| March 6, 1996
DRAFT CRUISE INSTRUCTIONS
NOAA Ship: MILLER FREEMAN
Cruise No: MF9609
May 1 Depart Dutch Harbor May 2 Arrive Dutch Harbor
NOAA Pacific Marine Environmental Laboratory (PMEL)
Fisheries Oceanography Coordinated Investigations (FOCI) is a joint effort by scientists at PMEL and AFSC to understand the biological and physical processes which cause recruitment variability of commercially valuable fish and shellfish stocks in Alaskan waters. The Bering Sea FOCI program is presently studying the effects of the biotic and abiotic environment on the early life stages of walleye pollock spawned in the eastern Bering Sea. There are two aspects to the study: the acquisition and analysis of time-series data, and specific research topics to be covered on a cruise-by-cruise basis.
1.1. Chief Scientist: William Parker 526-6180
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; (4) alter the general intent of these project instructions.
1.2 Participating Scientists
William Parker M/USA PMEL Carol DeWitt F/USA PMEL Dan Dougherty M/USA PMEL Lisa Britt F/USA AFSC
1.3 Ship Operations Contact:
2.1. SUMMARY OF ACTIVITIES:
Deploying FOCI biophysical platforms 2 and 3 is the first priority of this cruise. This is scheduled to be completed in MF96-07. The moorings will be loaded onto the ship in Dutch Harbor prior to MF96-07. If circumstances prevent deploying the moorings on MF96-07, the moorings will remain onboard and will be deployed on this cruise.
These deployments entail recovering subsurface moorings 2 and 3. The equipment will be turned around and redeployed with the surface moorings. Subsurface mooring 2 site has a witness buoy and 2 subsurface moorings, subsurface mooring 3 site has a witness buoy and one subsurface mooring. Standard CTD casts will be done at each mooring recovery and deployment. Bongo tows, Tucher trawls and CalVET will also be conducted at the mooring sites.
The second priority of this cruise is to recover the 7 EPA moorings around St. Paul Island. (See appendices) These are subsurface moorings, each moorings has a release, a current meter and a 28" float. (One of the 7 moorings has 2 current meters). This will also involve standard CTDs at the mooring locations, and occupation on a CTD transect.
In the event that the Pribilof Islands (St Paul) have ice around them, CTD operations will be conducted in the Bering Sea. These will include: a transect across moorings 6 & 7, a transit around Unimak Pass, and a transit between FOCI BP 2 & 3. kTucker sled tows will be conducted on the middle and outer shelf (1 day & 1 night tow each site) to determine the fraction of the total population which resides on the bottom, thus avoiding our tradditional samplers.
2.2 PROCEDURES FOR OPERATIONS:
2.2.1 CTD/Water Sample Operations
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.
2.2.2 MARMAP bongo tows
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.
2.2.3 CalCOFI Vertical Egg Tow (CalVET) Net
2.2.4 Tucker trawls
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 degrees C freezer is required for sample storage.
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.
ADCP Data Collection:
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)
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:
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:
ADCP Absolute Backscatter Calibration:
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.
3.2 Equipment to be Provided by the Project
3.3. 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.
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.
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.
The FOCI SCS co-administrators are:
3.3. 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.
4.1. Data Disposition and Responsibilities:
The Chief Scientist is responsible for the disposition, feedback on data quality, and 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 AFSC/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.
4.2.1. 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.
Complete meteorological observations will be logged on the NOAA Form 77-13d at hourly intervals for scientific data purposes.
The Chief Scientist and Commanding Officer will jointly prepare a cruise report for submission to the Director, PMC, as required NOAA Directives Manual 17-17. The Commanding Officer's report will follow formats and reporting requirements prescribed in PMC Oporder 1.3.6.
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.
1. SEAS Data Collecting and Transmission (PMC OPORDER 1.2.1.)
2. Marine Mammal Reporting (PMC OPORDER RP-12-94)
3. Nautical Charting (PMC OPORDER 1.2.6.)
4. Bathymetric Trackline (PMC OPORDER 1.2.5.)
5. Alaska Weather Reporting (PMC OPORDER 1.2.7.)
6. Sea Turtle Observations (SP-PMC-2-95, Sea Turtle Observation Program, 1995)
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. Planning Meeting
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
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 Directive 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.
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:
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 JFT at least once a week.
7.4 Important phone numbers:
PMEL/CARD Fax: (206) 526-6485
Important Internet e-mail addresses are:
The Chief Scientist, or designee will have access to, and assistance provided for transmitting and receiving communications through INMARSAT as needed during the cruise.
1. Positions for FOCI biophysical platforms 2 & 3
2. Positions for subsurface moorings 2 & 3
4. Biophysical platform descriptions