Dataset: CTD AR29, RB1904 and TN3638

Name: CTD casts from the SPIROPA project from R/V Neil Armstrong cruise AR29, Ronald H. Brown cruise RB1904 and R/V Thomas G. Thompson cruise TN368 to the New England Shelfbreak in 2018 and 2019
Published: 2022-08-10
Keywords: temperature, salinity, fluorescence, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.807119.4

Spatial Extent: N:41.391 E:-70.0012 S:39.1242 W:-71.337

Temporal Extent: 2018-04-17 - 2019-07-16

Project:

Collaborative Research: Shelfbreak Frontal Dynamics: Mechanisms of Upwelling, Net Community Production, and Ecological Implications (SPIROPA)

Principal Investigator:

Dennis J. McGillicuddy (Woods Hole Oceanographic Institution, WHOI)

Co-Principal Investigator:

Christian Petitpas (Massachusetts Division of Marine Fisheries)

Walker O. Smith (Virginia Institute of Marine Science, VIMS)

Heidi M. Sosik (Woods Hole Oceanographic Institution, WHOI)

Rachel Stanley (Wellesley College)

Jefferson Turner (University of Massachusetts Dartmouth, UMass Dartmouth)

Weifeng Gordon Zhang (Woods Hole Oceanographic Institution, WHOI)

Data Manager:

Olga Kosnyrev (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Mathew Biddle (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-08-10

Restricted:

Validated:

Current State:

Final no updates expected

CTD casts from the SPIROPA project from R/V Neil Armstrong cruise AR29, Ronald H. Brown cruise RB1904 and R/V Thomas G. Thompson cruise TN368 to the New England Shelfbreak in 2018 and 2019

Abstract:

CTD casts from the first, second and third cruises of the SPIROPA project. The first cruise (AR29), took place aboard the R/V Neil Armstrong in April 2018, the second cruise (RB1904) on the Ronald H. Brown in May 2019 and the third cruise (TN368) took place on the R/V Thomas G. Thompson cruise in July of 2019.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2022-08-10	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.807119.4	2022-08-11
2021-11-08	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.807119.3	2021-11-08
2021-04-20	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.807119.2	2021-04-21
2020-03-27	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.807119.1	2020-04-08

Description

Standard station CTD profiles measurements (down casts) with water sampling (up casts).

Methods & Sampling

Hydrographic data and water samples were collected at standard CTD stations: CTD profiles measurements (down casts) with water sampling (up casts). The CTD rosette was equipped with a SBE 911 plus CTD system, conductivity, temperature and pressure sensors (SeaBird Electronics), WetLabs ECO-AFL/FL fluorometer, WET Labs ECO-NTU turbidity sensor, Sea-Bird SBE 43 dissolved oxygen sensor, photosynthetically active radiation (PAR) sensor and also surface radiation (SPAR) sensor.

Location: New England Shelfbreak 40 S 71 W, depth 0-2000m

Data Processing Description

This dataset was not cleaned to remove outliers. See processing notes below about missing data identifiers.

Sea-Bird Software used for AR29 data:
Data acquisition: SBE Seasave, version 7.23.2
Data processing: SBE Data Processing, version 7.26.7.114

Sea-Bird Software used for RB1904 and TN368 data:

Data acquisition: SBE Seasave, version 7.26.7.107
Data processing: SBE Data Processing, version 7.26.7.114

Bad data is indicated with a flag:
Bad data flag=-9.990e-29

BCO-DMO Processing Notes (Data Version 1, 2020-03-27, AR29):
- submission contained ctd casts of cruise AR29 with numbers [133-143]
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- converted latitude and longitude coordinates to decimal degrees in the lat and lon columns
- concatenated all downcast seabird data files into one dataset.
- added ISO_DateTime_UTC field
- converted values indicated in seabird files as bad (-9.990e-29) to nd.

Dataset Version 2 (2021-04-20) replaces Dataset Version 1 (2020-03-27).
- This dataset update was made to add data from TN368 data in 2019.
- Imported seabrid .cnv files from TN368 and reimported the .cnv files from AR29 into the BCO-DMO data system. Imported the AR29 files again in this version instead of using the data from the previous version 1 of this dataset because temperature data t090C and t190C for cast 134 between depths 110 to 120 was not imported correctly in the version 1 data. It appears to have been an error when uploading the fixed with seabird file.
- Combined all the data into one table with additional columns for Cruise and Cast from information in the file names.
- As was done in version 1 of this dataset, the NMEA Lat, Lon and Time (UTC) in the seabird header was used as the data source for columns lat, lon, and ISO_DateTime_UTC.
- lat,lon rounded to 5 decimal places.
- column names renamed to match version 1 of this dataset which conform to the BCO-DMO naming conventions.
- Only -9.990e-29 was interpreted as a missing data identifier. These values will be displayed differently based on the file type downloaded by the user. It will be blank values in .csv files, NaN in matlab files, etc.
- The data submitter indicated this dataset was not cleaned for outliers. The following values are in this dataset: 90e-29, 9.0E-28,9.90E-27, 9.90E-27,-9.990e-29, 990e-29, 1.0000E-12. CPar data in AR29 cast 143 had some values: 9.2221E-13, 9.1837E-13, 9.2295E-13, 9.2564E-13, 9.2370E-13
- Data sorted by datetime then pressure (prDM).

Dataset Version 3 (2021-09-28) replaces Dataset Version 2 (2021-04-20).
- This dataset update was made to add CTD casts from AR29 cruise (added cast 001-011, 022-040, 047-068, and 079-095).
- Imported newly submitted seabird .cnv files from AR29 and imported the existing .csv from v2.
- Combined all the data into one table with additional columns for Cruise and Cast from information in the file names.
- As was done in version 1 & 2 of this dataset, the NMEA Lat, Lon and Time (UTC) in the seabird header was used as the data source for columns lat, lon, and ISO_DateTime_UTC.
- lat,lon rounded to 5 decimal places (same as v2)
- column names renamed to match version 2 of this dataset which conform to the BCO-DMO naming conventions
- Only -9.990e-29 was interpreted as a missing data identifier. These values will be displayed differently based on the file type downloaded by the user. It will be blank values in .csv files, NaN in matlab files, etc.
- Data sorted by datetime then pressure (prDM)

BCO-DMO data manager notes version 4 (replaces version 3)
- merged all available ctd cast .cnv files for all 3 cruises
- converted latitude and longitude to decimal degrees
- As was done in version 1, 2 & 3 of this dataset, the NMEA Lat, Lon and Time (UTC) in the seabird header was used as the data source for columns lat, lon, and ISO_DateTime_UTC.

Data Files

File
ctd_all.csv (Comma Separated Values (.csv), 24.67 MB) MD5:80e46264e58be7bb2a1e75de28a10f7c Primary data file for dataset ID 807119
Seabird CTD Data V1 filename: seabird_ctd_v1.zip (ZIP Archive (ZIP), 167.94 KB) MD5:de2963625a39967bf2e80b05dce86997 Original Seabird CTD files (.cnv) for the dataset 807119, version 1. This data file contains ctd data from the AR29 cruise with cast numbers [133-143].
Seabird CTD Data V2 filename: seabird_ctd_v2.zip (ZIP Archive (ZIP), 376.95 KB) MD5:20bf08b04e7cd4747a322b1bb972468e Original Seabird CTD files (.cnv) submitted for the dataset 807119, version 2. This data file containes ctd data from the TN368 cruise with numbers 039, 062, 070, 071,081, 082, 086, 086b, 089, 100, 118.
Seabird CTD Data V3 filename: seabird_ctd_v3.zip (ZIP Archive (ZIP), 847.86 KB) MD5:a42e9f7adf085e0220402ef84688cd94 Original Seabird CTD files (.cnv) for the dataset 807119, version 3. This data files contains ctd data from the AR29 cruise with cast numbers [001-011], [022-040], [047-068] & [079-095].
Seabird CTD Data V4 filename: seabird_ctd_v4.zip (ZIP Archive (ZIP), 8.60 MB) MD5:e6c72cdd30aa460200232dc9b475969f Original Seabird CTD files (.cnv) submitted for the dataset 807119, version 4. This data file containes ctd data from the cruises AR29, TN368 and RB1904.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1657803

Deployments

Deployment	Start Date	Platform	Investigator
AR29	2018-04-16	R/V Neil Armstrong	Dennis J. McGillicuddy (Chief Scientist)	data info
RB1904	2019-05-12	NOAA Ship Ronald H. Brown	Dennis J. McGillicuddy (Chief Scientist)	data info
TN368	2019-07-05	R/V Thomas G. Thompson	Dennis J. McGillicuddy (Chief Scientist)	data info

Instruments

CTD Sea-Bird 9

Supplied Name: Sea-Bird SBE 9

Supplied Description:

Sea-Bird SBE 9

Instrument Type

Generic Name: CTD Sea-Bird 9

Acronym: CTD SBE 9

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Sea-Bird SBE 9 is a type of CTD instrument package. The SBE 9 is the Underwater Unit and is most often combined with the SBE 11 Deck Unit (for real-time readout using conductive wire) when deployed from a research vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorometer, altimeter, etc.). Note that in most cases, it is more accurate to specify SBE 911 than SBE 9 since it is likely a SBE 11 deck unit was used. more information from Sea-Bird Electronics

CTD Sea-Bird SBE 911plus

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: CTD Sea-Bird SBE 911plus

Acronym: CTD SBE 911plus

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/

Generic Description:

The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics

LI-COR Biospherical PAR Sensor

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: LI-COR Biospherical PAR Sensor

Acronym: LI-COR Biospherical PAR

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0074/

Generic Description:

The LI-COR Biospherical PAR Sensor is used to measure Photosynthetically Available Radiation (PAR) in the water column. This instrument designation is used when specific make and model are not known.

Photosynthetically Available Radiation Sensor

Supplied Name: LI-COR Biospherical SPAR

Supplied Description:

Instrument Type

Generic Name: Photosynthetically Available Radiation Sensor

Acronym: PAR sensor

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/122/

Generic Description:

A PAR sensor measures photosynthetically available (or active) radiation. The sensor measures photon flux density (photons per second per square meter) within the visible wavelength range (typically 400 to 700 nanometers). PAR gives an indication of the total energy available to plants for photosynthesis. This instrument name is used when specific type, make and model are not known.

Pressure Sensor

Supplied Name: Pressure, Digiquartz with TC

Supplied Description:

Instrument Type

Generic Name: Pressure Sensor

Generic Description:

A pressure sensor is a device used to measure absolute, differential, or gauge pressures. It is used only when detailed instrument documentation is not available.

Sea-Bird SBE 43 Dissolved Oxygen Sensor

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Sea-Bird SBE 43 Dissolved Oxygen Sensor

Acronym: SBE-43 DO

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0036/

Generic Description:

The Sea-Bird SBE 43 dissolved oxygen sensor is a redesign of the Clark polarographic membrane type of dissolved oxygen sensors. more information from Sea-Bird Electronics

Turbidity Meter

Supplied Name: Turbidity, WET Labs ECO

Supplied Description:

Instrument Type

Generic Name: Turbidity Meter

Generic Description:

A turbidity meter measures the clarity of a water sample. A beam of light is shown through a water sample. The turbidity, or its converse clarity, is read on a numerical scale. Turbidity determined by this technique is referred to as the nephelometric method from the root meaning "cloudiness". This word is used to form the name of the unit of turbidity, the NTU (Nephelometric Turbidity Unit). The meter reading cannot be used to compare the turbidity of different water samples unless the instrument is calibrated. Description from: http://www.gvsu.edu/wri/education/instructor-s-manual-turbidity-10.htm

(One example is the Orion AQ4500 Turbidimeter)

Wet Labs ECO-AFL/FL Fluorometer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Wet Labs ECO-AFL/FL Fluorometer

Acronym: ECO AFL/FL

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0172/

Generic Description:

The Environmental Characterization Optics (ECO) series of single channel fluorometers delivers both high resolution and wide ranges across the entire line of parameters using 14 bit digital processing. The ECO series excels in biological monitoring and dye trace studies. The potted optics block results in long term stability of the instrument and the optional anti-biofouling technology delivers truly long term field measurements.
more information from Wet Labs

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
ISO_DateTime_UTC	Cast date and time in UTC ISO8601 format. From NMEA Time UTC.	yyyy-MM-dd'T'HH:mm:ss'Z'	ISO_DateTime_UTC
Latitude	Cast latitude. From NMEA latitude.	decimal degrees	lat
Longitude	Cast longitude; west is negative. From NMEA longitude.	decimal degrees	lon
Cruise	Cruise name	unitless	cruise_id
Cast	Cast number	unitless	cast
prDM	Pressure	decibar (db)	press
t090C	Temperature from primary sensor (ITS-90)	degrees Celsius (C)	temp
t190C	Temperature from secondary sensor (ITS-90)	degrees Celsius (C)	temp
c0S_m	Conductivity from primary sensor	Siemens per meter (S/m)	cond
c1S_m	Conductivity from secondary sensor	Siemens per meter (S/m)	cond
sbeox0V	Oxygen raw SBE 43	volts (V)	O2_v
flECO_AFL	Fluorescence, WET Labs ECO-AFL/FL	milligrams per meter cubed (mg/m3)	chl_a_fluor
wetCDOM	Fluorescence, WET labs CDOM	milligrams per meter cubed (mg/m3)	chl_a_fluor
upoly0	Upoly 0, SUNA 2km ASY-NTR-00081. SUNA UserPoly.	micromolar nitrate (mmol nitrate per m^3)	turbidity
CStarTr0	Beam Transmission, WET Labs C-Star	%	trans
turbWETntu0	Turbidity, WET Labs ECO	NTU	turbidity
altM	Altitude	meters (m)	altitude
sal00_DC	Salinity practical from primary sensor (output from Data Conversion)	Practical Salinity Units (PSU)	sal
spar	SPAR/surface irradiance	microEinsteins/m^2/second	SPAR
par	PAR/irradiance	microEinsteins/m^2/second	PAR
cpar	CPAR/Corrected Irradiance	percent (%)	irradiance
v0	Fluorometer WET Labs ECO-AFL/FL Voltage.	volts (V)	fluor
v6	UserPoly Voltage	volts (V)	fluor
depSM	Depth	meters (m)	depth
sal00	Salinity practical from primary sensors	Practical Salinity Units (PSU)	sal
sal11	Salinity practical from secondary sensors	Practical Salinity Units (PSU)	sal
sbeox0ML_L	Dissolved oxygen concentration from Oxygen SBE 43	milliliters per liter (ml/l)	O2
svCM	Sound velocity (chen-millero) from primary sensors	meters per second (m/s)	sound_vel
sigma_e00	Sigma-theta density from primary sensors	kilograms per meters cubed (kg/m^3)	sigma_0
sigma_e11	Sigma-theta density from secondary sensors	kilograms per meters cubed (kg/m^3)	sigma_0
flag	Bad data flag -9.990e-29	unitless	flag
File_Name	Name of corresponding .cnv file (see data files section)	unitless	file_name

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Dataset: CTD AR29, RB1904 and TN3638