FOCI STANDARD
OPERATING INSTRUCTIONS FOR NOAA SHIP RONALD H. BROWN
Date Last Modified: December
11, 2000
(Adapted from FOCI Standard Operating
Instructions for NOAA Ship Miller Freeman)
PARTICIPATING
ORGANIZATIONS:
NOAA - Alaska Fisheries
Science Center (AFSC)
NOAA - Pacific Marine
Environmental Laboratory (PMEL)
University of Alaska
Fairbanks (UAF)
University of
Washington (UW)
Southampton Oceanography
Centre
PROGRAM DESCRIPTION
Fisheries-Oceanography Coordinated
Investigations (FOCI) is an
effort by NOAA and academic scientists.
At present, FOCI consists of a Shelikof Strait (western Gulf of Alaska)
walleye pollock project, and a NOAA Coastal Ocean Program project: Southeast
Bering Sea Carrying Capacity. FOCI
also supports associated projects, such as the Arctic Research Initiative, U.S.
GLOBEC and North Pacific Marine Research Program, that address scientific
issues related to FOCI's. FOCI's
goal is to understand the effects of abiotic and biotic variability on
ecosystems of the North Pacific Ocean and Bering Sea in order to discern the
physical and biological processes that determine recruitment variability of
commercially valuable finfish and shellfish stocks in Alaskan waters.
1.0 PERSONNEL
1.1 & 1.2 CHIEF
SCIENTIST AND PARTICIPATING SCIENTISTS:
See specific FOCI Cruise
Instructions for Chief Scientist and scientific personnel.
The Chief Scientist has
the authority to revise or alter the technical portion of the instructions as
work progresses provided that, after consultation with the Commanding Officer,
it is ascertained that the proposed changes will not: (1) jeopardize the safety
of personnel or the ship; (2) exceed the overall time allotted for the project;
(3) result in undue additional expenses or (4) alter the general intent of
these project instructions.
1.3 NOAA MARINE
OPERATIONS CENTER-PACIFIC CONTACT:
CDR Jon Rix, Chief
Chief, Operations Division
Marine Operations Center-Atlantic
439 W York St
Norfolk VA 23510
Phone: (757)
441-6842
Fax: (757)
441-6495
E-mail: Jon.E.Rix@noaa.gov
LCDR Jim Meigs
Marine Operations Center-Atlantic
439 W York St
Norfolk VA 23510
Phone: (757)
441-6844
Fax: (757)
441-6495
E-mail: Jim.Meigs@noaa.gov
1.4 FOCI FIELD
OPERATIONS LEADERS:
Dr. Phyllis Stabeno
PMEL
7600 Sand Point Way NE
Seattle, WA 98115-6349
Phone: (206) 526-6453
Fax: (206)
526-6485
E-mail: Phyllis.Stabeno@ noaa.gov
Dr. Jeff Napp
AFSC
7600 Sand Point Way NE
Seattle, WA 98115-6349
Phone: (206) 526-4148
Fax: (206)
526-6723
E-mail: Jeff.Napp@ noaa.gov
2.0 OPERATIONS
Scheduling of individual
activities will depend upon weather conditions and progress of scientific
work. Therefore, firm advance
scheduling of events will not be possible, and a continual dialogue between
scientific and ship's personnel will be important. To insure fulfillment of all scientific objectives, the ship
is asked to steam at maximum cruising speed whenever time in transit or between
stations is greater than one hour.
2.1 SUMMARY OF
ACTIVITIES:
A summary of activities
for each FOCI cruise is provided in the FOCI Cruise Instructions.
2.2 PROCEDURES FOR
OPERATIONS:
The following is a
comprehensive list of FOCI operations including gear and procedures for
collecting data. A listing of
specific operations to be conducted on each cruise is listed in the FOCI Cruise
Instructions. Changes or
alterations to these standard procedures will be noted in the Cruise
Instructions.
2.2.1 CTD / Water
Sample Operation
A Sea-Bird 9Plus CTD
with dual thermistor and conductivity cells will be the primary system. The primary system will be provided and
maintained by PMEL. A backup
Sea-Bird 9Plus CTD is required and shall be maintained by the vessel. When available, and where possible, the
FOCI fluorometer, light meter, and chlorophyll absorbance meter (ChlAM) should
be mounted on the CTD stand for all casts. However, the ChlAM cannot exceed 300 m, the fluorometer
cannot exceed 500 m, and the light meter cannot exceed 1000 m. On
selected casts, biological samples will be collected. Water for microzooplankton samples will be collected using
10-l Niskin bottles. When only
nutrient or chlorophyll water samples are required, smaller Niskin bottles may
be used.
Once the CTD has been
deployed, it should be lowered to 10 m, and then the deck unit should be
turned on. If a ChlAM is attached,
the CTD should remain at 10 m for three minutes; otherwise after
45 seconds the CTD can be returned to just below the surface. Then the data acquisition program and
VHS cassette CTD tape backup system should be started. The CTD should descend at a rate of
30 m/min for the first 200 m and 45 m/min below that. The ascent rate should be
50 m/min. One exception to the descent rates occurs on the Bering Shelf in
water less than 150 m deep.
In this case, the CTD should descend at 10 m/min during the entire
cast. An entry in the MOA should
be made for each CTD cast at the maximum cast depth.
CTD data will be
acquired using SEASOFT software on the ship's computer. The capability to
display CTD data using the SCS system and monitors will be available. Survey technicians and scientists will
keep the "CTD Cast Information/Rosette Log". Pressure, primary salinity,
primary temperature, secondary temperature, fluorescence, ChlAM chlorophyll
concentration and light levels will be recorded on the "CTD Cast
Information/Rosette Log" for all water bottle samples.
CTD Calibration:
Salinity samples will be taken on every cast (or as specified by the Chief
Scientist). No reversing
thermometers will be required. The CTD systems will be equipped with dual thermistors. A survey technician will run AutoSal
analysis during the cruise and record the readings on an AutoSal log.
2.2.2 MARMAP Bongo
Tow
A 60-cm bongo net with
0.505-mm nets (or 0.333-mm before mid May), hard plastic codends,
and a 40-kg lead weight for a depressor will be used in standard MARMAP
tows. The nets will be deployed at
a constant wire speed of 40 m/min to a maximum depth of 100 m (or
200 m before mid May) or 10 m off bottom in shallower waters. However, at stations on Lines 8, 16 and
17 in Shelikof Strait, nets will be towed from 10 m off bottom to the
surface. In addition, one side of
the 60-cm bongo will be changed to 0.333-mm mesh. Furthermore the 20-cm bongo with
0.150-mm mesh nets will be attached to the wire 1 m above the 60-cm
bongo frame at Line 8, and at selected other stations. A CTD (SeaCat) or electronic BKG will
be attached to the wire to provide real-time tow data. The scientists will monitor the depth
of the nets, and issue commands to stop the winch. The winch will be stopped and the nets allowed to stabilize
for up to 30 sec. The nets are
then retrieved at a wire speed of 20 m/min. The ship speed is adjusted to maintain a wire angle of 45
degrees during the entire tow.
When the nets reach the surface they are brought aboard and hosed to
wash the sample into the codend.
The sample is preserved appropriately. In some cases, larvae are sorted and preserved separately. Flow meters in the nets record the
amount of water filtered and an electronic CTD or bathykymograph records the
depth history of the tow. The
Scientists on watch are responsible for recording times and maximum depth
obtained in the SeaCat logbook.
Tows not meeting specifications may be repeated at the discretion of the
scientific watch.
The PMEL SeaCat data will
be acquired on the ship's computer using SEASOFT software. The option to display SeaCat data using
the SCS system and monitors will be available.
2.2.3 Bongo Larval
Condition Tow
A live tow for larval
pollock uses the 60-cm bongo with 0.333-mm or 0.505-mm net
mesh with taped codends. The
selection of the mesh size will depend on the time of field collections, larval
size, amount of algae, etc. This
is a vertical tow with the ship's speed used only to maintain a zero wire
angle. The SeaCat is on the
wire and data is saved for each haul.
The bongo is lowered at 25-30 m/min to a gear depth of
70 meters. The wire-in speed
should be 10 m/min. Begin
timing the tow when the net starts up.
Do not rinse down the nets when they return to the deck, but do open the
codends immediately into clean (live) 5-gallon buckets. The samples are carefully transferred
into a bowl over ice and are sorted quickly for live larvae. Preserve larvae immediately, as
specified in FOCI field manual or sample collection request forms. Rinse the net between tows.
2.2.4 Live
Zooplankton Ring Net Tow
Tows to collect
experimental animals for secondary productivity experiments will be taken
during large-scale surveys and patch studies. These collections use a special net that minimizes damage to
the organisms. The net will be
deployed using the same CTD winch used for bongo tows. The ship will be asked to keep station
for this vertical tow. A 0.8-m
ring net with a large polycarbonate codend and the SeaCat will be "book
clamped" to the wire. The net
will be lowered at a rate of 20 m/min to near the bottom, and then
retrieved at a rate of 10-20 m/min.
2.2.5 MOCNESS Tow
Deck Machinery -- The
Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) is deployed
whenever possible using the Traction winch and the A-frame. The instrument will require
600-1500 m of single conductor wire. In addition, a set of slip rings is
requested for the winch. The
manufacturer states that the maximum drag observed on a 1-m2
MOCNESS system was 3,000 pounds.
If we include a 2-3X safety factor, the conducting cable should have a
minimum breaking strength of 6,000-9,000 pounds.
Electronics -- The
MOCNESS telemeters, in real time, conductivity, temperature, depth, and flow
meter data to the surface. FOCI
owns two, separate electronic systems for the MOCNESS frame. The older system consists of two
6" OD pressure cases that sit in separate cradles on the net frame and
telemeter data to the ship at 1 frame every four seconds. The signal is received on a MOCNESS PC
computer by a data acquisition deck box and simultaneously routed to an old 286
Compaq luggable computer and a VCR for analog signal backup. A dot matrix printer is used to print
data from every other scan. Serial
input (RS-232) from the ship's scientific GPS unit is required to obtain
continuous position data for the data stream. The data acquisition system (DAS) software requires a single
NMEA-0183 string ($GPGGA) for input to COM2. All acquisition programs are written in TurboPascal 5.0 and
exist as both source code and compiled executable code. All DAS hardware components sit in the
electronics rack.
The newer system
consists of two 4" OD pressure cases that sit in the same cradle on the
MOCNESS frame and telemeter data to the ship as fast as 1 frame per
second. The signal is received by
a serial modem and is routed to a PC Pentium computer under the bench on the
starboard bulkhead. The analog
signal is not recorded. The
MOCNESS acquisition station shares a monitor with the CTD/SeaCat data
acquisition system. Serial input
of GPS data is required as for the older system. The data acquisition software is written in Visual Basic
running under Windows 3.1, and we only have the compiled executable file.
Launch, Fishing, &
Recovery -- The movable MOCNESS support frame will be used. The MOCNESS is launched and recovered
from the stern. For safe,
efficient launch and recovery of the MOCNESS, the survey technician is asked to
lead those procedures, giving orders to the trawl house while the scientific
watch handles the tag lines. When
the weather is rough, a member of the deck dept may be requested to assist in
the deployment and recovery.
The MOCNESS pilot will
relay instructions to the winch operator and the bridge to control the
descent/ascent of the net system.
It is essential that the ship maintain a constant speed through the
water during the tow. Wire-in/out
rates must be available to the winch operator and should be available to the
MOCNESS pilot as well. The MOCNESS
is deployed and recovered while under way (1.5 knots). Wire is paid out at a rate of
5-25 m/min and is retrieved at 5-20 m/min under the direction of the
pilot. The MOCNESS pilot will
inform the bridge as each net is closed and request that the bridge record the
position in the MOA. After
recovery, the MOCNESS nets are washed down on the aft deck.
2.2.6 CalCOFI
Vertical Egg Tow (CalVET)
Vertical tows to collect
microzooplankton and free-floating copepod eggs will be conducted, sometimes in
conjunction with CTD/bottle casts.
When done in conjunction with a CTD cast, the CTD will be stopped at
15 m during its descent, and the net frame's top and bottom will be
attached to the wire so that the net flushes during its descent while the ship
stands hove to. After descent to
desired depth (usually 60 m), the net will then be retrieved at a rate of
60 m/min. The samples will be
washed into the codends, and then preserved in 32-oz jars with formalin
for later analysis. Once the net
frame has been removed from the wire, then the CTD/bottle cast can begin. The CalVET net can also be deployed
from the starboard quarterdeck.
When done without the CTD, the SeaCat should be attached below the net.
2.2.7 Chlorophyll
Sample
Chlorophyll samples will
be taken from the 10-l Niskin bottles.
Sampling depths depend on the fluorescence or ChlAM profile. A typical strategy would be samples at
0, 10, 20, 30, 40, and 50 or 60 m, depending upon which is closest to the
fluorescence or chlorophyll maximum.
If the maximum is deeper than 60 m, sampling should be moved deeper
with fewer samples in the mixed layer.
When microzooplankton
samples are to be collected from the same Niskin bottle, 500 ml of water
is first removed from the water bottle using a graduated cylinder. Chlorophyll and nutrient samples are
obtained from the 500 ml in the graduated cylinder. See the FOCI Field manual for sampling
collection, filtration and preserving details. Chlorophyll and nutrient samples will be stored in
conventional freezers.
2.2.8 Satellite-Tracked Drifter Buoy
Two to three working
days before deployment, the Chief Scientist or designated person will secure
the drifter on the back deck, turn it on (usually by removing the magnet), and
send an e-mail message to Dr. Phyllis Stabeno (stabeno@ pmel.noaa.gov) stating
the serial number that is stamped on the drifter and the time that it was
turned on. The method of
deployment of the drifter is dependent upon the particular make of drifter and
is to be directed by the Chief Scientist or designated person.
2.2.9 ADCP Operation
ADCP Observations: The
purpose of the Vessel-Mounted Acoustic Doppler Current Profiler (VM-ADCP) is to
measure the ocean current velocity continuously over the upper 300 m of
the water column, usually in 8-m depth increments. Current velocities relative to the
earth at this spatial and temporal resolution cannot be measured by CTD
sections, current meter moorings, or drifting buoys. ADCP data is also used to estimate the abundance and
distribution of biological scatterers over the same depth range and in the same
depth increments.
ADCP Data Collection:
ADCP measurement requires four instruments working in concert: the ADCP, the
ship's gyrocompass, a GPS receiver, and a GPS Attitude Determination Unit (ADU),
such as the Seapath 200. The ADCP
is connected to a dedicated PC and controlled by RD Instruments' Data
Acquisition System (DAS) software.
Version 2.48 of DAS software will be used as the controlling
software. The DAS software shall
be configured to use the user-exit programs AGCAVE.COM and UE4.EXE. Separate written instructions detailing
the ADCP setup and configuration files are kept in the ADCP notebook in the
Computer lab.
The ADCP PC is
interfaced to the ship's gyrocompass, to the primary scientific GPS receiver,
and to the GPS Attitude Determination Unit. The navigation GPS shall be configured to send only
NMEA-0183 messages $GPGGA and $GPVTG at the maximum fix update rate for the
receiver (usually a 1- or 2-second rate), and with the maximum number
of digits of precision (optimally 4).
The Attitude Determination Unit shall be configured to send the $PASHR
message at least once, preferably twice per second, and the NMEA-0183 message
$GPGGA once each second. The
user-exit program UE4.EXE shall be configured to control acquisition and
processing of GPS and ADU messages, and to synchronize the PC clock with the
time reported by the primary GPS.
The ADCP PC logs data
from the profiler to Iomega Zip disks and optionally sends a complete data
structure to SCS for logging on that system. This redundancy in data logging is desirable for post-cruise
processing flexibility. The
user-exit program UE4.EXE should be configured to send an "RDI-style"
ensemble to SCS.
PMEL supplies the Iomega
Zip drives for FOCI projects. No
more than one Iomega Zip disk will be required for the cruise. At the end of the cruise, a backup of
the Iomega Zip disks should be made to a unique subdirectory of another disk
maintained by the ship for this purpose until the original data is certified
"error free" at PMEL.
Detailed, post-cruise
processing of ADCP data is designed to take advantage of a higher quantity of
navigation data than is retained by the ADCP acquisition software. Thus, the ship's SCS is relied on to
log GPS navigation data at maximum available rates. The SCS system shall log output from the best two navigation
receivers at all times during a cruise.
For the purpose of designating a primary and secondary GPS system,
precedence shall be assigned according to the following list of GPS receivers
available on the Ron Brown:
1. P-code GPS receiver
2. Differential GPS
receiver (DGPS)
3. P-code GPS receiver
operating without encryption key (SPS-GPS)
4. Differential GPS
receiver without differential corrections (SPS-GPS)
Changes in the
availability of GPS equipment shall be communicated to PMEL to allow the above
list to remain current. It is the
responsibility of the ship to install and enable the appropriate encryption key
for use of a PPS-GPS receiver.
The SCS file SENSOR.DAT
should be configured to enable logging only of the NMEA-0183 format messages
$GPGGA and $GPVTG from navigation sources; derived sensor messages are not
desirable for post-cruise processing.
Similarly, only raw messages from the gyrocompass ($HEHDT) are desirable
for logging. SCS should log the
primary GPS data at 1-second intervals, the secondary GPS data at 10-second
intervals, and gyro data at 10-second intervals. The latter are used for adjusting the
acoustic backscattered signal strength to absolute levels and relating the
signal to biological scatterers.
ADCP Underway
Operations: The ADCP operates continuously during the entire cruise. At the start of a cruise, the system
shall be configured and started according to the provided checklists
"Before Leaving Port" and "Underway to Operations
Area". The ADCP and its
interface to the gyro and navigation must be checked daily by completing the
"ADCP Daily Log" and also at the end of the cruise with the ship tied
to the pier.
In case of problems
please describe the problem, error message numbers, flashing lights, etc. on
the log sheets. Also contact Ned
Cokelet (206-526-6820, e-mail cokelet@pmel.noaa.gov) at PMEL as soon as
possible.
Dedicated ADCP transects
should be run at constant heading (not constant course-over-ground) if
practical, thus minimizing gyro lag.
However, transects along lines of current-meter moorings should remain
on the line with the ship's heading gradually adjusted to accomplish this. Sharp turns should be avoided. The ship's speed should be
constant. Twelve knots is often
satisfactory, but the ship may have to slow down if the ADCP's "percent
good pings" decreases below 75% in the upper 200-250 m due to sea
state.
The ADCP should operate
in bottom-track mode when the water depth is less than about 500 m for
more than a few hours. This gives
currents that are better compensated for transducer misalignment but somewhat
lower in statistical significance because the number of pings is reduced. For extended periods in deeper water,
an ADCP configuration without bottom tracking should be used.
ADCP Backtrack-L
Calibration: One backtrack-L calibration maneuver per cruise may be executed to
test the instruments and to calibrate the transducer misalignment angle for
which a 0.5° error can seriously bias the measurements. The "misalignment angle" may
change with the ship's trim as well as with remounting the ADCP transducers. The basic idea is to measure the
current twice on closely spaced parallel tracks of opposite heading when the
ADCP and GPS are working well. The
maneuver consists of 4 legs (N, S, E and W headings) connected by simple
U-turns forming an L shape. Each
leg should be 30 minutes long.
The first 10 minutes are to allow the ship and instruments to stabilize
on the new heading. The entire
calibration should require about 2 1/2 hours with 5 minutes allowed
for each turn. The following
should be considered:
1. Negligible currents
are best, but stronger currents are acceptable as long as they are reasonably
uniform and steady. Avoid regions
of strong horizontal shear due to topography, flow through passes, eddies and
current boundaries. In tidal
currents, measure when the current is steadiest, often at maximum flood and ebb
rather than at slack water.
2. Calibration legs can
be done in any order provided opposite-headed legs are sequential.
3. Opposite-headed legs
should be parallel and closely spaced, but not retraced. Use U-turns to minimize gyro
oscillations. Avoid Williamson and
hairpin turns.
4. The ADCP's PC screen
should show at least 75%-good pings down to 250 m.
5. The ship should go
fast enough to detect a misalignment error (over 5 kts), but slow enough
to satisfy condition 4. This
depends on sea conditions. Ten to
twelve knots is often satisfactory.
6. Choose a time when
GPS is navigating and is expected to remain so over the next 2 hours.
2.2.10 Radiometer
The Ron Brown will provide a radiometer to measure solar
energy. The data stream should be logged by the SCS.