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  					                                    March 22, 1996


Cruise No: MF 96-08 (FOCI 4MF96)
Area: Western Gulf of Alaska


	May 1, 1996	Depart	 Kodiak, AK

	May 15, 1996	Arrive	 Dutch Harbor, AK

Participating Organizations:
NOAA Alaska Fisheries Science Center (AFSC)
NOAA Pacific Marine Environmental Laboratory (PMEL)

Cruise Description and Objectives

Fisheries Oceanography Coordinated Investigations (FOCI) is a joint effort by scientists at PMEL and AFSC to understand the biological and physical processes which cause variability of recruitment to commercially valuable fish and shellfish stocks in Alaskan waters. One component of the FOCI program is studying the effects of the biotic and abiotic environment on the early life stages of walleye pollock spawned in Shelikof Strait. There are two aspects to the study: the acquisition and analysis of time-series data, and specific process-oriented studies on a cruise-by-cruise basis.

This cruise plan is designed to achieve maximum coordination with sampling by the Discover (April 23-May 5). The Discover will conduct a pre-survey of the region and also conduct a broader scale picture, within which the Miller Freeman's process-oriented sampling will be nested. The principal objective of this cruise is to examine several important biophysical conditions as they related to larval pollock distribution, abundance and mortality. The physical conditions include the occurrrence of storms, eddies, and fronts. Each of these conditions have important consequences to larval pollock survival, but by nature their occurrence is sporadic and their duration is ephemeral. Since the occurrence and discovery of any one of these features is risky, the cruise is designed with that risk in mind and to optimize contingencies. Secondary objective are: (1) to continue acquisition of long-term biological and physical time series; (2) to conduct a survey of larval pollock for use in estimating distribution, drift and mortality rates; and (3) to collect samples of larval pollock and their prey for studies on growth and condition.


1.1. Chief Scientist: Kevin Bailey (AFSC) 526-4243

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.

1.2. All foreign nationals must have Department of Commerce security clearance.

1.3. Participating Scientists

	Kevin Bailey	M/USA	NOAA/AFSC>


	Morgan Busby	M/USA	NOAA/AFSC

	Annette Brown	F/USA	NOAA/AFSC

	Lorenzo Ciannelli	M/Italy	NOAA/AFSC

	Sigrid Salo	F/USA	NOAA/PMEL




1.4. Ship Operations Contact:

Larry Mordock
1801 Fairview Ave E.
Seattle, Washington 98102-3767


2.1. Summary of Activities

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 especially important. To insure fulfillment of all the scientific objectives, the ship will steam at maximum cruising speed whenever time in transit and between stations is greater than three hours.

A standard oceanographic watch will be utilized which consists of a winch operator, a scientific staff of three, and a Survey Tech on deck. Operations will be conducted 24 hours a day. The fishing crew will be required to assist with the Methot trawl, if it is decided to deploy it.

The first operation will be sampling of FOCI Lines 3,5 and 8. Immediately after occupation of Line 8, the ship will proceed to the region of a larval patch located and subsequently marked with a satellite-tracked drifer by the Discoverer. Bongo tows will be the standard survey gear. It is aniticipated that this patch will be located to the southeast of Sutwik I.

In the event that an eddy is located before or during the cruise, the eddy will be intensively sampled using ADCP and EK500 observations, bongo, MOCNESS, and CALVET tows, and CTD casts with the suite of associated biological samples. If a storm passes through the area of operation, the sampling schedule will be altered to efficiently sample before and after the storm, and if weather conditions are reasonable, to sample during the storm. If no eddy is found, efforts will be concentrated on locating a frontal region, and then conducting an intensive sampling of the feature using the suite of instruments listed above.

A special study on larval extrusion through the meshes of the plankton nets may be conducted at the discretion of the chief scientist. This study may include up to 30 Marmap bongo tows with a special net, and may also include several bongo tows where live pollock larvae are released into the nets using a specialized jar that is held in front of the plankton net with a pole while the net is at the water surface.

Two satellite drifters will be deployed during the cruise to study patch/eddy dynamics. In addition, the eddy/patch will be marked by deployment of a GPS or radar-tracked recoverable drifter. All drifters will be drogued at 40m. Surface drift cards may be deployed during the cruise.

At the end of the cruise and if time permits, sampling will be conducted on the FOCI grid of stations from the vicinity of the Discover's southwestern-most station to Unimak Pass. The standard gear for this sampling will be the bongo tow. Stations will be chosen from among those listed in Appendix B. Stations to the southwest of the normal FOCI grid will be provided before the cruise departure. The exact station grid will not be determined before the cruise begins, but will be continually updated by the Chief Scientist as the cruise proceeds. Stations may be added or subtracted at any time at his discretion.

FOCI Lines 8(additional sampling), 16 and 17 will be occupied opportunistically during cruise. CTD casts will be done using the PMC Sea Bird 911+ CTD system. Water samples will be collected for microzooplankton and chlorophyll content. CTD station locations are given in Appendix A. 60 cm bongo tows with .333 mm mesh nets and 20 cm bongo tows with 0.153 mm mesh nets will be done at each station on the FOCI lines.

2.2. CTD/Water Sample Operations

PMC's Sea-Bird 911+ CTD will be the primary system used. (PMEL's CTD stand, which has been modified for the attachment of a Sea-Tech fluorometer, will be used). CTD data will be acquired on a PMEL computer using SEASOFT software. The cabability 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" in addition to the wire usage log. The CTD should descend at a rate of 30m/min for the first 200m and 45m/min below that. The ascent rate should be 50m/min. The FOCI, light meter and chlorophyll absorbance meter (ChlAM) should be mounted on the rosette for all casts where possible. However, the ChlAM can not exceed 300m and the light meter cannot exceed 500 m. Water samples will be collected with 10-l Niskin bottles. Depth and light levels will be recorded on the "CTD Cast Information/Rosette Log" for all water bottle samples.

CTD Calibration: Salinity comparisons will be conducted 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 the AutoSal analysis during the cruise and record the readings on an AutoSal log.

Nutrient, chlorophyll and microzooplankton samples will be obtained from 10-l Niskin bottles deployed on the rosette sampler. Bottle samples will be obtained during the "upcast" after a CTD profile is obtained. If more than one deployment is necessary to meet our water requirements, then CTD data may be requested from the second cast. Depth and light readings should be recorded on the CTD/rosette log for all water bottle samples.

2.3. Drifter deployments: Satellite-tracked drifters will be drogued at 40m and deployed in the standard method. Two drifters will be deployed on this cruise. A recoverable GPS (if it is available and tested before the cruise) or radar-tracked drifter will be deployed in the standard method. Surface drift cards will be deployed by scientists using standard methods.

2.4. Biological Operations:

While the region of operation is established here, the exact position of eddy, patch or frontal stations will be determined just prior to departure or even while the cruise is underway. Approximately 24h will be utilized to characterize the patch/eddy feature. Intensive sampling of the patch/eddy is anticipated to last 5d. For the standard grid larval survey, approximately 150 stations will be occupied. The stations will be selected (from those listed in Appendix B) and may be updated as sampling proceeds. The stern platform will be used for MOCNESS tows.

2.4.1. MARMAP bongo tows: A 60-cm bongo net with 333 mm nets, (or .505 mm if clogging is significant) 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 200 m or 10 m off bottom in shallower waters. However, at stations on Lines 8, 16 and 17 nets will be towed from 10 m off bottom to surface. In addition at least one side of the 60 cm bongo will be .333 mm mesh. Furthermore the 20 cm bongo with .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 depth of the nets will be monitored from DataPlot and commands given 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 down to wash the sample into the codend. Larvae are sorted and preserved appropriately. 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 a PMEL computer using SEASOFT software. The option to display Seacat data using the SCS system and monitors will be available. Watch scientists are responsible for monitoring the quality of the Seacat data.

2.4.2. Bongo live tows: A live tow for larval pollock uses the 60cm bongo with 0.333mm or 0.505mm 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 meant to be a vertical tow with ship speed used only to maintain a zero wire angle. The bongo is lowered at 50 m/min to a gear depth of 70 meters. The wire in speed should be 10 m/min, begin timing tow when 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 due to time restrictions are sorted quickly for live larvae.

2.4.3. Tucker trawls:
The Tucker trawl will be used as both a backup for the MOCNESS and for dedicated predator studies. When used as a backup sampler it will have 333 um mesh netting and will be used in the standard manner. When used for predator studies it will have 505 um mesh with a 1 mm cod end bucket. In either case, the depth of the net will be monitored with the ScanMar quarterdeck hydrophone(or the SeaCat depending on circumstances). The net is deployed at constant wire speed of 40 m/min to a desired depth. The winch is stopped and the net allowed to stabilize for 30 sec. A messenger is sent, opening the first net. Then at the next desired depth, a second messenger is sent, closing the first net and opening the second. Again the net is allowed to stabilize and then is retrieved as before. The nets are retrieved at a wire speed of 20 m/min. The ship speed is adjusted to maintain a 45 degree wire angle during the entire tow. When the nets reach the surface, they are brought aboard and hosed down to wash the sample to the codend. Flow meters are read. Tows not meeting specifications may be repeated at the discretion of the scientific watch. Four Tucker tows are required to substitute for one oblique MOCNESS tow.

2.4.4. Methot trawl: The Methot trawl is deployed using the Marco winch off the stern of the vessel. A ScanMar acoustical depth sensor, with a readout in the trawl house (or alternatively, an electronic BKG or CTD), will be used to receive real-time depth information. A scientist or Survey Tech in the trawl house will relay orders for stopping and starting the winch to the winch operator based on trawl depth. The ship's speed should be 2.5 to 3.0 kts. This trawl will be deployed at 40 m/min and retrieved at 20 m/min. Tows will be oblique or stepped oblique from 100 m to the surface. Methot trawls may be conducted in daytime or at night with little or no advanced warning, as where and when they will be done depends on plankton catches or acoustic sign. Because this information is instantaneous, the trawl will need to be activated quickly with little time lost. Location and time of tows is at the discretion of the chief scientist or scientific watch leader.

2.4.5. CALVET sampling: Vertical tows to collect microzooplankton and free-floating copepod eggs will be conducted during patch studies, 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 standard 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 cod ends, 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. The mesh size is 40 um.

2.4.6. MOCNESS sampling: A Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) will be used during the cruise. The MOCNESS is deployed from the stern platform using the Rowe winch and the A-frame. The instrument will require 600-1500 m of single conductor wire. In addition, a set of slip rings are requested for the winch. The load requirement of the MOCNESS system is 0-3000 pounds, so including a 2-3X safety factor, the conducting cable should have a minimum breaking strength of 6000-9000 pounds. The MOCNESS telemeters, in real time, conductivity, temperature, depth, and filtered-volume to the surface. A scientist in DataPlot will relay instructions to the winch operator and the bridge to control the descent/ascent of the net system. Wire in/out rates must be available to the winch operator and should be a display in DataPlot. The MOCNESS is deployed while under way (2.5 knots). Wire is paid out at a rate of 5-50 m/min and is retrieved at 5-20 m/min.

This year we would also like to acquire ship's position data from the GPS port in DataPlot and display the MOCNESS depth trajectory using the SCS. Assistance from shoreside Engineering and the ship's ET is requested. Our deck unit for the GPS requires a single NEMA string via RS232 serial communications. The GPS unit should be programmed to transmit only the $GPGLL string. The operating software can not handle more than one type of string.

The movable MOCNESS support frame will be used (as in the past) and will be secured to the deck near the net reel. We will need assistance from the ship in building a plywood platform (4' x 16') with 2" x 4" side rails to attach to the stern platform. Similar to the one built in previous years.

During the cruise, Survey Technicians will be asked to jointly share responsibility with the scientists for the successful operation of the MOCNESS. A member of the fishing crew may be requested to assist in the deployment and recovery of the MOCNESS.

2.4.8. Biological sampling: Samples from the bongo or Tucker trawls will be processed as soon as possible in the laboratory by the scientists. A subsample will be taken and pollock larvae will be removed from the codend over ice and rough counts made. Individual larvae from the subsample will be preserved in 95% ethanol. The rest of the sample will be fixed in ethanol. Larvae from live tows will be frozen or fixed in Bouins solution. The approximate number of chaetognaths and jellyfishes observed in the subsample will be recorded and the number with larval pollock in their guts will be noted.

2.4.9. Chlorophyll samples: Chlorophyll samples will be taken from the 10-l Niskin bottles. Sampling depths depend on the fluorescence 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 maximum. If the maximum is deeper, sampling should be moved deeper with less 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. The -70 degree C freezer is required for sample storage.

2.5. Other Operations

2.5.1. Seachest and Uncontaminated Seawater: Sea surface temperature, conductivity and fluorescence will be continuously monitored. A Sea-Bird thermosalinograph will be mounted in the sonar void amidships and will send its data to the SCS. In addition, the uncontaminated seawater from this chest will be pumped to the Chemistry Laboratory and through a fluorometer. The scientists will be responsible for regularly cleaning the cuvette inside the fluorometer and obtaining and processing the calibration samples. Calibration samples will be taken at each bongo station or one hour apart, whichever is more frequent.

Prior to the cruise (while dockside), the seachest should be opened and the sensors visually inspected and cleaned in the presence of the Chief Scientist or his delegate.

At the beginning of the cruise, the ship's Chief Survey Technician will be responsible for ensuring that the data streams from the instruments are correctly logged by the SCS. During the cruise, the Survey Technicians are responsible for checking the logger once per watch to determine that the instruments are functioning, and for taking salinity calibration samples every other day. After the cruise, the Chief Survey Technician should prepare an ASCII dos formatted diskette that contains 1 minute averages of time, position, T, S, F and water depth.

2.5.2. Radiometer: The ship will be equipped with a radiometer to measure solar energy. PMEL scientists will supply the calibrated instrument, mounting hardware and cable to run to Data-plot. We will need the assistance of the ship's Electronic Tech. and SCS Manager to correctly install the instrument and make sure that the data stream is being logged by the SCS.

2.5.3. 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 other methods: 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 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). 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 DataPlot compartment.

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 1 or 2 second rate), and with the maximum number of digits of precision (optimally 4). The Ashtech 3DF Attitude Determination Unit shall be configured to send the $PASHR,ATT 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 SyQuest 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 progam UE4.EXE should be configured to send an "RDI-style" ensemble to SCS.

PMEL supplies the SyQuest disks for FOCI projects. No more than one SyQuest disk will be required for the cruise. At the end of the cruise, a backup of the SyQuest should be made to a unique subdirectory of another disk maintained by the ship for this purpose until the original data is certified 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 Miller Freeman:

1. Trimble Centurion with encryption key installed and enabled (PPS-GPS)
2. Northstar 941X receiving differential corrections from radiobeacon (DGPS)
3. Trimble Centurion operating without encryption key (SPS-GPS)
4. Northstar 941X without differential corrections (SPS-GPS)
5. Magnavox MX-200 (SPS-GPS)
6. Ashtech 3DF ADU (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 ($HEHDT) and GPS ADU ($PASHR,ATT) are desirable for logging.

SCS should log the primary GPS data at 1 second intervals, the secondary GPS data at 10 second intervals, gyro data at 10 second intervals, GPS ADU messages at 10 second intervals, and the temperature and input voltage of the ADCP electronics (deck unit) at 60 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. The centerboard height affects the depth of sampling. The centerboard shall be lowered as soon as practical upon leaving port and remain lowered throughout the cruise. If it is necessary to raise the centerboard during the cruise, the times of raising and lowering must be logged in the Marine Operations Abstract (MOA).

In case of problems please describe the problem, error message numbers, flashing lights, etc. on the log sheets. Also contact Dan Dougherty (206-526-6844; e-mail DOUGHERTY@PMEL.NOAA.GOV) or 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 practicable, 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. 12 kts 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 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:
At least one backtrack-L calibration maneuver per cruise should 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. 10-12 kts is often
6. Choose a time when GPS is navigating and is expected to remain so over the next 2 hours. ADCP Absolute Backscatter Calibration:
A test to calibrate the absolute backscatter strength and to determine the background noise level of the ship-ADCP system may be performed once per cruise at the discretion of the Chief Scientist. Specific instructions in such event will be provided by PMEL personnel aboard, and cannot be anticipated in advance of the cruise.

Typically, such a test will be attempted in conditions when weather is relatively calm, and the water depth exceeds 250 m. This test may require that the main power plant, pumps, sonars, and other sources of acoustic and electronic noise be shut down. If conducted in the course of normal operations, the work will require about 1 hour. There may be opportunities for variations of the test any time the ship is at anchor, requiring the cooperation of the ship's officers and engineering watch.

2.5.4. EK-500 Monitoring: The Simrad EK-500 Scientific 38 kHz Echosounding System in the acoustics van will be turned on during all scientific operations and should be monitored regularly for the presence of unusual acoustic signals or heavy fish sign. The bridge should notify the scientific watch on duty if any unusual sign appears on the bridge echosounder. Because of the vast amount of data and paper generated by this system, the PC data-logger and color printer should only be turned on when in an area of interest or when unusual sign begins to show up. A trained scientist should be available on each watch to begin logging data and to record ship speed and course changes on the traces and file names in the notebook provided. Files should be closed after a maximum of two hours and backed up onto 3.5" floppy disks or other storage medium before the end of the cruise. The printer pen cartridges and paper should be replaced as needed. The EK-500 settings will be set at the beginning of the cruise and remain the same throughout the cruise.


The following systems and their associated support services are essential to the cruise. Sufficient consumables, back-up units, and on-site spares and technical support must be in place to assure that operational interruptions are minimal. All measurement instruments are expected to have current calibrations, and all pertinent calibration information shall be included in the data package.

3.1 Equipment and Capabilities to be Provided by the Ship

  1. Oceanographic winch with slip rings and 3-conductor cable terminated for CTD (port winch)
  2. Oceanographic winch for bongo net and Tucker trawl sampling with slip rings and 3-conductor cable terminated for Seacat or electronic Time-Depth recorder. Wire should be capable of 1200 lb loading
  3. Meter block for plankton tows
  4. Laboratory space with exhaust hood, sink, lab tables and storage space
  5. Sea water hoses and nozzles to wash down nets 6. Adequate deck lighting for night-time operations 7. 10-liter sampling bottles for use with rosette (12 plus spares)
  6. Navigational equipment,including satellite, radar and Loran-C systems
  7. For CTD field corrections: Copenhagen standard water,AUTO-SAL salinometer with back-up AGE mini-sal and two pingers 10. Wire-angle indicator and readout for oceanographic winch to be used with bongo and Tucker
  8. Wire speed indicator and readout
  9. For meteorological observations:2 anemometers (one interfaced to the SCS), calibrated air thermometer(wet-and dry-bulb) and a calibrated barometer and/or barograph
  10. Aft Rowe winch with single conductor cable and slip rings for MOCNESS
  11. Aft metering block and trawl house Data-Plot readout for MOCNESS and Methot
  12. Freezer space for storage of samples (blast and storage freezers)
  13. Simrad EQ50 echo sounder
  14. JRC JFV-200R color sounder recorder
  15. RDI ADCP with PC compatible data acquisition computer and SyQuest disk drive
  16. Stern platform (in place)
  17. Bench and rack space in Data Plot for PC computer and peripherals to fly MOCNESS
  18. Radar-tracked buoy
  19. Electrical connections between Rowe winch and Data Plot 23. Use of 386 computer in Data Plot and laser printer 24. SeaCat SBE-19(backup)
  20. MX2000 GPS unit for MOCNESS
  21. Display to MOCNESS depth trajectory by SCS Computer system
3.2 Equipment Provided by the Project
  1. Complete 60-cm bongo sampling arrays
  2. Complete 1-M Tucker sampling arrays
  3. Spare wire angle indicator
  4. ScanMar
  5. SeaCat SBE-19 for bongo tows
  6. Complete Methot frame trawl
  7. 2 PMC Sea-Bird CTD 911+ systems, SBE 36 deck unit, SBE Power Data Interfact module (PDIM), and SBE 5T pump(primary system)
  8. Scientific ultra-cold freezer
  9. Electronic BKG, computer, printer and software 10. Miscellaneous scientific sampling and processing equipment 11. 20 cm bongo arrays
  10. CALVET net array
  11. Complete MOCNESS sampling array
  12. 2 ARGOS Satellite-tracked drifters
  13. GPS recoverable buoy and drogue
  14. Surface drift cards
  15. Simrad EK-500 system and van
  16. Tucker net array
  17. Radiometer
  18. Holey sock drogue for Radar drifter
  19. Light meter and ChlAM to be mounted on CTD
  20. PMEL PC with SEASOFT for CTD data collection and processing
  21. Temperature thermistors for CTD's (one for primary system, one for back up system)
  22. Rosette sampler
3.2. Ultra-cold Freezer Requirements

The scientific ultra-cold freezer will remain on the ship in operating condition from the beginning of the first FOCI cruise until the ship returns to Seattle and the samples within can be unloaded. Since valuable samples will be in the unit, operation must be continuous without interruption. Therefore, the unit should be hardwired into the ships electrical system or connected with a threaded plug. The unit must be securely fastened to a bulkhead or counter, easily accessible, with a minimum of 4" on each side around the bottom. The location, fastening and wiring should be similar to last year. In addition, a weight should be taped to the top of the unit to prevent the lid from lifting in heavy seas.

The freezer has an alarm, but the ship's personnel are requested to check the digital temperature display twice daily to insure that the operating temperature is below -60 degrees C. The unit will be locked between cruises, and a key left with the Chief Survey Tech. In the event that the unit fails, the temperature will maintain for about 12 hours if the lid isn't opened. If the unit fails and cannot be fixed on the ship, the scientific blast freezer should be pre-cooled to its minimum (-38 degrees C), and all frozen specimens should be transferred to it immediately, without thawing. Kevin Bailey (206/526-4243, 4239) must be notified.

A daily record of the temperature (digital readout) on the scientific ultra-cold freezer will be submitted to K. Bailey (AFSC) upon the ship's return to Seattle.

3.3 The Scientific Computer System (SCS):

The ship's Scientific Computer System (SCS) shall operate throughout the cruise, acquiring and logging data from navigation, meteorological, oceanographic, and fisheries sensors.

The SCS data acquisition node will provide project scientists with the capability of monitoring sensor acquisition via text and graphic displays. A data processing node will be available to project scientists throughout the cruise, configured according to the specifications of the FOCI SCS administrators.

Sensor identification, and data acquistion and logging parameters are specified in the system file SENSOR.DAT. This file shall be maintained in a current state by the ship's SCS manager. Specific FOCI requirements for the content of the SENSOR.DAT file were provided by the FOCI SCS administrators at the start of the 1996 field operations season. A listing of the sensor specifications is attached as an appendix to these instructions. Changes to the SENSOR.DAT specifications may be made by the ship's SCS manager on a cruise-by-cruise basis, at the request of the chief scientist. All changes in content of the SENSOR.DAT file shall be communicated to the FOCI SCS administrators.

SCS sensor data logged to disk files are organized into several logical groupings according to intended post-cruise processing. These logical groupings were specified by the FOCI SCS administrators at the start of the 1996 field operations season. The ship's SCS manager will assign data elements from newly-installed sensors to the appropriate logical group(s), and inform the FOCI SCS administrators of such changes.

At regular intervals, not to exceed every 5 days, SCS ship's manager will archive data from disk files to 8-mm tape cartridge for delivery to the project representative at the end of the cruise. To ensure compatibility with the laboratory tape drive mechanisms, backup 8-mm tapes shall not be recorded with hardware compression options.

Real-time data will also be logged to QIC tapes to provide additional data security in the event of disk failure; these tapes will be archived by the ship until project data tapes have been received and verified by the laboratories.

The ship's SCS manager will ensure data quality through the administration of standard SCS protocols for data monitoring. If requested by the chief scientist, standard SCS daily quality assurance summaries will be prepared for review.

Additional recording of processed data may be requested of the ship's SCS manager; if so, specific instructions will be found elsewhere in this document. During the cruise, the scientific party may require the assistance of the ship's SCS manager to determine if all sensors are functioning properly and to monitor some of the collected data in real time to make sampling strategy decisions .


4.1. Data Disposition and Responsibilities:

The Chief Scientist is responsible for the disposition and feedback on data quality along with the archiving of data and specimens collected on board the ship for the primary project. The Chief Scientist will be considered to be the representative of the NMFS/PMEL Lab Director for purpose of data disposition. A single copy of all data gathered by the vessel will be delivered to the Chief Scientist upon request for forwarding to the lab director, who in turn will be responsible for distribution of data to other investigators desiring copies.

4.2. Data requirements:

The following data products will be included in the cruise data package:

bullet Marine operations abstracts,

bullet Marine weather observation logs,

bullet PMEL CTD weather observation logs,

bullet CTD audio cassettes,

bullet CTD Cast Information/Rosette Log,

bullet Calibration sheets for all ship's instruments used,

bullet Autosalinometer logs,

bullet ADCP daily log sheets,

bullet ADCP SyQuest 105 MB disks,

bullet SCS 8 mm backup tapes,

bullet SeaPlot Files, disk and hard copy. NOS chart or overlay not required,

bullet Ultra-cold freezer temperature daily log, (end of field season).

4.2.1. Marine Observation Log: A Marine Operations Abstract (MOA) form will be maintained by the ship's officers during the cruise. The Chief Scientist and the Commanding Officer or designee will negotiate the details regarding forms required by the project for each operation.

4.2.2. Station Plot: The position of each operation and station will be maintained in a SeaPlot file. A diskette and hard copy of the file will be given to the Chief Scienist. The requirement to plot on NOS nauticalcharts and provide the Chief Scientist with the chart or mylar overlay has been temporarily waived.

4.2.3. Navigation: Observations and reliable fixes shall be plotted and identified by date/time group or equivalent. Fixes shall be evaluated for course and/or speed made good. Primary navigational control shall be provided by satellite, Loran-C, radar range and bearing, and visual fixes. Loran-C fixes shall be recorded as both the rates and as latitude and longitude.

4.2.4. Synoptic Weather Reports: In accordance with OMO Instruction 3142 dated December 5, 1985 and Amendment 3142B dated August 4, 1986, a weather log of NOAA Form 72-1A will be maintained by ships personnel, and data will be transmitted via SEAS. The completed logs will be forwarded to NWS port meteorologists.

Complete meteorological observations will be logged on the NOAA Form 77-13d at hourly intervals for scientific data purposes.

4.2.5. Scientific Ultra-cold Freezer Log: A daily record of the temperature (digital readout) on the scientific ultra-cold freezer will be submitted to K. Bailey (AFSC) upon the ship's return to Seattle.

4.3. Cruise Reports: The Chief Scientist and Commanding Officer will jointly prepare a cruise report for submission to the Director, PMC, as required by NOAA Directives Manual 17-17. The Commanding Officer's report will follow formats and reporting requirements prescribed in PMC Oporder 1.3.6.

4.4. Evaluation Report: One Ship Operations Evaluation Report is required for each leg of the primary project only, using the form provided for that purpose.


5.1. Additional Investigations: Any other work done during the cruise period will be subordinate to the main project and performed so as not to interfere with that outlined in these instructions. The Chief Scientist will be responsible for determining the priority of additional work relative to the main project.

5.2. Ancillary and Piggyback Projects:

(a) SEAS Data Collecting and Transmission (PMC OPORDER 1.2.1.)
(b) Marine Mammal Reporting (RP-12-93)
(c) Nautical Charting (PMC OPORDER 1.2.6.)
(d) Bathymetric Trackline (PMC OPORDER 1.2.5.)
(e) Loran-C Comparison Data (PMC OPORDER 1.2.4.)
(f) Alaska Weather Reporting (PMC OPORDER 1.2.7.)
(g) Sea Turtle Observations (SP-PMC-2-94, Sea Turtle
Observation Program, 1994)

5.3. Piggyback Projects: None at this time.


6.1. Radio Interference
Some scientific equipment is sensitive to radio frequency interference. If interference occurs, it may be necessary to adjust operations and communications schedules if efforts to electronically isolate the equipment are unsuccessful.

6.2. Pre-cruise and Post-cruise Meetings:

A precruise meeting between the Commanding Officer and the Chief Scientist will be held prior to the start of the cruise. Its purpose is to identify the day-to-day requirements of the project in order to best utilize shipboard personnel resources and to identify overtime requirements. A brief meeting of all scientific personnel, the Field Operations Officer, Chief Boatswain, survey department, and other relevant ship's personnel should be held before the vessel reaches the experiment area for the purposes of:

a) introducing new scientific personnel to ship's procedures, proper channels, etc.;

b) discussing operating procedures for deploying various pieces of sampling equipment; and

c) coordinating scientific watch assignments.

A post-cruise debriefing will be held between the Chief Scientist and the Commanding Officer. If serious problems are identified, the Commanding Officer shall notify the marine center by the most direct means available. The Chief Scientist shall document identified problems in the Ship Operations Evaluation Form.

6.3. Meals
All scientists (passengers) will pay for their meals at a rate of $8.20 per day for two or more meals and $4.10 a day for one meal, in accordance with NOAA Administrative Order 203-100, and PMC Directives #87-04. The Commanding Officer will furnish NOAA Form 75-90, Authorization of Mess Obligation, for the Chief Scientist's and Commanding Officer's signature for all the scientists' meals.

6.3.1. Midnight Lunches: The scientific staff will work 12 hour watches (12 to 12). A hot midnight lunch will be required for the watch.

6.4. Hazardous Materials: The Chief Scientist shall be responsible for complying with NC Instruction 6280A, Hazardous Waste; policy, guidance, and training, dated February 4, 1991, paragraph 7.g and paragraph 9. By federal law, the ship may not sail without a complete inventory of MSDS, and appropriate neutralizing agents, buffers, and/or absorbents in amounts adequate to address spills of a size equal to the amount aboard.

The following hazardous materials will be provided and controlled by the scientists with the Chief Scientist assuming responsibility for the safe handling of such substances:
(a) Ethanol
(b) Formalin
(c) Z-fix
MSDS data will be provided when the chemicals are loaded.


7.1. A daily JFT schedule will be maintained between KVJ and the MILLER FREEMAN Monday through Friday. Radio contact will be maintained when possible. A scientific progress report will be sent to AFSC via INMARSAT voice, Fax, or JFTt at least once a week.

7.2. Since it is sometimes necessary for the scientific staff to communicate with other research vessels, commercial vessels, and shore based NOAA facilities, the Chief Scientist or designee may request the use of radio transceivers aboard the vessel.

7.3. The Chief Scientist anticipates the need for daily reports on the position of satellite-drifters in the study area and the health of the biophysical mooring(s). These will be sent either by Fax from PMEL over INMARSAT or over Internet from PMEL to the PMC radio room and forwarded to the ship via the PC-T-Post-INMARSAT route.

7.4 Important phone numbers:

PMEL/CARD Fax: (206) 526-6485

PMEL/ADMIN Fax: (206) 526-6815

AFSC/RACE Fax: (206) 526-6723



Program contacts:

Phyllis Stabeno -PMEL- (206) 526-6453

Kevin Bailey -AFSC- (206) 526-4243

Important Internet e-mail addresses are:

Phyllis Stabeno:
Kevin Bailey:
Jeff Napp:

PMC radio room:

Direct to ship:

7.4. The MILLER FREEMAN is equipped with INMARSAT, a telephone/teletype satellite communication system. If the scientific staff uses this system, they will be obligated to pay for their calls, which are estimated at $7.70 per minute and Rapid fax and $4 per minute for Telex.

The Chief Scientist, or designee will have access to, and assistance provided for transmitting and receiving communications through INMARSAT as needed during the cruise.

7.5 The MILLER FREEMAN is equipped with a cellular telephone. If the Scientific Party uses this system, they will pay for incoming and outgoing calls. Cost is approximately $0.90 per minute, plus applicable long distance fees charged to the ship's number.


A. Locations of FOCI lines 3,5 and 8: CTD stations.

B. Locations of potential larval survey stations.

C. Map of standard FOCI grid region and general area of survey (delimited by box).

D. 1996 FOCI SCS sensor specifications.

Appendix A. Locations of FOCI lines 3,5 and 8 stations.

Station	Lat-deg	Lat-min	Long-deg	Long-min
(Shelikof; FOCI Line 3) 19 58 39.2 152 39.1 20 58 40.6 152 43.8 21 58 42.7 152 49.5 22 58 44.5 152 55.5 23 58 46.4 153 2 24 58 48.5 153 8 25 58 51 153 13.5 (Shelikof; FOCI Line 5) 33 57 59.2 153 34 34 58 0.5 153 37.5 35 58 3 153 43 36 58 5.4 153 49 37 58 8 153 54.6 38 58 10.7 154 0.9 39 58 13 154 7.6 (Shelikof; FOCI Line 8) 56 57 30.9 154 47 57 57 33.1 154 52.5 58 57 36.3 155 0.5 59 57 38.5 155 4.2 60 57 41 155 10 61 57 43.2 155 15.6

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