18 April 2023

Overview

This class will focus on use of existing data. We will review data repositories, what kinds of data they hold, and how to find data within them. We will learn about one innovative data repository linked to a data manipulation and display application, which is freely available to everyone (Case study: GeoMapApp). We will also discuss selected examples of physical repositories that contain seafloor and subseafloor samples, and talk about how researchers can find out what is available and place requests to obtain samples.

Goals

• Familiarize COBRA MC Fellows with existing data repositories

• Enhance data discoverability by learning to find desired data types and datasets for your region of interest

• Determine the usability and whereabouts of at-home data use and what requires pro-software (availability vs usability)

• Case Study: GeoMapApp - How to make a site diagram / intro user activity

  • All students will research one or more specific locations/regions to identify and access data and prepare a map. If your project is not location specific, please choose a location/region on which you will focus for some short exercises.

Pre-Class Activities

• Please post on Slack! What is the approximate Latitude/Longitude for your dream cruise?

  • We will use this information to group you regionally for the in-class Data Scavenger Hunt

  • When we are working with GeoMapApp during the class, we can see how well your dream cruise area is represented, and consider if external (local) data may help with generating maps.

• Download and install GeoMapApp and prepare for use (15-20 minutes)

  • Access GeoMapApp resources here: https://www.geomapapp.org/

  • Download and install GeoMapApp on your local computer - versions are available for MacOS, PC (Windows), and Linux

  • There is a comprehensive GeoMapApp user guide that is useful to download for local use, and numerous short, video tutorials are available online. Please skim through p. 11 in the User Guide to get a short overview of the GeoMapApp interface. Next section goes through menus in detail.

  • It is helpful to have GeoMapApp open as you skim the first part of the User Guide, so you can follow along on your own computer. Please launch the application, you will be greeted with the "splash screen" shown below - choose your preferred map projection and press button labeled <Agree>. 

    

• If needed, download and install a utility capable of "unarchiving" datasets that will be delivered to you from data repositories, often in zip, gz, tar, or tgz formats (10 min):

  • If using MacOS, you should have built-in unarchiving (unpacking) abilities using the Archive Utility. Double-click on an archive to unpack it into a folder in the same location as the archive. FYI, you can create an archive in MacOS using the terminal window (explained here), or download a free archive manager that allows point-and-click control of archiving/unarchiving processes (some options here). 

  • If using Windows 10, you can right-click on a downloaded zip file and select Extract All. This will generate a folder containing the contents of the archive. Alternatively, double-click on the archive and it will open into a window (still compressed, but showing you contents), then drag or copy into a working folder. There are several excellent free archive managers for Windows, one of the best being 7zip (available here). Once installed, you can use 7zip to open and extract files from an archive, add files to an archive, or create a new archive.

Class Plan & Materials

• Hour 1 

  • 20 min: Andy - GeoMapApp overview (save 3-5 min for questions)

    • Capabilities, data types and linking, app versus local data

  • 20 min: Randi - Digital data repositories and overviews (save 3-5 min for questions)

    • Intro to R2R

    • Ocean Networks Canada

    • National Centers for Environmental Information (NCEI)

    • Video annotation resources - e.g., animal guides

  • 10 min: Physical data repositories and overviews 

    • IODP Core Repository (Andy - 3-4 min)

    • Intro to Smithsonian, Geological databases, MCZ (Randi - 5 min)

  • Break (5-10 min)

• Hour 2

  • Data Scavenger Hunt activity in Breakout Rooms (30 min)

    • Breakout groups:

      • Breakout A: Albano, Frates, Niyazi

      • Breakout B: Anthony, Gajigan, Jammalamadaka

      • Breakout C: Antonio, Barnhill, Weston

      • Breakout D: Ladd, Lejzerowicz, Ramírez Ortiz

    • 15 min: For your Dream Cruise area, what is the latest cruise that you can find with Multibeam data for your area (e.g., Year, Platform (Ship), Chief Scientist, Study Area)?

    • 15 min: Find one other type of data from a public repository from the area that works for your Dream Cruise. These are examples of potentially useful data, but you might find others that are especially useful (O2, pCO2, pH, fluorometer, multibeam, CTD, singlebeam sonar, XBT). For that data, tell us:

      • (a) file type (format, ASCII/binary)

      • (b) can you access the data

      • (c) is it what you expected it to be (why or why not?)

      • (d) is it useful to you (why or why not?)

  • 20 min: Data Scavenger Hunt report back

  • Wrap-up (5 min)

Additional Resources

• Look through the links on the “Class Plan” above

  • Scroll to the bottom of the GeoMapApp tutorials page for in-depth training and workflows

• Other tools:

  • Spatial Data Analysis:

    • qGIS: a free and open source geographic information system

    • arcGIS (ESRI)

    • QPS Fledermaus 

    • Google Earth

  • Species Identification:

    • World Register of Marine Species (WoRMS)

    • Deep Sea ID app

    • FathomNet

    • HURL deep sea animal guide

    • MBARI deep-sea guide

    • NOAA OE benthic deepwater animal identification guide v3

    • World Register of Deep-Sea Species (WoRDSS)

  • Video Annotation:

    • Squidle+

    • MBARI VARS 

    • Canadian Scientific Submersible Facility Ropos IRLS 2.0

    • Ocean Video Lab

    • Ocean Networks Canada SeaTube Pro

    • FathomNet

    • WHOI NDSF Alvin Frame-Grabber and Jason Virtual Van

  • NOAA OE Capstone Data links and usage:

    • Kennedy, B.R., Cantwell, K., et al, 2019. The unknown and the unexplored: insights into the Pacific deep-sea following NOAA CAPSTONE expeditions. Frontiers in Marine Science

Class Slides

Post-Class Dream Cruise Project Development

See the Dream Cruise Project Overview Template for additional context.

• Finish preparing the list of data for your Dream Cruise

• Consider creating a relevant, preferably bathymetric map (i.e. a global index map and a regional / local base map with available data layers) using a mapping tool (like GeoMapApp or the tool in the Marine Facilities Portal)