Metadata Report for BODC Series Reference Number 1012791

• Metadata Summary

• Problem Reports

• Data Access Policy

• Narrative Documents

• Project Information

• Data Activity or Cruise Information

• Fixed Station Information

• BODC Quality Flags

• SeaDataNet Quality Flags

Metadata Summary

Problem Reports

No Problem Report Found in the Database

Sea surface hydrography data quality document

During the cruise there were periods when the pump was switched off or the lines to the instruments were blocked with ice. These are easily identified as low values (~0) in the INFLTF01 flow rate channel. During these periods corresponding data in CNDCSG01, PSALSU01, TMESSG01 and SVELSG01 are flagged as suspect. The parameters CPHLUMTF and TMESFL01 lag the pump by up to 5 minutes or have slower response times and have extra values flagged around these periods.

While the ship was in port, TEMPHU01 values were flagged as suspect because the ship was warming the surrounding water.

Data Access Policy

Open Data supplied by Natural Environment Research Council (NERC)

You must always use the following attribution statement to acknowledge the source of the information: "Contains data supplied by Natural Environment Research Council."

Narrative Documents

Turner Designs 10AU Field Fluorometer

The Turner Designs 10AU is designed for continuous-flow monitoring or discrete sample analyses of fluorescent species. A variety of optical kits with appropriate filters and lamps are available for a wide range of applications. Individual filters and lamps are also available for customised applications.

Standard optical kits include those for chlorophyll-a (extracted and/or in vivo), phycocyanin, phycoerythrin, CDOM, ammonium, rhodamine and fluorescein dye tracing, crude oil, refined oil, histamine and optical brighteners.

The instrument's light source is a 4 watt lamp and the detector is a photomultiplier tube with a standard detection range of 300-650 nm. A red-sensitive version with a detetion range of 185-970 nm is also available.

Specifications

Further details can be found in the manufacturer's specification sheet.

Instrument Description (JR106 sea surface hydrography)

Data were collected using the integrated underway system on the RRS James Clark Ross. Contacts for specific instrumentation queries can be found on the British Antarctic Survey (BAS) website (BAS website).

The data were logged on a PC-based oceanlogger logging system, built in-house at BAS, with the primary purpose of logging measurements from various of the ship's continuously-run data sources. Accordingly, it drew data from the ship's pumped non-toxic supply, plus assorted meteorological parameters. The instruments with an analogue output were connected to self-contained digitising Nudam modules located close to the relevant instrument. The modules were then interrogated by the controlling PC using the RS485 protocol.

The following oceanographic instrumentation were connected to the ships non-toxic sea-water supply:

References

Cruise report - JR106b, RRS James Clark Ross, NERC AutoSub under ice thematic Programme, Kangerdlugssuaq Fjord and Shelf, East Greenland.

BODC JR106b documentation

Litre Meter flow meter

A flow meter used to monitor water flow rates for pumped systems such as ships' continuous seawater supplies.

SeaBird MicroTSG Thermosalinograph SBE 45

The SBE45 MicroTSG is an externally powered instrument designed for shipboard measurement of temperature and conductivity of pumped near-surface water samples. The instrument can also compute salinity and sound velocity internally.

The MicroTSG comprises a platinum-electrode glass conductivity cell and a stable, pressure-protected thermistor temperature sensor. It also contains an RS-232 port for appending the output of a remote temperature sensor, allowing for direct measurement of sea surface temperature.

The instrument can operate in Polled, Autonomous and Serial Line Sync sampling modes:

• Polled sampling: the instrument takes one sample on command
• Autonomous sampling: the instrument samples at preprogrammed intervals and does not enter quiescence (sleep) state between samples
• Serial Line Sync: a pulse on the serial line causes the instrument to wake up, sample and re-enter quiescent state automatically

Specifications

Further details can be found in the manufacturer's specification sheet.

Sea surface hydrography processing document

Originator's processing

Sea surface hydrography (ship's intake 6 m below surface) was recorded by the BAS Oceanlogger system. This comprised a thermosalinograph and fluorometer both of which were connected to the ship's non-toxic seawater supply. The system was set to record every 2 seconds. However, the pumps were switched off whenever the ship moved through sea ice to avoid damaging the pumps. Discrete samples were taken from the system for calibration.

The data from the oceanographic instrumentation were read into Unix daily to produce an ocean.*** file for the particular Julian day (where *** is the Julian day), at intervals from 2 seconds upwards. The data were mapped and converted to the same time interval as the navigational data, using the bestnav_all_jr106.mat file. Corresponding latitudes and longitudes from the bathymetry data were also included in the output file. The daily mapped data were saved in the oceanlog_30sec_all_jr106s.mat containing data for the entire cruise leg.

BODC Processing

Data were received as three binary .mat Matlab files named bestnav_all_jr106.mat, merged_all_jr106s and oceanlog_30sec_all_jr106s.mat. Each file held data from the navigation, bathymetry and oceanographic/meteorological respectively although each file contained both position and time data. The data covered the time period of 18:24:29 on the 29th August 2004 to 23:59:29 on the 10th September 2004, and so include data from the previous cruise (JCR106). Data from the previous cruise were trimmed from this series as they are included in the JCR016 data submission.

All underway sea surface hydrography, meteorology and ship's navigation files are merged into a single NetCDF file using time (GMT) as the primary linking key.

Following this, the NetCDF file was then split into three separate NetCDF files, with the data grouped by instrument position, by BODC generated Matlab code. One file contained data for sea surface hydrography, one for meteorology and the final NetCDF file held navigation data.

During transfer the original variables were mapped to unique BODC derived parameter codes. The parameter mapping is described in the table below.

Each data channel was visually inspected on a graphics workstation and any spikes or periods of dubious data are flagged as suspect. The capabilities of the workstation screening software allows all possible comparative screening checks between channels (e.g. to ensure corrected wind data have not been influenced by changes in ship's heading). The system also has the facility of simultaneously displaying the data and the ship's position on a map to enable data screening to take oceanographic climatology into account.

Calibration

Calibrations of the salinity, temperature and chlorophyll values against the underway salinity samples and CTD profiles were undertaken by BODC. For all parameters the offset (reference minus parameter to calibrate) failed the Anderson-Darling test for normality. All offsets appeared homogeneous so linear regression was used.

Salinity

Attempts to calibrate the salinity against discrete samples taken from the underway supply and against calibrated CTD profiles were undertaken. When the data were viewed initially it was clear that values of salinity were highly variable in the upper water column whilst the ship was within the Kangerdlugssuaq Fjord system. For this reason, only salinities outside the fjord are used in calibration.

Regression of salinity offsets vs time

Regression of discrete salinities vs the difference between discrete sample and TSG salinity

In both regressions the R² is too small (<95%) and the P value too large (>0.05) for the results to be considered significant.

When plotted a small offset from zero is visible throughout the series. This has a mean of 0.015 and a standard deviation of 0.031 (N=17). The high standard deviation suggests that the offset should not be applied.

Regression of salinity offsets vs time

Regression of salinity offsets vs the surface value

In both regressions the R² is too small (<95%) and the P value too large (>0.05) for the results to be considered significant.

When a mean offset is calculated for the entire series the values is 0.0547 (N=13) with a standard deviation of 0.797. The standard deviation is greater than a mean so the offset has not been applied

Sea Surface Temperature (SST)

An inter-comparison between the underway SST and the uncalibrated CTD temperature profiles was undertaken, this assumed a seawater intake depth on the ship of 6 m. When the data were viewed initially it was clear that values of temperature were highly variable in the upper water column whilst the ship was within the Kangerdlugssuaq Fjord system. For this reason, only temperatures outside the fjord are used.

Regression of temperature offsets vs time

Regression of temperature offsets vs the surface value

In both regressions the R² is too small (<95%) and the P value too large (>0.05) for the results to be considered significant.

There is a mean offset in temperature of -0.1101 with a standard deviation of 0.1138. The standard deviation is of a similar magnitude to the offset so the offset will not be applied to the series.

Chlorophyll

On visual inspection the chlorophyll did not exhibit the high variability observed when the ship was in the fjord like in the salinity and temperature series so the entire series of values is used for an inter-comparison between the underway and CTD values.

Regression of chlorophyll offsets vs time

The P value of 0.025 suggests a time dependence in the offsets which is confirmed by visual inspection of the data.

Regression of chlorophyll offsets vs the surface value

This shows there is not significant variation with chlorophyll though.

The mean offset for the series is -0.0028 with a standard deviation of 0.1058 so not offset is to be applied.

Because both the parameters considered are uncalibrated and no discrete samples were taken is not known which sensor is responsible for the suggested time dependent offset so no calibration will be applied.

Project Information

AutoSub Under Ice (AUI) Programme

AutoSub was an interdisciplinary Natural Environment Research Council (NERC) thematic programme conceived to investigate the marine environment of floating ice shelves with a view to advancing the understanding of their role in the climate system.

The AUI programme had the following aims:

• To attain the programme's scientific objectives through an integrated programme based on interdisciplinary collaborations and an international perspective
• To develop a data management system for the archiving and collation of data collected by the programme, and to facilitate the eventual exploitation of this record by the community
• To provide high-quality training to develop national expertise in the use of autonomous vehicles in the collection of data from remote environments and the integration of such tools in wider programmes of research
• To stimulate and facilitate the parameterising of sub-ice shelf processes in climate models, and to further demonstrate the value of autonomous vehicles as platforms for data collection among the wider oceanographic and polar community

Following the invitation of outline bids and peer review of fully developed proposals, eight research threads were funded as part of AUI:

Physical Oceanography

• ISOTOPE: Ice Shelf Oceanography: Transports, Oxygen-18 and Physical Exchanges.
• Evolution and impact of Circumpolar Deep Water on the Antarctic continental shelf.
• Oceanographic conditions and processes beneath Ronne Ice Shelf (OPRIS).

Glaciology and Sea Ice

• Autosub investigation of ice sheet boundary conditions beneath Pine Island Glacier.
• Observations and modelling of coastal polynya and sea ice processes in the Arctic and Antarctic.
• Sea ice thickness distribution in the Bellingshausen Sea.

Geology and Geophysics

• Marine geological processes and sediments beneath floating ice shelves in Greenland and Antarctica: investigations using the Autosub AUV.

Biology

• Controls on marine benthic biodiversity and standing stock in ice-covered environments.

The National Oceanography Centre Southampton (NOCS) hosted the AUI programme with ten further institutions collaborating in the project. The project ran from April 2000 until the end of March 2005, with some extensions to projects beyond this date because of research cruise delays. The following cruises were the fieldwork component of the AUI project:

Table 1: Details of the RRS James Clark Ross AUI cruises.

All the cruises utilised the AutoSub autonomous, unmanned and untethered underwater vehicle to collect observations beneath sea-ice and floating ice shelves. AutoSub can be fitted with a range of oceanographic sensors such as:

• Conductivity Temperature Depth (CTD) instruments
• Acoustic Doppler Current Profillers (ADCP)
• A water sampler
• Swath bathymetry systems
• Cameras

In addition to use of AutoSub during each cruise measurements were taken from ship. These varied by cruise but included:

• Ship underway measurements and sampling for parameters such as:
  • Salinity
  • Temperature
  • Fluorescence
  • Oxygen 18 isotope enrichment in water
  • Bathymetry using a swath bathymetry system
• Full-depth CTD casts for with observations of samples taken for parameters such as:
  • Salinity
  • Temperature
  • Fluorescence
  • Optical transmissivity
  • Dissolved oxygen
  • Oxygen 18 isotope enrichment in water
  • Water CFC content
• Sea floor photography and video using the WASP system
• Sea floor sampling with trawls/rock dredges
• Sea ice observations (ASPeCt), drifters and sampling

The AutoSub project also included numerical modelling work undertaken at University College London, UK.

The project included several firsts including the first along-track observations beneath an ice shelf using an autonomous underwater vehicle. The AutoSub vehicle was developed and enhanced throughout this programme and has now become part of the NERC equipment pool for general use by the scientific community. Further information for each cruise can be found in the respective cruise reports (links in Table 1).

Data Activity or Cruise Information

Cruise

Complete Cruise Metadata Report is available here

Fixed Station Information

No Fixed Station Information held for the Series

BODC Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

SeaDataNet Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle: