FOCI STANDARD OPERATING INSTRUCTIONS FOR NOAA SHIP MILLER FREEMAN

Date Last Modified: May 29, 2001

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:

Larry Mordock
NOAA/Marine Operations Center-Pacific (MOP1)
1801 Fairview Ave. East
Seattle, WA  98102-3767
 (206) 553-4764
Larry.Mordock@noaa.gov

1.4 FOCI FIELD OPERATIONS LEADERS:

Dr. Phyllis Stabeno
PMEL
7600 Sand Point Way NE
Seattle, WA  98115-6349
(206) 526-6453
Phyllis.Stabeno@ noaa.gov

Dr. Jeff Napp
AFSC
7600 Sand Point Way NE
Seattle, WA  98115-6349
(206) 526-4148
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 9 Plus 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 9 Plus CTD is required and will be provided 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 depth, the Wet-Star fluorometer cannot exceed 600 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 on a PMEL PC computer using SEASOFT software. Aboard the Miller Freeman, 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, secondary 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 analyses 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 from DataPlot, and they will issue stop commands for 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.  Ship’s speed is adjusted to maintain a wire angle of 45(±5)° 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 a CTD or electronic bathykymograph records the depth history of the tow.  The scientists on watch are responsible for recording times and maximum depth on the COD (Cruise Operations Database).  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.

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 are 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 immediately pour 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 and codend that minimizes damage to the organisms.  The net will be deployed using the starboard winch.  The ship will be asked to keep station for this vertical tow.  A 0.8 m diameter 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 from the stern platform using the Rowe winch and the A-frame.  On cruises where the trawl ramp is used, the MOCNESS may be carefully lowered and retrieved over the ramp under calm seas.  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 in DataPlot by a data acquisition deck box and simultaneously routed to a 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 in DataPlot.

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 in DataPlot 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; we only have the compiled executable file.  Data scans and tow summaries are printed on an inkjet printer located on the other side of DataPlot. 

Launch, Fishing, & Recovery -- The movable MOCNESS support frame (cart) will be used (as in the past).  On cruises not using trawl gear, the MOCNESS is launched and recovered from the stern grating.  We request that the deck crew construct a plywood platform (4' x 16') with 2" x 4" side rails to attach to the stern platform.  On these non-trawl cruises, the support frame will be secured to the deck near the net reel when not in use.  On cruises where trawling occurs, the MOCNESS is launched just forward of the trawl ramp and stored off the trawl way between the crane and sorting table.

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 fishing crew may be requested to assist in the deployment and recovery.

A scientist in DataPlot (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 displayed in DataPlot 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.  It may be necessary to remain on a course that minimizes waves coming up the stern trawl ramp during net washing.

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 Methot Trawl
The Methot trawl is deployed off the stern of the vessel (without the stern platform) using the Marco winch. A ScanMar acoustical depth sensor with readout in the trawl house will be used to receive real-time depth information.  A scientist or survey technician 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 30-40 m/min and retrieved at 20 m/min.  Tows will be oblique or stepped oblique, generally from 100 m to the surface.  Methot trawls may be conducted in daytime or at night with little or no advanced warning (where and when they will be done depends on plankton catches or acoustic sign).  Therefore, 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.

2.2.8 Midwater Trawl
Several Marinovich or Rope midwater trawls may be requested for examining predators.  Midwater trawls will be deployed using standard procedures for the gear requested.  The Chief Scientist or watch chief will decide trawl locations, times and depths.   As with the Methot trawls, the midwater trawls will be conducted day or night and will depend on plankton catches or midwater sign seen on the EK-500 echosounder.  Once a trawl is requested, regardless of the time of day, the fishing crew will need to be activated quickly, with little time lost.  A Furuno net sonde usually is mounted on the center of the headrope to provide real-time depth.  To record net depth and temperature with time, a microbathythermograph (MBT) or a Sea-Bird Electronics unit (SBE-39) can be mounted alongside the net sonde.

2.2.9 Tucker Trawl
The Tucker trawl may be used as the primary gear for late-larval surveys, as a backup for the MOCNESS, or for dedicated predator studies.  When used for late-larval surveys, it will have 0.505-mm mesh and be towed in a smooth oblique fashion with one net open.  When used as a backup MOCNESS sampler, it will have 0.333‑mm mesh netting and will be used in the standard manner.  Four Tucker tows are required to substitute for one oblique MOCNESS tow.  When used for predator studies, it will have 0.505-mm mesh with a 1‑mm codend bucket.  In all cases, the depth of the net will be monitored with the ScanMar quarterdeck hydrophone.  When used for discrete depth sampling, an electronic BKG or CTD/SeaCat will be attached.  The net is deployed at constant wire speed of 40 m/min to a desired depth.  The winch is stopped, and the net is 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.  Ship speed is adjusted to maintain a 45° wire angle during the entire tow.  When the nets reach the surface, they are brought aboard and hosed 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.

2.2.10 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.  The –70°C freezer is required for sample storage.

2.2.11 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.

2.2.12 EK-500 Monitoring
When requested, the Simrad EK-500 Scientific 38‑ and 120‑kHz echosounding system in the acoustics lab 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 echo sounder.  Because of the vast amount of data and paper generated by this system, the data logger and color printer should only be turned on 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 station data and file names in the notebook provided.  Files should be backed up onto optical disks and magnetic tape before the end of the cruise following instructions in the ARC manual.  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.  When data are being logged, the printers need to be checked every hour at a minimum.

2.2.13 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 are 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), presently the TSS POS/MV.  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 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 appropriate NMEA-0183 messages 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 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. Leica MX-412 (DGPS)

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, gyro data 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 for 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 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:  Occasionally, the ship may be requested to execute a backtrack-L calibration maneuver 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.

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 at other times when the ship is at anchor, requiring the cooperation of the ship's officers and engineering watch.

2.2.14 Radiometer

The Miller Freeman will be equipped with a radiometer to measure solar energy. The scientists will supply the calibrated instrument, mounting hardware and cable to run to DataPlot. The scientists will need the assistance of the ship's Electronic Technician and SCS Manager to correctly install the instrument and make sure that the data stream is being logged by the SCS.

3.0 FACILITIES AND EQUIPMENT

3.1 EQUIPMENT AND CAPABILITIES TO BE PROVIDED BY THE SHIP:
A complete list of equipment to be provided by the ship is contained in the FOCI Cruise Instructions for each cruise.

3.2 EQUIPMENT TO BE PROVIDED BY THE PROJECT:
A complete list of equipment to be provided by the program is contained in the FOCI Cruise Instructions for each cruise.

Additionally, the NOAA Ship Miller Freeman shall provide and/or service the following:

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 (see below).

Sensor identification, and data acquisition and logging parameters are specified in the system file SENSOR.DAT.  The ship's SCS manager shall maintain this file in a current state.  Specific FOCI requirements for the content of the SENSOR.DAT file are provided by the FOCI SCS Administrators at the start of the 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 is organized into several logical groupings according to intended post-cruise processing.  These logical groupings are specified by the FOCI SCS Administrators at the start of the 1997 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, the ship's SCS manager will archive data from disk files to CD for delivery to the project representative at the end of the cruise.  Additional recording of processed data may be requested of the ship's SCS manager; if so, specific instructions will be found in the Cruise Instructions.

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.  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.

The FOCI SCS co-administrators are:

Tiffany Vance: (206) 526-6767; e-mail: vance@pmel.noaa.gov
Dave Kachel: (206) 526-6195; e-mail: kachel@pmel.noaa.gov

3.4 SEACHEST AND UNCONTAMINATED SEAWATER:
Sea surface temperature, conductivity and fluorescence will be continuously sampled.  Data from the Sea-Bird thermosalinograph installed in the sonar void seachest shall be sent to the SCS.  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.

The ship’s SCS ASCII-Logger feature shall be configured to log one-minute averaged data throughout each FOCI cruise, including:
GPS Time
GPS Latitude
GPS Longitude
Water Depth in Meters
Seawater (seachest) temperature
Seawater (seachest) salinity
Laboratory Fluorometer voltage
Radiometer data (E m-2 s-1)
A standard template file specifying these data types shall be maintained for all FOCI cruises by the ship’s SCS manager.  ASCII Logger files will be included in the periodic backup of SCS data for distribution at the end of the cruise.  The Chief Scientist may request that these data be made available on DOS-formatted media at the completion of the cruise.

During 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 status display once per watch to determine that the instruments are functioning, and for taking salinity calibration samples every other day.

3.5 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 ship's 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 the configuration that FOCI has used in the past.  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 ship's personnel are requested to check the digital temperature display twice daily to insure that the operating temperature is below –60°C.  The unit will be locked between cruises, and a key left with the Chief Survey Technician.  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°C), and all frozen specimens should be transferred to it immediately, without thawing.  Kevin Bailey (206/526-4243, 4239; kevin.bailey@noaa.gov) must be notified.

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

4.0 DATA AND REPORTS

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 Directors of AFSC and PMEL 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 Directors, 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:
Marine Operations Abstracts,
Marine weather observation logs,
PMEL CTD weather observation logs,
CTD VHS videocassettes,
CTD Cast Information/Rosette Log,
Calibration sheets for all ship's instruments used,
Autosalinometer logs,
ADCP log sheets,
ADCP Iomega Zip,
SCS backup CD,
SeaPlot files, disk and hard copy.  NOS chart or overlay not required,
Ultra-cold freezer temperature daily log, (end of field season). 

4.2.1 Marine Observation Log: Ship's officers will maintain a Marine Operations Abstract (MOA) form during the cruise.  The critical information to record at each station is:
GMT date, 
GMT time, 
position, 
station #, 
haul #, 
gear type, and
bottom depth.

At present, a paper form (hard copy) MOA is the most secure method for ensuring that these data are recorded and preserved.  However, FOCI is willing to work with MOC-Pacific to develop an electronic version that is efficient, secure and could eventually replace the paper MOA.

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 Scientist.  The requirement to plot on NOS nautical charts 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 GPS satellite, radar range and bearing, and visual fixes.

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

Complete meteorological observations will be logged on 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 Kevin Bailey (AFSC) upon the ship's return to Seattle.

4.3 EVALUATION REPORT:  One Ship Operations Evaluation Report is required for each leg of the primary project only, using the form provided by the ship for that purpose.   The Chief Scientist will complete the report and submit it to their Lab or Center Director for forwarding to OMAO. 

5.0 ADDITIONAL INVESTIGATIONS AND PROJECTS

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 or in the specific FOCI instructions pertaining to the cruise.  The Chief Scientist will be responsible for determining the priority of additional work relative to the main project.

5.2 ANCILLARY PROJECTS:
Ancillary tasks will be accomplished in accordance with the NOAA Fleet Standing Ancillary Instructions.

5.3 PIGGYBACK PROJECTS:
See FOCI Cruise Instructions

6.0 MISCELLANEOUS

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

6.2 PRECRUISE MEETING:
A pre-cruise 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 operations area for the purposes of:
1.  introducing new scientific personnel to ship's procedures, proper channels, etc.;
2.  discussing operating procedures for deploying various pieces of sampling equipment; and
3.  coordinating scientific watch assignments.

6.3 POST-CRUISE DEBRIEFING:
A 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.

6.4 MEALS:
There is no charge to scientists for meals aboard NOAA vessels.

6.4.1 Midnight Lunches:  The scientific staff will work 12-hour watches (12 to 12).  A microwave oven will be available to reheat meals requested to be set aside for the watch.  

7.0 COMMUNICATIONS

7.1 METHODS AND PROGRESS REPORT:
The Miller Freeman does not maintain an exact JFT schedule w/ MOC-Pacific.  E-mail is used more often.  Radio contact will be maintained when possible. The Chief Scientist will send a scientific progress report to his or her respective Field Operations Leader via INMARSAT voice, Fax, or e-mail at least once a week.

7.2 USE OF RADIO TRANSCEIVERS:
Because 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 RECEIVING SCIENTIFIC STATUS REPORTS:
The Chief Scientist may anticipate the need for daily reports on the position of satellite drifters in the study area and on the status of biophysical mooring(s).  These will be sent either by Fax from PMEL over INMARSAT or over Internet from PMEL to the MOC-Pacific radio room and forwarded to the ship via JFT.

7.4 IMPORTANT PHONE NUMBERS, FAX NUMBERS AND E-MAIL ADDRESSES:

PMEL
OERD2 (FOCI):
206-526-4700 (voice)
206-526-6485 (fax)
Admin:
206-526-6810 (voice)
206-526-6815 (fax)
E-Mail: 	LastName@pmel.noaa.gov  OR  FirstName.LastName@noaa.gov

AFSC
RACE (FOCI):
206-526-4171 (voice)
206-526-6723 (fax)
E-Mail:	FirstName.LastName@noaa.gov

MILLER FREEMAN (The telephone methods listed here are in order of increasing expense)
Home port (Seattle, WA) – 206-553-4589, 4581, 8344
Cellular (First dial the roamer code, wait for dial tone, then dial cellular number.): 
Ship's cell number	206-660-7167
Roamer codes:
907-391-7626 - Dutch Harbor, AK 
907-528-7626 - Kodiak, AK 
907-321-7626 - Juneau, AK 
907-399-7626 - Homer, AK 
907-752-7626 - Sitka, AK 
907-254-7626 - Petersburg / Ketchikan, AK 
907-229-7626 - Anchorage, AK 
Inmarsat Mini-M
011-872-761-267-346 (voice/pbx)
011-872-761-267-347 (voice)
011-872-761-267-348 (fax)
Inmarsat B
011-872-330-394-113 (voice)
011-872-330-394-114 (fax)
E-Mail:	NOAA.Ship.Miller.Freeman@ noaa.gov (mention person's name in SUBJECT field)

Marine Operations Center, Pacific
Voice	206-553-4548
E-Mail:	FirstName.LastName@noaa.gov
E-Mail to radio room:	Radio.Room@noaa.gov

FOCI contacts: 
Dr. Phyllis Stabeno -PMEL- 206-526-6453; phyllis.stabeno@noaa.gov 
Dr. Jeffrey G.  Napp -AFSC- 206-526-4148; jeff.napp@noaa.gov

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 $6.02 per minute 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 CELL PHONE:
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.  The Scientific Party should keep a complete phone log (INMARSAT and cellular) for all calls, and turn it over to the Miller Freeman Executive Officer.

APPENDIX. FOCI SCS Sensor Specification