata Standard • Ocean Models (www.fgdc.gov/index.html) • Static

2) Data Management • Metadata • Data Formats

3) Software • Processing • Plotting/Visualization • Analysis/Statistics

Which data format? Which data format? • Appropriateness for your data • ASCII (text) files • Ease of use • Proprietary formats (Arc) • Flexibility • Portability • Relational databases • Ability to accommodate metadata • Scientific formats • Data easily transferred to collaborators → HDF → NetCDF

6 10/24/09

Resources Which data format? • ASCII (text) files NetCDF • Scientific data formats • Stores multidimensional → HDF (hdf.ncsa.uiuc.edu) • Proprietary formats (Arc) array data → NetCDF (www.unidata.ucar.edu/software/netcdf) • Excellent capacity for • Relational databases metadata • Platform-independent • Scientific formats (can share between any → HDF machine) • No compression (may → NetCDF not be the format of choice for archiving)

1) Oceanographic Data Sources Processing • In-situ • Remotely-sensed Software that will allow you to prepare your data • Climatologies for visualization and analysis • Ocean Models • Static Ideally, should be flexible to deal with any and all 2) Data Management features and idiosyncrasies in your data • Metadata → Extract regions of interest in satellite data • Data Formats → Extract features in in-situ data 3) Software → Editing/quality controlling sighting data • Processing • Plotting/Visualization • Analysis/Statistics

Resources 1) Oceanographic Data Sources • In-situ • Remotely-sensed • Processing • Climatologies → Matlab (www.mathworks.com) • Ocean Models → IDL (www.rsinc.com/idl) • Static → Perl (www.perl.org) → ArcView/ArcGIS (www.esri.com) 2) Data Management → IDRISI (www.clarklabs.org) • Metadata • Data Formats

3) Software • Processing • Plotting/Visualization • Analysis/Statistics

7 10/24/09

Plotting/Visualization Resources Software that will allow you to qualitatively • GIS → ArcView/ArcGIS (www.esri.com) examine your data AND convey your results in → GRASS (grass.itc.it) public communications (presentations and papers) → MapInfo (www.mapinfo.com) → Others (see software.geocomm.com) Ideally, should be flexible to deal with any and all • Mapping features and idiosyncrasies in your data → Generic Mapping Tools (GMT) (gmt.soest.hawaii.edu) → Online Map Creation (www.aquarius.geomar.de/omc) → Plot maps of distributions → Planiglobe (www.planiglobe.com/omc_set.html) → Plot environmental data in whatever form it comes in (e.g., temperature profiles) • Analytical software with plotting/visualization capabilities → Matlab (www.mathoworks.com) → Plot relationships between variables → IDL (www.rsinc.com/idl)

1) Oceanographic Data Sources Analysis/Statistics • In-situ • Remotely-sensed Software that will allow you to quantitatively • Climatologies examine your data • Ocean Models • Static Must have the tools you need 2) Data Management → Basic statistics (t-test, ANOVA) • Metadata → Advanced regression models (GLM, GAM) • Data Formats → Community analyses 3) Software • Processing • Plotting/Visualization • Analysis/Statistics

Resources Final thoughts on software…

• Analysis/Statistics • Beware of “push-button” processing and → R (www.r-project.org) → Splus (www.insightful.com/products/splus) analysis – make sure you know what’s going → SAS (www.sas.com) on behind the scenes → Matlab (www.mathoworks.com) → IDL (www.rsinc.com/idl) → ArcView/ArcGIS (www.esri.com) • Learn to program a computer → C, FORTRAN, BASIC → Matlab, IDL → Arc → Perl

8 10/24/09

dimensions: n = 179 ; variables: NetCDF header Thanks to my fellow Workshop Organizing float depth(n) ; depth:long_name = "depth" ; Committee members… depth:units = "meters" ; float temp(n) ; • Ed Gregr temp:long_name = "temperature" ; temp:units = "degC" ; • Toshihide Hamzaki float sal(n) ; sal:long_name = "salinity" ; • Ellen Hines sal:units = "PSU" ;

• Kristin Laidre // global attributes: :experiment = "North Atlantic Right Whale Ecology" ; • Daniel Palacios :platform = "NOAA Ship Albatross IV" ; :cruise = "AL0504" ; • Jessica Redfern :instrument_type = "SBE 19plus CTD" ; :serial_number = 4501 ; • Kathleen Vigness Raposa :comments = "CTD data for cast 186" ; :cast = 186 ; :date = "05/19/05 18:00:00" ; :lon = -69.2037 ; This presentation available at :lat = 41.2932 ; ftp://ftp.whoi.edu/pub/users/mbaumgartner/baumgartner_modeling.ppt :water_depth = 98.0 ; :designation = "DV40" ; :set_ctd_flag_min_speed = 0.3 ;

Summer Climatology of Bottom Temperature and Salinity

Loder, J.W., G. Han, C.G. Hannah, D.A. Greenberg and P.C. Smith. 1997. and baroclinic circulation in the Scotian Shelf region: winter versus summer. Canadian Journal of Fisheries and Aquatic Sciences 54:40-56.

9