Metadata Report for BODC Series Reference Number 1093461
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
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Problem Reports
No Problem Report Found in the Database
DIMES James Cook Cruise JC041 Underway Surface Hydrography Quality Control
Large sections of the cruise track are within Argentine waters and therefore data are unavailable for these time periods; 06/12/2009 4:29 to 07/12/2009 16:19 and 17/12/2009 07:20 to 20/12/2009 09:58.
The temperature, conductivity and salinity values were found to have regular spikes of 1 degree and 0.1 PSU every 12 hours or so, which is likely to be system maintenance. These have been flagged as suspect where necessary.
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
WET Labs WETStar Fluorometers
WET Labs WETStar fluorometers are miniature flow-through fluorometers, designed to measure relative concentrations of chlorophyll, CDOM, uranine, rhodamineWT dye, or phycoerythrin pigment in a sample of water. The sample is pumped through a quartz tube, and excited by a light source tuned to the fluorescence characteristics of the object substance. A photodiode detector measures the portion of the excitation energy that is emitted as fluorescence.
Specifications
By model:
| Chlorophyll WETStar | CDOM WETStar | Uranine WETStar | Rhodamine WETStar | Phycoerythrin WETStar | |
|---|---|---|---|---|---|
| Excitation wavelength | 460 nm | 370 nm | 485 nm | 470 nm | 525 nm |
| Emission wavelength | 695 nm | 460 nm | 530 nm | 590 nm | 575 nm |
| Sensitivity | 0.03 µg l-1 | 0.100 ppb QSD | 1 µg l-1 | - | - |
| Range | 0.03-75 µg l-1 | 0-100 ppb; 0-250 ppb | 0-4000 µg l-1 | - | - |
All models:
| Temperature range | 0-30°C |
|---|---|
| Depth rating | 600 m |
| Response time | 0.17 s analogue; 0.125 s digital |
| Output | 0-5 VDC analogue; 0-4095 counts digital |
Further details can be found in the manufacturer's specification sheet, and in the instrument manual.
Trimble Applanix Position and Orientation Systems for Marine Vessels (POSMV)
The Position and Orientation Systems for Marine Vessels (POSMV) is a real time kinematic (RTK) and differential global positioning system (DGPS) receiver for marine navigation. It includes an inertial system that provides platform attitude information. The instrument provides accurate location, heading, velocity, attitude, heave, acceleration and angular rate measurements.
There are three models of Applanix POSMV, the POS MV 320, POS MV Elite and the POS MV WaveMaster. POS MV 320 and POS MV WaveMaster are designed for use with multibeam sonar systems, enabling adherence to IHO (International Hydrographic Survey) standards on sonar swath widths of greater than ± 75 degrees under all dynamic conditions. The POS MV Elite offers true heading accuracy without the need for dual GPS installation and has the highest degree of accuracy in motion measurement for marine applications.
Specifications
POS MV 320
| Componenet | DGPS | RTK | GPS Outage |
|---|---|---|---|
| Position | 0.5 - 2 m 1 | 0.02 - 0.10 m 1 | <2.5 m for 30 seconds outages, <6 m for 60 seconds outages |
| Roll and Pitch | 0.020° | 0.010° | 0.020° |
| True Heading | 0.020° with 2 m baseline 0.010° with 4 m baseline | - | Drift <1° per hour (negligible for outages <60 seconds) |
| Heave | 5 cm or 5% 2 | 5 cm or 5% 2 | 5 cm or 5% 2 |
POS MV WaveMaster
| Accuracy | DGPS | RTK | GPS Outage |
|---|---|---|---|
| Position | 0.5 - 2 m 1 | 0.02 - 0.10 m 1 | <3 m for 30 seconds outages, <10 m for 60 seconds outages |
| Roll and Pitch | 0.030° | 0.020° | 0.040° |
| True Heading | 0.030° with 2 m baseline | - | Drift <2° per hour |
| Heave | 5 cm or 5% 2 | 5 cm or 5% 2 | 5 cm or 5% 2 |
POS MV Elite
| Accuracy | DGPS | RTK | GPS Outage |
|---|---|---|---|
| Position | 0.5 - 2 m 1 | 0.02 - 0.10 m 1 | <1.5 m for 60 seconds outages DGPS, <0.5 m for 60 seconds outage RTK |
| Roll and Pitch | 0.005° | 0.005° | 0.005° |
| True Heading | 0.025° | 0.025° | Drift <0.1° per hour (negligible for outages <60 seconds) |
| Heave | 3.5 cm or 3.5% 2 | 3.5 cm or 3.5% 2 | 3.5 cm or 3.5% 2 |
1 One Sigma, depending on quality of differential corrections
2 Whichever is greater, for periods of 20 seconds or less
Further details can be found in the manufacturer's specification sheet.
WETLabs C-Star transmissometer
This instrument is designed to measure beam transmittance by submersion or with an optional flow tube for pumped applications. It can be used in profiles, moorings or as part of an underway system.
Two models are available, a 25 cm pathlength, which can be built in aluminum or co-polymer, and a 10 cm pathlength with a plastic housing. Both have an analog output, but a digital model is also available.
This instrument has been updated to provide a high resolution RS232 data output, while maintaining the same design and characteristics.
Specifications
| Pathlength | 10 or 25 cm |
| Wavelength | 370, 470, 530 or 660 nm |
| Bandwidth | ~ 20 nm for wavelengths of 470, 530 and 660 nm ~ 10 to 12 nm for a wavelength of 370 nm |
| Temperature error | 0.02 % full scale °C-1 |
| Temperature range | 0 to 30°C |
| Rated depth | 600 m (plastic housing) 6000 m (aluminum housing) |
Further details are available in the manufacturer's specification sheet or user guide.
DIMES James Cook Cruise JC041 Underway Surface Hydrography Instrumentation
The surface hydrography suite of sensors forms part of the NMFD surfmet system and consists of a flow through system with a pumped pickup at 5.5 m depth. Thermosalinograph (TSG) flow is approximately 18 litres per minute whilst fluorometer and transmissometer flow is approximately 1.5 litres per minute. Flow to instruments is degassed using a debubbler with 24 litres per minute.
Details of these sensors are shown in the table below:
| Sensor | Serial number | Last calibration date |
| Falmouth Scientific Instruments Ocean Temperature Module (FSI OTM) remote sea surface and housing temperature sensor | - | - |
| Falmouth Scientific Instruments Ocean Temperature Module (FSI OCM) conductivity sensor | - | - |
| Sea-Bird MicroTSG SBE 45. For remote sea surface temperature, housing temperature, conductivity and salinity | 0230 | 25/02/2009 |
| Wetlabs WET-Star fluorometer | WS35-134 | 07/04/2009 |
| Wet Labs C-Star Transmissometer (25 cm path length) | CST-1132PR | 14/07/2008 |
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
| Conductivity | Temperature | Salinity | |
|---|---|---|---|
| Range | 0 to 7 Sm-1 | -5 to 35°C | |
| Initial accuracy | 0.0003 Sm-1 | 0.002°C | 0.005 (typical) |
| Resolution | 0.00001 Sm-1 | 0.0001°C | 0.0002 (typical) |
| Typical stability (per month) | 0.0003 Sm-1 | 0.0002°C | 0.003 (typical) |
Further details can be found in the manufacturer's specification sheet.
DIMES James Cook Cruise JC041 Underway Surface Hydrography Processing
Originator's Data Processing
Data from the sea surface hydrography suite of sensors were logged daily by the onboard logging system (TECHSAS). The data storage method used was NetCDF and pseudo-NMEA (ASCII). The NetCDF data files were manually parsed through an application in order to convert them to RVS format for data processing. Data were transferred from the TECHSAS system to the user Unix area and reformatted into Mstar format NetCDF using NOC-generated Mstar processing scripts on a daily basis. Transfer and formatting was achieved via Matlab with some of the data remaining in matlab format. Further details of the originator's data processing is detailed in the cruise report. The following files were submitted to BODC:
Data streams
| Sea surface hydrography data source | Format | Start of recording | End of recording | Frequency | Content |
| TSG | matlab format | 06/12/2009 14:17:30 | 20/12/2009 03:41:30 | 60 second bins | Date, temperature, conductivity, salinity and soundspeed |
| Surfmet (as above) | ASCII | 04/12/2009 21:54:35 | 20/12/2009 13:38:48 | 1 second | Fluorometer, transmissometer, TIR, PAR, humidity, air pressure, water temperature, conductivity, wind direction and wind speed |
BODC's Data Processing
Thermosalinograph measurements (TSG) were made by Falmouth Scientific Instruments OTM and OCM as well as a SBE45 Micro TSG. Only the SBE45 Micro TSG data were supplied from the originator as it was proven previously to have better reliability than the FSI sensors. All matlab formatted channels, which were 1 minute averaged bins, were reformatted to the internal QXF format (1 min data cycle intervals) via the nearest neighbour method. The ASCII formatted channels of 1 second cycles were also reformatted to the internal QXF format via the nearest neighbour method. The year, month, day, hour, minute were combined in matlab into one 'time' channel which the 1 min data cycle intervals were based on.
The salinity data and calibration as contained in the cruise report are different from that provided to BODC. The cruise report details that salinity was calculated from the conductivity and the remote temperature using the subroutine sw_salt (from the free CSIRO sea_water package) and then calibrated against 21 data points from salinity bottle samples, taken from the thermosalinograph (TSG) every 4-6 hours. The salinity data provided by BODC appears to have been calculated using conductivity and the housing temperature with no calibration applied. Therefore salinity was re-derived by BODC using conductivity housing temperature using the routine sw_salt based upon UNSECO (1983).
The following tables show how the variables within the files were mapped to appropriate BODC parameter codes:
TSG matlab file
| Originator's variable | Units | Description | BODC parameter code | Units | Comments |
| year | - | - | - | - | - |
| month | - | - | - | - | - |
| Day | - | - | - | - | - |
| Hour | - | - | - | - | - |
| minute | - | - | - | - | - |
| temp_h | Degrees Celsius | Water temperature (housing) | TMESSG01 | Degrees Celsius | - |
| temp_r | Degrees Celsius | Water temperature (remote) | TEMPHU01 | Degrees Celsius | - |
| cond | Conductivity | S/m | CNDCSG01 | S/m | - |
| salin | Salinity | PSU | - | Dimensionless | Not transferred, re-derived by BODC |
| sndspeed | Sound speed | m/s | - | - | Not transferred- derived variable from temperature and salinity channels |
| julian_day | - | - | - | - | - |
surfmet ASCII file
| Originator's variable | Units | Description | BODC parameter code | Units | Comments |
| time | Seconds | Time taken as the middle of the time averaged bin | - | - | Used as the time variable |
| temp_h | Degrees Celsius | Water temperature (housing) | - | - | Not transferred- loaded from TSG file |
| temp_r | Degrees Celsius | Water temperature (remote) | - | - | Not transferred- loaded from TSG file |
| cond | S/m | Conductivity | - | - | Not transferred- loaded from TSG file |
| fluo | Volts | Raw fluorometer output | FVLTWS01 | Volts | - |
| trans | Volts | Raw transmissometer output | TVLTDR01 | Volts | - |
Calibrations
The TSG SBE45 contains its own calibration coefficients and has outputted calibrated temperature and conductivity. The BODC derived salinity (PSALSU01) was calibrated against the bottle salinity data collected from the TSG. A total of 21 bottle salinity samples were provided by the originator, but only 18 bottle samples were used in the calibration as 4 samples did not have a corresponding underway date and time. The offset between the bottle salinity and the underway salinity was examined to identify any trends, outliers or steps in the data, with time or bottle salinity. No outliers were identified and regression analysis revealed there to be no trend in the relationship between the salinity offset and bottle salinity (p = 0.235, r2(adjusted) = 3.0%). A mean offset calibration equation was therefore used; calibrated underway salinity (PSALSG01) = raw underway salinity + 0.027977778.
The manufacturer's calibration was applied to the raw fluorometer output to calibrate the raw volts to concentration of chlorophyll-a per (milligrams per cubic metre) using the Wetlabs WET-Star fluorometer calibration sheet. The following equation was used: mg/m3= 14.7 * (output volts - 0.064).
The transmissometer was calibrated using the manufacturers calibration from volts to, light transmission (%) and beam attenuation (per metre). The equation below, taken from Sea-Bird electronics was calculated using values taken from the calibration sheet only. No field measurements were available to be used for the calibration.
M=(Tw/(W0-Y0))*((A0-Y0)/(A1-Y1)); B=-M*Y1 where;
A0 = Vair = manufacturer voltage output in air (4.806)
A1 = most recent voltage output in air (not known, 4.806 used)
Y0 = manufacturer dark or zero voltage (0.062)
Y1 = most recent dark or zero voltage (not known, 0.062 used)
W0 = manufacturer voltage output in pure water (4.698)
Tw = % transmission in pure water relative to water (100%)
Light transmittance (%) = M * output volts + B Beam attenuation (per metre) = -1/path length * ln (light transmittance).
All reformatted and calibrated data were visualised using the in-house Edserplo software. Suspect and missing data were marked by adding an appropriate quality control flag.
References
Unesco 1983. Algorithms for computation of fundamental properties of seawater, 1983. Unesco Technical Paper in Marine Science, No.44, pp.53.
Project Information
Diapycnal and Isopycnal Mixing Experiment in the Southern Ocean (DIMES) project document
DIMES is a US/UK field program aimed at measuring diapycnal and isopycnal mixing in the Southern Ocean, along the tilting isopycnals of the Antarctic Circumpolar Current.
The Meridional Overturning Circulation (MOC) of the ocean is a critical regulator of the Earth's climate processes. Climate models are highly sensitive to the representation of mixing processes in the southern limb of the MOC, within the Southern Ocean, although the lack of extensive in situ observations of Southern Ocean mixing processes has made evaluation of mixing somewhat difficult. Theories and models of the Southern Ocean circulation have been built on the premise of adiabatic flow in the ocean interior, with diabatic processes confined to the upper-ocean mixed layer. Interior diapycnal mixing has often been assumed to be small, but a few recent studies have suggested that diapycnal mixing might be large in some locations, particularly over rough bathymetry. Depending on its extent, this interior diapycnal mixing could significantly affect the overall energetics and property balances for the Southern Ocean and in turn for the global ocean. The goals of DIMES are to obtain measurements that will help us quantify both along-isopycnal eddy-driven mixing and cross-isopycnal interior mixing.
DIMES includes tracer release, isopycnal following RAFOS floats, microstructure measurements, shearmeter floats, EM-APEX floats, a mooring array in Drake Passage, hydrographic observations, inverse modeling, and analysis of altimetry and numerical model output.
DIMES is sponsored by the National Science Foundation (U.S.), Natural Environment Research Council (U.K) and British Antarctic Survey (U.K.)
For more information please see the official project website at DIMES
Data Activity or Cruise Information
Cruise
| Cruise Name | JC041 (UKD-1) |
| Departure Date | 2009-12-05 |
| Arrival Date | 2009-12-21 |
| Principal Scientist(s) | Alberto C Naveira Garabato (University of Southampton School of Ocean and Earth Science) |
| Ship | RRS James Cook |
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:
| Flag | Description |
|---|---|
| Blank | Unqualified |
| < | Below detection limit |
| > | In excess of quoted value |
| A | Taxonomic flag for affinis (aff.) |
| B | Beginning of CTD Down/Up Cast |
| C | Taxonomic flag for confer (cf.) |
| D | Thermometric depth |
| E | End of CTD Down/Up Cast |
| G | Non-taxonomic biological characteristic uncertainty |
| H | Extrapolated value |
| I | Taxonomic flag for single species (sp.) |
| K | Improbable value - unknown quality control source |
| L | Improbable value - originator's quality control |
| M | Improbable value - BODC quality control |
| N | Null value |
| O | Improbable value - user quality control |
| P | Trace/calm |
| Q | Indeterminate |
| R | Replacement value |
| S | Estimated value |
| T | Interpolated value |
| U | Uncalibrated |
| W | Control value |
| X | Excessive difference |
SeaDataNet Quality Control Flags
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
| Flag | Description |
|---|---|
| 0 | no quality control |
| 1 | good value |
| 2 | probably good value |
| 3 | probably bad value |
| 4 | bad value |
| 5 | changed value |
| 6 | value below detection |
| 7 | value in excess |
| 8 | interpolated value |
| 9 | missing value |
| A | value phenomenon uncertain |
| B | nominal value |
| Q | value below limit of quantification |
