Metadata Report for BODC Series Reference Number 1043415
No Problem Report Found in the Database
Data Quality Report
There is a large time interval in all data channels between 19/8/2007 07:05:19 and 17:14:20. This was due to an interruption in logging (see cruise report p211).
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."
Chelsea Technologies Group FASTtracka MKI FRRF
The FASTtracka is a Fast Repetition Rate Fluorometer (FRRF) designed to measure the variable fluorescence of marine phytoplankton. It can be deployed on its own or integrated in moorings, profiling systems or in towed applications.
The operation mode comprises a rapid series of high frequency flashes (200 kHz), which enable the measurement of the absorption cross section of photosystem II (PSII), the rate of electron transport and the level of photochemical quenching. A 16 MHz clock microcontroller monitors the digital acquisition of the stimulated fluorescence and the excitation flashes, while simultaneously measuring Photosynthetic Active Radiation (PAR). These concurrent measurements allow for estimates of phytoplankton primary productivity to be made.
A comparison of ambient-irradiated and dark adapted phytoplankton samples is possible due to the optical head dual (light and dark) chamber design. All measurements are stored on an internal memory card with a 24 MB capacity and are downloaded through an RS232 connector.
Additional specifications include a maximum depth rating of 500 m and a chlorophyll-a sensitivity of 0.1 to 30 µg l-1.
The Chelsea Technologies Group (CTG) FASTtracka TM I Fast Repetition Rate Fluorometer (FRRf) was connected to the ship's non-toxic supply within the bottle annex. Non-toxic seawater was pumped from a pick-up depth of approx. 5 m. The sensor was operated in flow-through mode. The manufacturer's calibration values for this instrument (Serial no. 05 5335 001) was 532.70 x 1010 quanta m-2 count-1 (30 Oct 2006).
Originator's Data Processing
The Fast Repetition Rate Fluorometer (FRRf) was run between the 27/07/2007 12:36:06 to the 22/08/2007 19:30:00. The data were stored internally on the instrument and downloaded at between 1-3 day intervals.
Data Acquisition and Processing
Variable fluorescence was measured and processed in a similar manner to that described by Moore et al. (2005). Saturation of the variable chlorophyll fluorescence was performed using 100 flashlets of 1.1 µs duration with a 2.3 µs repetition rate. Subsequent relaxation of fluorescence was monitored using flashlets provided at 9.8 µs spacing, giving a total relaxation protocol length of around 2 ms. Data were not blank-corrected.
Table 1. Chelsea FASTtracka TM I gain settings
|Originator's ID||Start date/time||End date/time||Gain|
|UW1||27/07/2007 12:27||28/07/2007 11:57||4|
|UW2||28/07/2007 12:28||30/07/2007 15:54||4|
|UW3||30/07/2007 16:42||31/07/2007 15:13||4|
|UW4||31/07/2007 13:52||02/08/2007 14:34||4|
|UW5||02/08/2007 14:49||04/08/2007 14:29||4|
|UW6||04/08/2007 14:45||07/08/2007 14:59||4|
|UW7||07/08/2007 15:22||09/08/2007 12:02||4|
|UW8||09/08/2007 12:21||10/08/2007 06:30||4|
|UW9||10/08/2007 06:38||10/08/2007 17:27||1|
|UW10||10/08/2007 17:43||11/08/2007 17:05||4|
|UW11||11/08/2007 17:14||12/08/2007 16:36||4|
|UW12||12/08/2007 16:37||13/08/2007 14:20||4|
|UW13||13/08/2007 14:35||14/08/2007 17:15||4|
|UW14||14/08/2007 17:24||15/08/2007 16:42||4|
|UW15||15/08/2007 16:47||16/08/2007 19:20||4|
|UW16||16/08/2007 19:43||17/08/2007 16:13||4|
|UW17||17/08/2007 16:21||18/08/2007 15:59||4|
|UW18||18/08/2007 16:07||19/08/2007 07:07||4|
|UW19||19/08/2007 16:58||20/08/2007 17:15||4|
|UW20||20/08/2007 17:21||21/08/2007 14:48||4|
|UW21||21/08/2007 14:55||22/08/2007 19:30||4|
Moore, C.M., Lucas, M.I., Sanders, S., and Davidson, R., 2005. Basin-scale variability of phytoplankton bio-optical characteristics in relation to bloom state and community structure in the Northeast Atlantic. Deep-Sea Research I 52:401-419
Processing at BODC
The data arrived at BODC in one Microsoft Excel file representing all of the processed measurements collected during cruises D321 and D321B (raw binary files were also received and are available on request). The Excel file was reformatted to two internal NetCDF format files (one for each cruise) using BODC generated code. The following table shows how the variables within the Excel file were mapped to appropriate BODC parameter codes:
|Originator's variable||Units||Description||BODC code||Units||Comments|
|Jday||day fractions||Julian day from the beginning of the year (0/0/2007 00:00:00)||-||-||Converted to BODC format|
|Long||decimal degrees||Longitude East||ALONGP01||decimal degrees|
|Lat||decimal degrees||Latitude North||ALATGP01||decimal degrees|
|Fo||arbitrary units||Minimal Fuorescence yields measured in the dark||FOMINI01||not specified|
|Fm||arbitrary units||Maximal Fuorescence yields measured in the dark||FMMAXI01||not specified|
|Fv/Fm||ratio||Maximum photochemical quantum efficiency in the dark||FVFMMI01||dimensionless|
|Sigma||x10-20 m-2*||Functional absorption cross-section of PSII in the dark||SIGPSII1||Angstroms squared quanta-1||x10-20 m-2 = 1 Angstrom squared|
*units were confirmed with originator as per quanta
The reformatted data were visualised using the in-house EDSERPLO software. Suspect data were marked by adding an appropriate quality control flag, missing data by both setting the data to an appropriate value and setting the quality control flag.
Oceans 2025 Theme 10
Oceans 2025 is a strategic marine science programme, bringing marine researchers together to increase people's knowledge of the marine environment so that they are better able to protect it for future generations.
Theme 10: Integration of Sustained Observations in the Marine Environment spans all marine domains from the sea-shore to the global ocean, providing data and knowledge on a wide range of ecosystem properties and processes (from ocean circulation to biodiversity) that are critical to understanding Earth system behaviour and identifying change. They have been developed not merely to provide long-term data sets, but to capture extreme or episodic events, and play a key role in the initialisation and validation of models. Many of these SOs will be integrated into the newly developing UK Marine Monitoring Strategy - evolving from the Defra reports Safeguarding our Seas (2002) and Charting Progress (2005), thus contributing to the underpinning knowledge for national marine stewardship. They will also contribute to the UK GOOS Strategic Plan (IACMST, 2006) and the Global Marine Assessment.
Oceans 2025 Theme 10, Sustained Observation Activity 4: The Extended Ellett Line
The Ellett Line (begun in 1975 and since 1996 the Extended Ellett Line from Scotland to Iceland) crosses important north Atlantic Meridional Overturning Circulation (MOC) components and thus provides an additional contribution to understanding the north Atlantic response to climate change. Sustained Observation Activity (SO) 4 will repeat this section annually collecting a wide variety of physical and biogeochemical measurements, and will, to enhance the time variable component, make use of Argo floats and gliders. SO 4 will be implemented by physical, biological and chemical scientists at the National Oceanography Centre, Southampton (NOCS) and the Scottish Association for Marine Science (SAMS).
SO 4 formally contributes to the Department for Environment, Food and Rural Affairs (DEFRA)-funded Marine Environmental Change Network (MECN). Established in 2002 to coordinate and promote the collection and utilisation of marine time-series and long-term data sets, the goal of the network is to use long-term marine environmental data from around the British Isles and Ireland to separate natural fluctuations from global, regional and local anthropogenic impacts.
The specific deliverables for SO 4 are:
- A time series of the evolution of the hydrography of the northeast Atlantic, together with a more formal understanding of the causes of any changes observed
- An archived data set available to the international community via the British Oceanographic Data Centre (BODC)
- A platform for further scientific research
More detailed information on this Work Package is available at pages 15 - 16 of the official Oceans 2025 Theme 10 document: Oceans 2025 Theme 10
Oceans 2025 - The NERC Marine Centres' Strategic Research Programme 2007-2012
Who funds the programme?
The Natural Environment Research Council (NERC) funds the Oceans 2025 programme, which was originally planned in the context of NERC's 2002-2007 strategy and later realigned to NERC's subsequent strategy (Next Generation Science for Planet Earth; NERC 2007).
Who is involved in the programme?
The Oceans 2025 programme was designed by and is to be implemented through seven leading UK marine centres. The marine centres work together in coordination and are also supported by cooperation and input from government bodies, universities and other partners. The seven marine centres are:
- National Oceanography Centre, Southampton (NOCS)
- Plymouth Marine Laboratory (PML)
- Marine Biological Association (MBA)
- Sir Alister Hardy Foundation for Marine Science (SAHFOS)
- Proudman Oceanographic Laboratory (POL)
- Scottish Association for Marine Science (SAMS)
- Sea Mammal Research Unit (SMRU)
Oceans2025 provides funding to three national marine facilities, which provide services to the wider UK marine community, in addition to the Oceans 2025 community. These facilities are:
- British Oceanographic Data Centre (BODC), hosted at POL
- Permanent Service for Mean Sea Level (PSMSL), hosted at POL
- Culture Collection of Algae and Protozoa (CCAP), hosted at SAMS
The NERC-run Strategic Ocean Funding Initiative (SOFI) provides additional support to the programme by funding additional research projects and studentships that closely complement the Oceans 2025 programme, primarily through universities.
What is the programme about?
Oceans 2025 sets out to address some key challenges that face the UK as a result of a changing marine environment. The research funded through the programme sets out to increase understanding of the size, nature and impacts of these changes, with the aim to:
- improve knowledge of how the seas behave, not just now but in the future;
- help assess what that might mean for the Earth system and for society;
- assist in developing sustainable solutions for the management of marine resources for future generations;
- enhance the research capabilities and facilities available for UK marine science.
In order to address these aims there are nine science themes supported by the Oceans 2025 programme:
- Climate, circulation and sea level (Theme 1)
- Marine biogeochemical cycles (Theme 2)
- Shelf and coastal processes (Theme 3)
- Biodiversity and ecosystem functioning (Theme 4)
- Continental margins and deep ocean (Theme 5)
- Sustainable marine resources (Theme 6)
- Technology development (Theme 8)
- Next generation ocean prediction (Theme 9)
- Integration of sustained observations in the marine environment (Theme 10)
In the original programme proposal there was a theme on health and human impacts (Theme 7). The elements of this Theme have subsequently been included in Themes 3 and 9.
When is the programme active?
The programme started in April 2007 with funding for 5 years.
Brief summary of the programme fieldwork/data
Programme fieldwork and data collection are to be achieved through:
- physical, biological and chemical parameters sampling throughout the North and South Atlantic during collaborative research cruises aboard NERC's research vessels RRS Discovery, RRS James Cook and RRS James Clark Ross;
- the Continuous Plankton Recorder being deployed by SAHFOS in the North Atlantic and North Pacific on 'ships of opportunity';
- physical parameters measured and relayed in near real-time by fixed moorings and ARGO floats;
- coastal and shelf sea observatory data (Liverpool Bay Coastal Observatory (LBCO) and Western Channel Observatory (WCO)) using the RV Prince Madog and RV Quest.
The data is to be fed into models for validation and future projections. Greater detail can be found in the Theme documents.
|Cruise Name||D321 (D321A)|
|Principal Scientist(s)||John T Allen (National Oceanography Centre, Southampton)|
Complete Cruise Metadata Report is available here
No Fixed Station Information held for the Series
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
|<||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.)|
|E||End of CTD Down/Up Cast|
|G||Non-taxonomic biological characteristic uncertainty|
|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|
|O||Improbable value - user quality control|
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
|0||no quality control|
|2||probably good value|
|3||probably bad value|
|6||value below detection|
|7||value in excess|
|A||value phenomenon uncertain|
|Q||value below limit of quantification|