ECS Observatory Collaboration

An open source project to provide the geosciences community with an example of the interdisciplinary potential of the Ocean Observatories Initiative.

This repository contains all of the necessary analyses and materials for Levine et al., 2020, "Open data, collaborative working platforms, and interdisciplinary collaboration: building an early career scientist community of practice to leverage Ocean Observatories Initiative data to address critical questions in marine science" currently under review. Code and data included are for investigation into air-sea interactions and water column impacts of Winter Storm Avery on the New England shelf break and subsequent surface cooling events. The notebooks, code, and data within this directory serve as an introduction to data acquisition and analysis of OOI data through the use of both Python via Jupyter Notebooks and MATLAB. While this repository may continue to evolve, a realease (v1.0) was created to maintain a copy of the repository at the time of publication and has been archived:

Data

Data included in the analyses and figures presented. See data folder for additional documentation on included files and original sources.

Analysis

Python and Matlab materials for data analysis and figure production. See analysis folder for additional documentation on included files.

• Figure 2

  • Datasets:
    • Met package Data from Pioneer Inshore Surface Mooring*: CP03ISSMmetpackage.mat
    • can be requested via M2M: M2M_Data_Figure2.m
  • Analysis:
    • Figure2.m
    • or Figure2.mlx (live editor)

• Figure 3

  • Datasets:
    • Meteorological Data from the Central Surface Mooring: deployment0010_CP01CNSM-SBD11-06-METBKA000-recovered_host-metbk_a_dcl_instrument_recovered_20181112T000012.513000-20181205T235959.678000.nc. or CP01CNSM_METBK1_2018-11-12_2018-12-06_RI.mat
  • Analysis:
    • plotOOImetbk.m, can use either netcdf or mat file, follow instructions in code comments.

• Figure 4

  • Datasets:
    • Global satellite sea surface temperature data (in netcdf) is retrieved from NASA's Jet Propulsion Laboratories Group for High Resolution SST webpage. Please find specifics located in the Data Availability statement of Levine et al. (2020).
  • Analysis:
    • plotGHRSST_ooi.jnl and corresponding functions to run code in ferret analysis folder

• Figure 5

  • Datasets:
    • Met package Data from Pioneer Inshore Surface Mooring*: CP03ISSMmetpackage.mat
    • CTD Profiler Data from Pioneer Central Offshore Profiler Mooring*: CP02PMCOProfilerCTD.mat
    • Oxygen Data from Pioneer Central Offshore Profiler Mooring*: CP02PMCOProfilerDO.mat
    • Flourometer and CDOM Data from Pioneer Central Offshore Profiler Mooring*: CP02PMCOProfilerFLORT.mat
    • can be requested via M2M: M2M_Data_Figure5.m
  • Analysis:
    • Figure5.m
    • or Figure5.mlx (live editor)

ProfilerCTD_RequestsAndAnalysis.ipynb in the analysis directory contains the necessary Python code for data acquisition, analysis, and creation of Figure 6 and Figure 7

• Figure 6
  • Datasets (*Available in a merged csv named CP02PMCO_combined.csv):
    • CTD Data from the Central Offshore Profiler*: CP02PMCO_ctd.csv
    • Oxygen Data from the Central Offshore Profiler*: CP02PMCO_DO.csv
    • Flourometer Data from the Central Offshore Profiler*: CP02PMCO_flor.csv
    • WOA-18 Decadal average of Temperature, Salinity, and Oxygen: woaDecadalAverage.csv
  • Analysis:
    • ProfilerCTD_RequestsAndAnalysis.ipynb, subsection titled: Figure 6 - Storm Profiles
• Figure 7
  • Datasets:
    • CTD Data from the 7 profiler sites: CP03ISPM_ctd.csv, CP02PMUI_ctd.csv, CP02PMCI_ctd.csv, CP02PMCO_ctd.csv, CP01CNPM_ctd.csv, CP04OSPM_ctd.csv, CP02PMUO_ctd.csv
  • Analysis:
    • ProfilerCTD_RequestsAndAnalysis.ipynb, subsection titled: Figure 7 - Spatial Variability of 1st Storm

Additional Examples for Accessing and Analyzing OOI data

dataAccess.ipynb

This notebook walks through searching for instrumentation and datasets at the OOI Coastal Endurance sites.

Copying/Running this repository

Local

• Make sure you have Git installed on your machine. For downloads/instructions for Windows/Mac/Linux, check out the Git website and/or the great tutorial video by UW eScience.
• In command line, navigate to where you would like the cloned directory, and run the following in your command line:

git clone https://github.com/ooi-ecs/ECS-Observatory-Collaboration.git

Google Colaboratory

• Through your Google account, open Google Drive
• On the top left side of your screen, select New > More > Colaboratory to launch a new Google Colaboratory notebook
• Under File, select Upload notebook and click on GitHub at the top of the window
• Insert https://github.com/ooi-ecs/ECS-Observatory-Collaboration into the search bar and press Enter
• Click on dataAcces.ipynb to launch the notebook in a new window.
• To connect to a runtime, run any notebook cell.
• To save any changes to the notebook, select Copy to Drive on the top left of the site or go to File > Save a copy in Drive...

Other Resources

Quick Jupyter keyboard shortcuts for new Users

• Esc + A: add new cell above
• Esc + B: add new cell below
• Esc + M: convert to Markdown cell
• Esc + Y: convert to code cell
• Esc + D + D (D twice): Delete current cell
• ctrl + Enter: execute the current cell
• Shift + Enter: execute the current cell and advance to the next cell