CRUISE REPORT:  SR01b
(Updated DEC 2016)






Highlights

                            Cruise Summary Information

               Section Designation  SR01b
                             alias  JR15003
Expedition designation (ExpoCodes)  74JC20151217
                  Chief Scientists  Yvonne Firing / NOC
                             Dates  2015 DEC 17 - 2016 JAN 13
                              Ship  RRS James Clarke Ross
                     Ports of call  Port Stanley, Falkland Islands -South Powell 
                                    Island - Signy Island - Coronation Island - 
                                    Rothera Research Station - Verndasky 
                                    Research Base - Port Stanley

                                                       54° 40' S
             Geographic Boundaries  70° 10' 14.8" W                54° 35' 16"W
                                                     67° 48' 13" S

                          Stations  28
      Floats and drifters deployed  4 SOCCOM floats deployed
    Moorings deployed or recovered  0

                                Contact Information:
                                   Yvonne Firing 
                     National Oceanography Center, Southampton
                 Tel: 02380 599669 • email: yvonne.firing@noc.ac.uk



















National
Oceanography Centre
NATURAL ENVIRONMENT RESEARCH COUNCIL








                       National Oceanography Centre Cruise

                                  Report No. 38

                       RRS James Clark Ross Cruise JR15003

                              17 DEC – 13 JAN 2016
                 Hydrographic measurements on GO-SHIP line SR1b
                  and investigations of circulation and isotope
                       cycles in coastal West Antarctica

                              Principal Scientist
                                    Y Firing






                                      2016










National Oceanography 
Centre, Southampton 
University of Southampton 
Waterfront Campus European Way
Southampton Hants 
SO14 3ZH 
UK

Tel: +44 (0)23 8059 9669
Email: yvonne.firing@noc.ac.uk


© National Oceanography Centre, 2016



DOCUMENT DATA SHEET

AUTHOR                                                               PUBLICATION
    FIRING, Y et al                                                  DATE   2016
TITLE
    RRS James Clark Ross Cruise JR15003, 17 Dec 2015 - 13 Jan 2016. 
    Hydrographic measurements on GO-SHIP line SR1b and investigations of 
    circulation and isotope cycles in coastal West Antarctica.
REFERENCE
    Southampton, UK: National Oceanography Centre, Southampton, 41pp.
    (National Oceanography Centre Cruise Report, No. 38)
ABSTRACT
    This cruise comprised work contributing to five projects. The 
    twenty-first complete occupation of the Drake Passage GO-SHIP 
    section SR1b obtained full-depth temperature, salinity, and 
    lowered ADCP velocity profiles at 28 stations, along with underway 
    measurements, with the objectives of investigating and monitoring 
    interannual variability and trends in Antarctic Circumpolar 
    Current structure and property transports and Southern Ocean water 
    mass properties. Turnarounds of bottom pressure recorder (BPR) 
    moorings contributed to the long time series of bottom pressure in 
    Drake Passage.

    Biogeochemically-equipped Argo floats were deployed as part of the 
    Southern Ocean Carbon and Climate Observations and Modelling (SOCCOM) 
    project to increase climate-quality observations in the Southern Ocean. 
    Gliders were deployed over the Western Antarctic Peninsula continental 
    shelf to measure properties and circulation with the aim of 
    understanding flow and mixing of warm waters onto the shelf. 
    Hydrographic profiles and water column and sediment samples taken over 
    the continental shelf will be used to investigate stable isotope 
    nutrient cycling processes.






KEYWORDS

ISSUING ORGANISATION  National Oceanography Centre
                      University of Southampton Waterfront Campus
                      European Way
                      Southampton SO14 3ZH    UK
                      Tel: +44(0)23 80596116  Email: nol@noc.soton.ac.uk
A pdf of this report is available for download at: http://eprints.soton.ac.uk





Contents

1  Personnel                                                                  6
2  Itinerary and Cruise Track                                                 7
3  Objectives                                                                 7
4  Narrative                                                                  8
5  Slocum glider deployments                                                 10
   5.1  Glider 438                                                           11
   5.2  Glider 331                                                           11
6  CGS: Understanding the cycling of stable isotopes in coastal Antarctic 
        waters                                                               12
   6.1  Objectives                                                           12
   6.2  Project report                                                       12
   6.3  Comments and recommendations                                         13
7  Continuous Ocean Monitoring Methods: Drake Passage                        14
8  Hydrographic Measurements                                                 14
   8.1  CTD Systems Operation                                                15
8.1.1  CTD operation and processing                                          15
8.1.2  Data Processing                                                       16
   8.2  Water Sample Analysis                                                17
   8.3  Data calibration                                                     19
   8.4  Lowered Acoustic Doppler Current Profiler (LADCP)                    19
        8.4.1  Instrument setup and performance                              19
        8.4.2  Data processing                                               20
   8.5  References                                                           22
9  SOCCOM (Southern Ocean Carbon and Climate Observations and Modeling) 
          float deployments and CTD stations                                 23
   9.1  Float Deployments                                                    23
   9.2  CTD/Rosette Sampling                                                 24
   9.3  Dissolved Oxygen                                                     24
   9.4  Sampling and Data Processing                                         24
   9.5  Equipment and Techniques                                             24
   9.6  Volumetric Calibration                                               25
   9.7  Standards                                                            25
   9.8  pH/Alkalinity                                                        25
   9.9  Nutrients                                                            25
   9.10  Salinity                                                            25
   9.11  HPLC and POC                                                        25
   9.12  References                                                          26
10  Underway Data Collection and Processing                                  26
    10.1  Computing and SCS data processing                                  26
          10.1.1  Configuration of linux workstation ’fola’                  26
          10.1.2  SCS data streams                                           27
          10.1.3  Access to SCS data                                         27
          10.1.4  The mscs source directory                                  29
    10.2  Underway surface water sampling                                    29
          10.2.1  Underway surface thermosalinograph                         29
    10.3  Surface water sampling for Nd isotope analysis                     30
    10.4  Daily processing of SCS streams                                    30
          10.4.1  Navigation                                                 30
          10.4.2  Surface meteorological sampling (SURFMET)                  31
          10.4.3  Bathymetry                                                 31
          10.4.4 EA600                                                       32
          10.4.5 EM122                                                       32
          10.4.6  Chernikeef EM log                                          33
    10.5  Vessel Mounted ADCP                                                33
          10.5.1  Real-time data acquisition and VMDAS files                 33
          10.5.2  Settings                                                   34
11  Instrumentation, extracted from AME Report                               35
12  Acknowledgments                                                          36
CCHDO Data Processing Notes                                                  37


List of Figures

 1  JR15003 cruise track with glider deployment sites (red 
    triangles), CGS CTD sites (filled green circles), CGS underway 
    surface Nd sampling (open green circles), BPRs (gray stars), 
    SR1b CTD sites (magenta squares), and float deployment sites 
    (black square outlines).                                                  8
 2  Calibrated temperature on SR1b, with bottle firings (corresponding 
    to SBE35 samples) shown by black circles and float deployment 
    stations by squares.                                                     22
 3  Calibrated salinity on SR1b, with bottle salinity samples shown by 
    black circles and float deployment stations by squares.                  22
 4  Calibrated dissolved oxygen on SR1b, with bottle oxygen samples shown 
    by black circles and float deployment stations by squares.               22
 5  Profiles of zonal (top) and meridional (bottom) velocity from 
    LADCP at each station in Drake Passage, offset to the latitude 
    of that station, with dashed zero lines. Right hand panels show 
    northern profiles including the Subantarctic Front jet, with a 
    common zero line.                                                        22

List of Tables

 1  CGS CTD and sediment core sites.                                         12
 2  CTD stations times and positions, with number of bottle salinity and 
    oxygen samples obtained for calibrating CTD sensors.                     14
 3  LADCP deployment commands, contained in JR15003 ladcp.cmd.               20
 4  SOCCOM floats with deployment times and positions.  I = ice enabled; 
    O = oxygen sensor; N = nitrate sensor; F = fluorometer (WetLabs 
    FLBB); p = pH sensor                                                     23
 5  Times (from log sheet) and locations (from ship track) of surface 
    water samples for Nd isotope analysis                                    30
 6  Lab instruments used                                                     35
 7  Acoustic instruments used                                                35
 8  Oceanlogger                                                              35
 9  CTD                                                                      35
10  AME unsupported instruments logged                                       36









1  PERSONNEL

Scientific Personnel

Yvonne Firing (Principal Scientist)  NOC 
Alexander Brearley                   BAS
Sian Henley                          U Edinburgh
David Byrne                          NOC, U Liverpool
Lucie Cassarino                      U Bristol
Tianyu Chen                          U Bristol
Casimir de Lavergne                  LOCEAN
Damien Desbruyeres                   NOC
Jennifer Mecking                     U Southampton
Daniel Schuller                      Scripps Institution of Oceanography 


Technical Personnel

Johnny Edmonston                     BAS IT
Paul Morgan                          BAS AME


Ship’s Personnel

Graham Chapman                       Master
Simon Wallace                        Chief Officer
Christopher Hipsey                   2nd officer
Georgina Delph                       3rd Officer
Harry Taylor                         3rd Officer
Charles Waddicor                     ETO Comms
Luke Parnell                         Chief Engineer
Edel Trearty                         2nd Engineer
Stephen Gardiner                     3rd Engineer
Steven Eadie                         4th Engineer
Simon Wright                         Deck Engineer
Julian Klepacki                      ETO
James Gibson                         Purser
Tim Osborne                          Doctor
George Stewart                       Bosun/Sci Ops
Clifford Mullaney                    Bosun
John O’Duffy                         Bosuns Mate
Kevin Cambell                        AB
Colin Leslie                         AB
Lasse Pedersen                       AB
Martyn Dyer                          AB
Stephen Pictor                       Motorman
Kristian Bates                       Motorman
Padraig Molloy                       Chief Cook
Brian Robertson                      2nd Cook
Derek Lee                            Senior Steward
James Newall                         Steward
Thomas Patterson                     Steward
Roger Route                          Steward



2  ITINERARY AND CRUISE TRACK

JR15003 sailed from Port Stanley, Falkland Islands on 17 December 2015, 
called at three of the South Orkney Islands December 20-22, at Rothera 28 
December - 2 January, 2016, at Vernadsky on 4 January, and returned to Port 
Stanley on 13 January 2016. Science operations were conducted on both the 
southbound leg along the western Antarctic Peninsula between 24 December 
and 28 December, and the northbound leg in Drake Passage between 6 January 
and 11 January, along with standard underway sampling during much of the 
time at sea. The cruise track and sites of science work are shown in Figure 2.



3  OBJECTIVES

RRS James Clark Ross cruise JR15003 included work contributing to five projects: 

• What causes the influx and mixing of warm waters on polar ocean shelves?
  A Brearley, M Meredith, and M Inall, BAS 
  To deploy gliders to measure water mass properties and circulation on 
  the West Antarctic Peninsula continental shelf.

• Understanding the cycling of stable isotopes in coastal Antarctic waters
  K Hendry and L Cassarino, U Bristol; S Henley, U Edinburgh; Y Firing, 
  NOC; R Mills and T Stichel, U Southampton; M Meredith, BAS
  To sample the stable isotope composition of nitrogen, silicon, and 
  neodymium through the water column and in the upper sediments in order 
  to understand the key biological and non-biological processes setting 
  these profiles in different parts of the western Antarctic Peninsula 
  continental shelf.

• Continuous Ocean Monitoring Methods: Drake Passage 
  S Mack, NOC
  To maintain the long time-series of transport through Drake Passage by 
  recovering and redeploying two bottom pressure recorders (BPRs), one on 
  either side of the passage.

• Hydrographic measurements in Drake Passage 
  Y Firing, NOC
  To make high-quality repeat hydrographic measurements on GO-SHIP line 
  SR1b, continuing a near-annual time series begun in 1993, as part of 
  the Drake Passage repeat hydrography National Capability programme 
  designed to monitor Southern Ocean watermasses and Antarctic Circumpo- 
  lar Current volume and property transport; to obtain complementary 
  station and underway currents and underway meteorology.

• Southern Ocean Carbon and Climate Observations and Measurements (SOCCOM)
  L Talley and A Dickson, Scripps Institution of Oceanography; S Riser, U 
  Washington; K Johnson, MBARI; E Boss, U Maine; R Feely, NOAA PMEL; L 
  Juranek, Oregon State U; J Sarmiento and   R Key, Princeton U
  To increase the sampling of physical and biogeochemical parameters in 
  the Southern Ocean by deploying four biogeochem-equipped Apex floats 
  and acquiring climate-quality calibration measurements.

The glider work was funded by NERC. The BPR and hydrography components are 
part of National Capability projects funded by NERC. The isotope cycling 
experiment was funded by NERC through the BAS Collaborative Gearing Scheme 
(CGS, now Collaborative Antarctic Science Scheme). SOCCOM is funded by the 
USA National Science Foundation and float deployment was performed 
opportunistically alongside the NERC-funded hydrography.


Figure 1: JR15003 cruise track with glider deployment sites (red 
          triangles), CGS CTD sites (filled green circles), CGS underway 
          surface Nd sampling (open green circles), BPRs (gray stars), SR1b 
          CTD sites (magenta squares), and float deployment sites (black 
          square outlines).


4  NARRATIVE
   Yvonne Firing
   
JR15003 sailed from Port Stanley, Falkland Islands the evening of 17 
December 2015 in calm conditions, headed for the South Orkney Islands. 
Underway data logging, including VMADCP and tsg, commenced on 18 December. 
It took a bit of trial and error to find a useable configuration of the 
acoustic sampling run through the k-sync program, as the previous year’s 
configuration did not seem to work. The ship called at South Powell Island 
on 20th December, dropping off a field party of three, and allowing some of 
the scientists and fids to visit the island for a few hours. At Signy the 
following day four fids disembarked, and most science and passengers 
visited the station, where we were kindly provided with a tour of the area. 
Finding and setting up a camp at Coronation Island on 22 December proved 
challenging due to ice conditions (which slowed operations around the South 
Orkneys in general), but in the end the two scientists and their gear 
were landed and settled in. Late on the 22nd we were again underway headed 
for the first planned glider deployment site off Anvers Island. Some wind, 
sea, and swell were encountered on the 24th, and the VMADCP was turned off 
in favour of obtaining swath bathymetry data along a new track.
   
Due to ice conditions the JCR took a course outside Anvers Island, and we 
decided to move the first glider deployment location and CTD/sediment 
core site from Palmer Deep to off the western tip of Anvers Island. The 
first glider deployment, in the early hours of 25 December, went smoothly, 
with a successful test dive. We did a CTD cast including water sampling for 
nutrients and trace metals adjacent to the glider deployment site, 
followed by a sediment core. However, as we were continuing southward 
several hours later, the glider data indicated that it had leaked.  We 
therefore returned to recover it, and deployed the second glider at that 
site. A forensic examination of the first glider did not reveal a reason 
for the leak. Up-to-date satellite imagery was limited due to cloud cover 
but appeared to indicate continued heavy ice over the continental shelf; 
therefore we abandoned plans to deploy a second glider and CTD with 
nutrient sampling between Anvers and Adelaide and attempted to go around 
the ice until closer to Adelaide Island. Progress toward Rothera was slow 
through 3/10 to 8/10 ice, exacerbated by a problem with one of the two 
main engines. Our next planned CTD site was completely ice-covered but we 
found open water just 6 kilometers to the southeast, and were able to 
conduct a CTD cast and sediment core at a comparable depth there on 27th 
December.
   
As the first glider hull appeared to be in good shape and the electronics 
undamaged, o-rings were changed and it was decided to deploy it in Ryder 
Bay for test dives, with the hope that it could then be sent out onto the 
shelf to complete some of the original sampling plan throughout the summer. 
Upon our arrival in Ryder Bay early on the morning of the 28th, we found 
that our last southbound CTD site, the RaTS site, was also too icy, and 
therefore moved to the backup RaTS site a few km away to redeploy the first 
glider and do a CTD cast and sediment core. On the first two core attempts 
a small rock was stuck in the corer jaws, so the sediment leaked out; 
however the third attempt recovered enough mud to work with.
   
The JCR was alongside at Rothera from 28th December to 2nd January, 2016, 
performing cargo resupply for the station. The NOCL technicians also 
serviced the Rothera tide gauge during this call.   Due to ice damage to 
the wharf the fore and aft decks had to be offloaded separately. The 
station personnel generously organised crevassing and skiing expeditions 
for the ship party and welcomed us to their New Year’s Eve celebrations as 
well as dinner exchanges with outgoing and incoming winterers. During the 
Rothera call the glider in Ryder Bay became stuck under ice, but otherwise 
at first appeared to be functioning as designed. On the 1st, however, the 
leak detect flagged again. The glider was therefore recovered by the JCR 
upon departure from Rothera on the morning of 2nd January.
   
We then headed offshore, emerging from the ice late on the 3rd, and 
coming into Verndasky the morning of the 4th. There the NOCL technicians 
serviced the tide gauge and the science party, officers, and crew were 
treated to the station hospitality. We departed Vernadsky on the evening of 
the 4th and passed Elephant Island early on the 6th. The SR1b CTD stations 
were begun at 0600 on the 6th. CTD casts over the slope were only conducted 
to 30 m above the bottom due to fluctuating echosounder depth readings.   
The SACCF appears to have been relatively far south, as the influence of 
CDW was visible early on, before SR1b site 6 (cast 009). At this point it was 
discovered that the LADCP beam 2 had been bad (unnoticed earlier, as 
reasonable solutions were still obtained from 3 beams). The LADCP was switched 
for the spare unit before cast 007.
   
The south slope BPR at first did not respond to acoustic transmissions, 
but did respond to the ship’s transponder, implying an issue with the NOCL 
deck unit. Following this the release and recovery, and deployment of the 
replacement, went smoothly.
   
The CTD power cable between the rosette swivel and the CTD had to be 
replaced as it was smashed (broken connector and bent pin) just below the 
swivel, apparently due to hitting the insufficiently-opened roller door over 
the water sampling bay. The data do not appear to have been affected.
   
Floats were deployed following CTD casts 009, 012, 016, and 020 (SR1b 
sites 6, 9, 13, and 17). In addition to the calibration water samples taken 
at the four float deployment stations, oxygen samples were taken at 11 
additional sites (casts 004, 006, 008, 010, 011, 015, 017, 019, 021, 028 
and 029) for calibration of the CTD oxygen sensor.
   
Following some misfired bottles on early casts we decided to rinse and 
clean the bottle carousel more frequently. The CTD secondary temperature 
and conductivity sensors on cast 016 looked bad, but the problem was solved 
by flushing with a detergent solution.
   
In mid-passage the passage the weather worsened, with forecasts 
predicting rougher conditions to-  ward the end of our science time. We had 
a weather delay of approximately 4 hours on the 8th, moving on after the 
10th SR1b station (13th cast of the cruise) to a station halfway between 
the originally-planned 11th and 12th SR1b stations, and then to the 
originally-planned 13th station (thus, a spacing of 2 rather than 3 
stations over 70 km). Following this, with the forecast still predicting 
more heavy weather, station spacing was increased from the nominal 20 nm to 
25 nm to make progress across the passage.
   
We stopped work and hove to for weather mid-day on the 10th, stopping the 
underway sampling at approximately 2000Z as we approached the Argentine 
EEZ. We resumed at 0900Z on the 11th with a CTD cast in 2200 m, still in 
some wind and swell. As the conditions were then improved enough to 
consider BPR operations, we first visited the BPR at 2000 m to check its 
communications and battery levels, which were good. We then moved on to the 
1000 m BPR, which was successfully recovered and replaced. A nearby BPR 
which failed to release in 2013 proved to be still communicating, but did 
not release. CTD stations were resumed starting at 1700 m, and finished at 
2100 on 11 January. The swell picked up for our steam over Burdwood Bank, 
supplying additional liveliness to the end-of- cruise festivities, but by 
the following day wind and seas had abated enough for the ship to take care 
of unwinding and respooling a winch cable from a previous cruise. We 
returned to Port Stanley the morning of the 13th.



5  SLOCUM GLIDER DEPLOYMENTS
   Alexander Brearley, Alvaro Lorenzo Lopez

   
Two Slocum gliders from the National Marine Equipment Pool were deployed 
on the southbound leg of JR15003, as part of the project “What causes the 
influx and mixing of warm waters on polar ocean shelves?”, led by Alexander 
Brearley. The first glider, serial number 438 and named Frazil, 
incorporated pumped Seabird CTD, WetLabs Ecopuck, Satlantic PAR sensor, 
Aanderaa oxygen optode and thruster.  The second, serial number 331 and 
named Coprolite, incorporated unpumped Seabird CTD, WetLabs Ecopuck and 
oxygen optode. Both gliders had previously been ballasted in Oban during 
the BAS trials week on 22 to 26 June 2015. Standard functional checkouts 
were completed on the transit south from Stanley at the start of the 
cruise.




5.1  Glider 438
   
It was initially planned to deploy 438 in Palmer Deep, and 331 just to 
the northwest of Adelaide Island. However, inspection of in situ ice 
conditions and SAR satellite images of the Peninsula revealed extensive sea 
ice close to the planned deployment sites. The first deployment site was 
thus moved to west of Anvers Island and Glider 438 was deployed at 
64°30.478S, 64°50.868W at 0430Z on 25 December 2015. The ice coping 
software was loaded onto the gliders using loadmission ice.mi, and the 
mission filename for this season is shelf.mi. A concurrent CTD was 
completed at the site.
   
Unfortunately, at 0956Z, the glider aborted for a leak in the aft 
compartment. The JCR scrambled   and recovered the glider at 1454Z on 25 
December 2015. Subsequent inspection of the aft compartment revealed a 
trickle of salt crystals from close to the rear leak detector into the rear 
hull, and a significant pool of water sitting under the Teflon protecting 
the steatite battery.  No evidence of O-ring damage was apparent, but we 
removed and changed out all the aft compartment O-rings as a precaution. As 
we had not definitively determined the root cause of the leak, we decided 
to redeploy in Ryder Bay where small-boat support was available from 
Rothera.
   
The glider was redeployed at 67034.476S, 68008.392W on 28 December 2015 at 
0910Z (immediately before the final CTD site). We chose two closely spaced 
waypoints in Ryder Bay. Unfortunately, after two dives, the glider became stuck 
under a layer of sea ice, and no communications were received until 0541Z on 29th 
December (abort for MS ABORT NO TICKLE ICE). By this time, the glider had 
drifted significantly to a point between Leonie and Kirsty Island. Efforts 
to get the glider back into Ryder Bay were inhibited by further glider 
aborts for the thruster and digifin (presumably because both became stuck in 
ice). The glider finally returned to deep water around 2000Z on the 29th 
December, but aborted again for a leak in the aft compartment at round 
2130Z at 277 m depth. An unsuccessful attempt to recover the glider was 
made early on the 30th using the Rothera rib Nimrod, but the site could not 
be reached because of heavy sea ice. Leaving the glider on a surface 
callback script, we tracked the glider as it drifted quickly southwards 
over the next three days (on lastgasp.mi), ultimately reaching a position 
to the south of Adelaide Island. By this stage, we were concerned that the 
glider was approaching a line of heavy sea ice, beyond which it may have 
become unrecoverable. We thus programmed the glider to do shallow dives 
(initially to 10 m, later to 100 m, with 3 yos) to prevent further 
southward drift. The glider was collected by the JCR after its departure 
from Rothera after relief, at around 1345Z on January 2nd, at a position of 
67°59.567S, 68°23.449W. The source of the leak has still not been 
identified, so we will conduct a closer analysis once back in the UK.


5.2  Glider 331
   
It had initially been planned to deploy 331 to the northwest of Adelaide 
Island.  However, upon the failure of 438, it was deployed close to the 
original deployment position of 438, at 64°28.700S, 64°50.787W at 1600Z. No 
significant issues were encountered with 331 during the duration of the 
cruise, other than the altimeter terminating dives slightly early (⇠100-200 
m from the bottom). We resolved this by setting:

sensor: u alt reqd good in a row(nodim)    5
in the yo11.ma file.


Piloting logs

Piloting notes for each glider were maintained on the Cambridge dockserver, 
Under /home/localuser/438 pilot log and /home/localuser/331 pilot log.




6  CGS: Understanding the cycling of stable isotopes in coastal Antarctic waters
   Sian Henley, Lucie Cassarino, Tianyu Chen, Yvonne Firing


6.1  Objectives

The aim of this CGS project was to examine the biogeochemical cycling of 
silicon (Si) and nitrogen (N) in surface waters, throughout the water column and 
in sediments along the west Antarctic Peninsula. Stable isotopic signatures of 
silicon and nitrogen in each of the different biogeochemical system components 
will be used to understand biological production, remineralisation and nutrient 
recycling processes occurring during sinking and sedimentation of organic 
matter. Neodymium (Nd) isotopes will be used to trace relevant water masses 
and local freshwater inputs, with relevance for trace metal fluxes to the 
water column. These two work packages combined will inform on processes 
influencing biological drawdown of carbon in this climatically and 
environmentally-sensitive region, as well as providing insight into the 
past.


6.2  Project report
   
Water column sampling and sediment box-coring were conducted at three 
sites along the Antarctic Peninsula, listed in Table 1 and shown in Figure 2.


Table 1: CGS CTD and sediment core sites.

             Station   Latitude     Longitude   Depth (EM122)
             -------  -----------  -----------  -------------
               001    64 30.5391S  64 50.8731W      594 m
               002    66 50.9766S  70 09.9624W      565 m
               003    67 34.9440S  68 08.7666W      388 m
   
   
Water column samples were taken in full depth profiles and were processed 
in the main laboratory. Oxygen isotope samples were taken first, followed 
by nutrients, particulates, Nd isotopes and salts. Oxygen isotope samples 
were taken into glass bottles, which were crimp-sealed immediately and 
stored in the dark at +4C. Nutrient samples were filtered through 0.2 um 
supor membrane filters. Nutrient and nitrate isotope samples were snap-
frozen at -80C then stored at -20C. Silicic acid samples were stored    in 
the dark at +4C. Particulate organic carbon (POC) and nitrogen (PON) 
samples were obtained by filtration using GF/F filters and a custom-built 
overpressure system. Samples were snap-frozen at -80C and stored at -20C. 
This large volume filtration was also conducted using polycarbonate 
filters; filtrate was acidified with HCl (1mL/L) and stored in the dark 
for Nd isotope analysis, whilst filters were stored in the dark at +4C for 
biogenic silica analysis. Salts samples to calibrate the shipboard CTD were 
taken into glass bottles, brought to room temperature at least overnight 
and analysed onboard using the ships Guildline Autosal instrument 
(described in Section 8.2).
   
Upper sediment samples were collected at each CTD station by box-coring. 
Interface waters were collected immediately, then sub-cores were taken from 
the box core for pore fluid extraction and core sectioning. Pore fluids 
were extracted using rhizon syringe filters every 2 cm and were stored for 
analysis of nutrient concentrations, Si isotopes and N isotopes as for sea 
water samples. Separate cores were sectioned in 2 cm intervals, and stored 
at +4C, for analysis of sedimentary Si and N isotopes.
   
All samples have been processed and shipped back to the UK for analysis. 
As such, there are no preliminary results to be included in this cruise 
report.


6.3  Comments and recommendations
   
CGS-109 was completed successfully as part of cruise JR15003. Ice 
conditions dictated that all three proposed sites had to be moved, but this 
was done in consultation with the Captain, and without compromising the 
scientific objectives. A fourth water column sampling station was lost due 
to logistic constraints, but this again did not compromise the objectives 
set out in the bid.
   
All sampling and processing was completed successfully within the time 
constraints of the cruise.  Large volume filtration of water column samples 
was time-consuming and could be optimised for future work of this type. 
Nutrient filtrations were complete within one hour of sampling and POC 
filtrations were complete within four hours.  Samples were kept in the 
dark at +4 C to limit biological activity and upper ocean samples were 
processed first. For Station 001, Nd and biogenic silica filtrations were 
completed within 12 hours of sampling. For Stations 002 and 003, samples 
were kept in the dark at +4 C and were processed within 36 hours of 
sampling. For future cruises where samples for both biogenic silica and Nd 
are required, a recommendation would be that these filtrations should not 
be combined. Nd samples should be filtered through large-diameter filters, 
due to their large volume requirement, whilst biogenic silica samples 
should be filtered using 25 mm polycarbonate filters.
   
Box cores were taken successfully at all three stations. At Station 003, 
three attempts were necessary to take a successful box core, due to rocks 
preventing full closure on the first two attempts. More detailed echo-
sounding using the TOPAS system onboard JCR might be used in future to 
prevent this occurrence, although the presence of small dropstones is an 
inevitable possibility in the nearshore Antarctic.
   
All samples are expected to be analysed and the data available 24 months 
from sampling, in agreement with NERC protocols.




7  CONTINUOUS OCEAN MONITORING METHODS: DRAKE PASSAGE
   Jeff Pugh and Emlyn Jones

   
A BPR was recovered and a new one deployed at both the south and north 
sides of the passage. Communications with the BPR at 2000 m on the northern 
slope were successful. Details are available    in NOC cruise report No. 
58, “Sea Level and Bottom Pressure Measurements in Drake Passage and the 
Southern Ocean”.




8  HYDROGRAPHIC MEASUREMENTS
   Yvonne Firing

   
The 31 CTD casts, including 3 contributing to the CGS project and 28 on 
SR1b, are summarised in Table 2.


Table 2:  CTD stations times and positions, with number of bottle salinity 
          and oxygen samples obtained for calibrating CTD sensors.

                 Bottom                               CTD
                  time                        water   max   N      N
stn    date      (UTC)   latitude  longitude  depth  press   salt   oxy
---  ----------  ------  --------  ---------  -----  -----  -----  ----
 1   2015/12/25  06:12   -64.5090   -64.8479    589    587     6     0
 2   2015/12/27  06:12   -66.8497   -70.1708    566    562     6     0
 3   2015/12/28  10:12   -67.8036   -68.8146    387    383     6     0
 4   2016/01/06  09:01   -61.0500   -54.5878    361    356     6     6
 5   2016/01/06  11:01   -60.9811   -54.6299    582    580     6     0
 6   2016/01/06  13:01   -60.8502   -54.7102    974    975     8     6
 7   2016/01/06  18:01   -60.8332   -54.7217   1735   1731    10     0
 8   2016/01/06  20:01   -60.7995   -54.7424   2649   2664     8     6
 9   2016/01/07  01:01   -60.6666   -54.8248   3094   3136    24    24
10   2016/01/07  06:01   -60.3333   -55.0313   3437   3489    12     6
11   2016/01/07  11:01   -60.0112   -55.2300   3496   3548    11     7
12   2016/01/07  16:01   -59.6667   -55.4444   3674   3732    23    24
13   2016/01/07  20:01   -59.3332   -55.6512   3755   3815    12     0
14   2016/01/08  01:01   -58.9998   -55.8581   3776   3833    12     0
15   2016/01/08  10:01   -58.5246   -56.1543   3787   3845    10     6
16   2016/01/08  16:01   -58.0500   -56.4466   3970   4035    23    23
17   2016/01/08  21:01   -57.6537   -56.6892   3467   3518    12     6
18   2016/01/09  02:01   -57.2588   -56.9334   3949   4013    12     0
19   2016/01/09  08:01   -56.8639   -57.1778   3014   3053    12     6
20   2016/01/09  13:01   -56.4685   -57.4128   3826   3886    24    24
21   2016/01/09  18:01   -56.0756   -57.6656   3847   3908    13     6
22   2016/01/10  00:01   -55.6817   -57.9093   4524   4604    11     0
23   2016/01/10  04:01   -55.5167   -57.9829   4211   4279    12     0
24   2016/01/10  09:01   -55.2154   -57.9622   3928   3985    12     0
25   2016/01/10  12:01   -55.1686   -57.9680   3106   3148    11     0
26   2016/01/10  15:01   -55.1171   -57.9682   2691   2721     8     0
27   2016/01/11  10:01   -55.0685   -57.9750   2186   2209     8     0
28   2016/01/11  12:01   -55.0067   -57.9782   1673   1683     8     8
29   2016/01/11  17:01   -54.9779   -57.9827   1062   1063     8     8
30   2016/01/11  18:01   -54.9224   -57.9825    712    711     6     0
31   2016/01/11  20:01   -54.6668   -57.9830    166    158     4     0


8.1  CTD Systems Operation
  
One stainless steel CTD system was prepared with a 24-way carousel. The 
details of the instrumentation are given in Section 11.
   
The instrumentation on the underwater package operated normally on the 31 
stations conducted during the cruise, with two exceptions. 1) During 
station 16, both temperature and conductivity sensor pairs diverged. 
Comparison with bottle salinity data showed that the secondary sensor was 
in error, and as the processed data default to using the primary sensor, 
no change to processing was required. Flushing with a detergent solution 
fixed the problem, so no further action was taken. 2) One beam of the 
LADCP was not functioning (zero amplitude) during the first four casts; 
the LADCP was switched for a backup unit (see Section 11).


8.1.1  CTD operation and processing

Data were acquired with SeaSave V 7.22.3.
   
SBE35 temperature data were uploaded using SeaTerm immediately after 
finishing a cast. SBE35 temperature data can be logged when a Niskin 
bottle is fired. If the SBE35 is set to 8 samples, it requires 
approximately 13 seconds to make a measurement, calculated as 8 * 1.1 
seconds plus an overhead. Data are stored internally and must be 
downloaded at the CTD deck unit as a separate process from the CTD data 
transfer. The SBE35 data are then transferred as a collection of ASCII 
files. The SBE35 clock was initially set to the wrong date, requiring 
editing of the files after the fact (the processing matches by bottle 
number and merely searches for SBE35 data within a few days of the CTD 
casts to be compared, so accurate time stamps are not required).
   
After each cast SBE processing software was run in three steps to export 
as text file (.cnv), to apply time alignment of oxygen data (5s for 
sbeox0Mm/Kg and sbeox0V, but note that the hysteresis correction is 
applied later in mexec processing, NOT here), and to apply a cell thermal 
mass correction for conductivity (alpha = 0.03. tau = 7.0000 on both 
primary and secondary). The resulting files have suffix align ctm. 
Following this processing, a batch script, BASSvp, was run to 
prepare a sound velocity profile and a CTD listing for transmission to 
the UK Met Office. This batch script also copied the raw and processed 
data onto the network drive, legdata.


8.1.2  Data Processing
   
The CTD data processing followed the methods used on previous SR1b and 
other NOC MPOC cruises, using the mexec software suite. The initial 
SeaBird data conversion, align, and cell thermal mass corrections were 
performed using SBE Data Processing, Version 7.22.2 software. The network  
data drive, legdata, was linked to ctd/ASCII FILES/jcrfs ctd and ctd 
linkscript was used to copy files to fola and set up additional symbolic 
links to filenames following mstar convention.
   
For each cast the following m-files were then run, using wrapper script 
ctd all part1: mctd 01, mctd 02a, mctd 02b, mctd 03, mdcs 01, mdcs 02.

The processes completed by these scripts include

read ASCII cnv data from ctd/ASCII FILES/ctd jr15003 001 ctm.cnv
convert variable names from SBE names to mexec names using 
data/templates/ctd jr15003 renamelist.csv copy raw file to 24hz file
make oxygen hysteresis adjustment on 
24hz file average to 1hz
calculate dereived variables psal, potemp
extract information from bottom of cast identified by maximum pressure.

   
Subsequently mdcs 03g was run to inspect the profiles and hand-select 
cast start and end times. The way oxygen time lag is handled in the SBE 
align algorithm, and the weak dependence of oxygen calculation on 
salinity, means that when air is ingested into the conductivity cell at 
the end of the cast, the oxygen becomes biased a few seconds earlier than 
the psal. Care should therefore be taken to select a cast end time for 
which all the important variables are free from bias. The mdscs 03g 
program was modified so that the pressure record is coloured red at times 
when the CTD pumps status indicated that the pumps were off. This 
highlighted one instance (station 15) where the pumps went off when the 
package was hauled too close to the surface after soaking. On that station 
it was necessary to delete approximately the first 27 metres of the 
downcast, until the pumps restarted and the sensors stabilised.
   
The start, bottom and end data cycles are stored in files with names 
like dcs jr15003 001.nc. After selecting the limits for start and end, ctd 
all part2 was then run, executing mctd 04, mfir 01, mfir 02,mwin 01, mwin 
03, mwin 04. The processes completed by these scripts include
Extract down and upcasts using scan numbers stored in dcs jr15003 001, and 
average into 2 dbar files (2db and 2up)
Read the data/ctd/ASCII FILES/ctd jr15003 001.bl file and extract scan 
numbers corresponding to bot- tle firing events.
Add time from CTD file, merging on scan number
Add CTD upcast data (P,T1,T2,S1,S2, etc) corresponding to bottle firing events 
Paste these data into the master sample file data/ctd/sam_jr15003_001.nc
Load winch telemetry data from winch SCS file  
Add winch wireout data to the fir jr15003 001 file 
Paste winch 
wireout data into the master sample file

   
Processed data could then be examined using mctd checkplots to view 
sensor and up-down cast differences as well as compare nearby profiles, 
with particular attention paid to any drift in deep tem- perature or 
salinity (expected to be relatively stable) over time. The 24-Hz data were 
checked for spikes in either of the temperature or conductivity sensors 
using mctd rawshow and, if necessary, edited using mctd rawedit.
   
A variety of extra steps is available after other processing has been 
carried out; these steps can be run in any order.
   
After LADCP processing has been completed there is a best estimate of 
water depth available from the LDEO IX processing. This is found in cast 
processing log files by searching for “bottom found at”; the list of 
stations and depths is placed in station depths/station depths.txt. 
populate station depths can be run to convert station depths jr15003.txt 
to station depths jr15003.mat, which is the file required by mdep 01. 
populate station depths.m also allows missing depths to be set or bad 
depths to be overwritten using switch/case for each cruise.
   
After navigation data processing has been completed the file 
data/nav/seapos/bst jr15003 01 will be available. mdcs 04 will generate 
files dcs jr15003 001 pos.nc which include position at start, bottom and 
end of profiles. mdcs 05 will then paste the position at the bottom of the 
cast into the header of all relevant files in data/ctd.
   
mdep 01 and mdcs 05 can be run multiple times. The headers will not be 
updated if the updating values are identical to the values already in the 
file.


8.2  Water Sample Analysis

Dissolved oxygen analysis is described in Section 9.
   

For each CTD cast, one water sample was drawn per Niskin bottle for 
salinity analysis, from bottles that were fired, up to 12 per station. The 
distribution of bottle sample locations in Drake Passage is shown in 
Figure 2 and 3. Samples were taken in 200ml glass sample bottles, which 
were rinsed three times and sealed with a new clean dry disposable 
plastic stopper, after drying the neck of the bottle. The crate was then 
transferred to the bench in the Prep Lab. Caps were rinsed in freshwater 
and dried before being added to secure the stoppers. Samples were stored 
in the Bio Lab for a minimum of 8 hours before analysis to allow 
equilibration to the laboratory temperature (the conductivity ratio drift 
mentioned above did not appear to be connected to length of time samples 
had been in the lab). A logsheet was maintained of when crates were moved 
into the Bio Lab to keep track of when they would be ready to analyse.
   
Salinity sample analysis was performed on the BAS Guildline 8400B 
Salinometer, Serial No. 65763, in the Bio Lab. The temperature of the ship 
air conditioning fluctuated throughout the cruise and we had considerable 
trouble keeping the autosal lab within the desired temperature range. We 
started by using a bath temperature of 24 C and attempting to keep the lab 
temperature between 21 and 22.5 C, but towards the end of the cruise we 
were unable to get the lab temperature above 17 C, so we switched the bath 
temperature to 21 C. The autosal did appear to be able to maintain a 
constant bath temperature, with the heater lights switching on and off as 
expected while it was in use. However, conductivity ratio readings for 
many sets of samples took an unusually long time to stablise.

All watchkeepers carried out the analysis following standard procedure. 
A sample of IAPSO Standard Seawater was run before and after each set 
of up to 24 samples for salinometer calibration. We used Standard 
Seawater batches P156 and P158, with K15 values of 0.99984 and 0.99970, 
respectively. Standard seawater batch P156 was used to analyse samples 
from stations 1-14 and the first set of tsg samples, and batch P158 was 
used for stations 158 and the second set of tsg samples. We flushed the 
volume with expired P155 before starting new sets of runs to bring it 
closer to the standard salinity, and with milli-Q for intervals between 
runs.
   
Bottle sample conductivity readings were read from the autosal and 
logged by hand as we did not have a laptop capable of running autosal 
2009 or connecting to the autosal. Three readings were taken for each 
sample. In some cases, where the values did not stabilise (see above), 
four or more readings   were taken, but, because drawing down the sample 
bottle volume permits more evaporation, readings past the third were not 
used. Due to the stabilisation problem (see above) all readings were 
examined, and a few outlier readings were excluded.
   
Before comparison with the CTD data, the sample readings are 
adjusted for the salinometer off- set, or the difference between the 
standard reading and its label value, by linearly interpolating be- 
tween the initial and final standard for each set of samples. These 
offsets ranged from 1.03  10-3 to 1.41  10-3 (2xK15) for all but the last 
two sets of samples, with drifts within a sample set of 0.05  10-3 to 0.10  
10-3. Offsets for the last two sets of samples, run at a higher bath 
temperature, were 3.8  10-3  to 5.8  10-3 (2xK15). These sets comprised 
the second set of tsg samples and CTD casts 30 and 31. Bottle-sensor 
conductivity differences stations 30 and 31 were not different from those 
for other stations. Samples from sets analysed using batch P156 (stations 
1-14) were further adjusted for the batch- batch offset between P156 and 
P158. This offset of 0.6  10-3 psu was supplied by H. Uchida (pers. 
comm.) based on laboratory measurements following Kawano et al. 
(2006). The scatter in bottle-CTD comparisons was too large for this 
offset to be visible in this dataset.


8.3  Data calibration
   
After calibration sample data were obtained, they were read in using 
msbe35 01, msbe35 02, msal 01y, msal 02, moxy 01y, moxy 02, and 
concatenated into master sample file sam jr15003 all.nc for comparison 
with sensor temperature, salinity, and oxygen. These comparisons were made 
ashore after the cruise. The locations of calibration samples from Drake 
Passage are shown in Figures 2, 3, and 4.

Constant temperature offsets of -4  10-40C (-8  10-40C) were applied 
first using temp apply cal.
   
344 Niskin bottle salinities samples were analysed. During comparison 
with CTD conductivities us- ing ctd evaluate sensors, 20 of these 
comparisons were judged to be questionable or bad, either due to 
questionable bottle analysis or to strong salinity gradients, and were 
flagged accordingly. Based on the 324 good conductivity comparisons 
calibration factors with linear pressure and station number de- 
pendence were applied to the two sensors to minimise the median of the 
bottle conductivity to CTD conductivity ratio. These factors, applied 
using cond apply cal, were approximately equivalent to salinity 
offsets of (5.38 to 4.09)  10-3 psu at the surface and (0.6 to -0.69)  
10-3 psu at 5000 dbar for the primary sensor, and (2.48 to 1.64)  10-3 psu 
at the surface and (-3.73 to -4.57)  10-3 psu at 5000 dbar for the 
secondary sensor (with factors in both cases decreasing over time).
   
After temperature and conductivity calibrations were applied, oxygen 
was converted from µmol/L to µmol/kg using msam oxykg, and bottle and 
sensor values compared using ctd evaluate oxygen. 166 bottles were 
analysed for oxygen, but 2 of the comparisons were flagged as 
questionable. The calibration function obtained by least-squares 
fitting to the bottle data, and applied by oxy apply cal, was Ocal = 
O0(1.0603 + 0.0005N) + (1.0384 + 0.0007P), where Oo is the uncalibrated 
CTD oxygen, N is the station number (1 to 31), and P is pressure.



8.4  Lowered Acoustic Doppler Current Profiler (LADCP)

8.4.1  Instrument setup and performance
   
The 300-kHz Workhorse LADCP was installed in a downward-looking 
configuration on the CTD rosette (see Section 11). The instrument was 
configured (Table 3) to sample 16 x 10m bins, with data collected in beam 
co-ordinates and rotated to earth co-ordinates during processing. The 
LADCP was connected to a charger and by a serial cable to a BAS AME-
supplied laptop in the Chem Lab for programming prior to each station and 
data download after each station, using BBTalk. Pre-deployment   tests 
were performed at least once daily. Data downloaded after each station 
were copied to the legwork portion of the network drive in ladcp/JR15003, 
with names of the form JR15003 NNN.000, along with deployment logs, 
JR15003 NNN.txt.


Table 3: LADCP deployment commands, contained in JR15003_ladcp.cmd.

CR1
RN JR15003 
WM15
TC2 
LP1
TB 
00:00:02.80 
TP  
00:00.00 TE 
00:00:01.30 
LN25
LS0800 
LF0 
LW1 
LV400 
SM1 
SA011 
SB0 
SW5500 
SI0
EZ001110
1 
EX00100 
CF11101 
CK
CS


8.4.2  Data processing
   
Data for each station were processed on fola using the LDEO-IX software 
package, developed at Lamont-Doherty Earth Observatory (LDEO). The 
software uses an inverse method to calculate veloc-   ity profiles, 
optionally including LADCP bottom tracking and/or VMADCP upper ocean 
velocities as constraints. At-sea processing was performed using only ship 
navigation (ladcp/ix/DL GPS) or navi- gation and bottom tracking 
(ladcp/ix/DL BT). The LADCP profiles in Drake Passage produced by the 
LDEO-IX inverse including navigation and bottom tracking are shown in 
Figure 5.

There is a link to the ladcp directory on legdata:

cruise/data/ladcp/raw/rawdata → ../../jcrfs/current/work/ladcp/JR15003/. 
After a cast, unix script exec/lad linkscript ix is run to update the raw 
data directory (calling exec/lad syncscript) and making links to files 
with IX processing name convention files. lad linkscript ix will need to 
be edited for the cruise name.


Linking to CTD data
   
Each processing suite also expects CTD filenames to have a certain 
form. 1-Hz CTD data can be exported from mexec into ascii using the mexec 
command list ctd 1hz(nnn) for station number nnn. This exports the 
variables time, press, temp, psal, latitude, longitude. Note that lat and 
lon are required for the IX processing, and become the source of 
navigation data for that suite. If list ctd 1hz   has been run from 
Matlab, then ladctd linkscript ix will make those ascii files available 
to the IX processing in the correct locations and with the correct file 
names. In IX, links to CTD data are made in ladcp/ix/data/CTD/1Hz/ctd →  
ctd and ladcp/ix/data/CTD/1Hz/ctd jr15003 028 1hz txt ctd/ctd jr15003 028 
1hz txt. ladctd linkscript ix should not require modification for each 
cruise.

Edits to .m files required at start of a cruise for IX processing
   
In addition to setting up directories, links and linkscripts, the set 
cast params*.m files must be edited with cruise details. These scripts 
reside in data/ladcp/ix/data/.
Edits required (lines from jr15003 set_cast_params*.m shown): 
f.sadcp = sprintf(’SADCP/os75_jr15003_ctd_%03d.mat’,stn); 
f.ctd = sprintf(’CTD/1Hz/ctd_jr15003_%03d_1hz_txt’,stn); 
p.cruise id = ’jr15003’;
p.whoami = ’Y. Firing’;

The different versions of set cast params*.m are called by different 
versions of process cast*.m to run IX processing of the LADCP data 
with different constraints:
  • process cast v5.m calls set_cast_params_v5.m to include only 
    navigation data
  • process cast v4.m calls set_cast_params_v4.m to include navigation and 
    bottom tracking data
  • process cast v3.m calls set_cast_params_v3.m to include navigation, 
    bottom tracking, and VMADCP data

set_cast_params.m (and thus process_cast.m) are currently set to use v5 
(navigation only).

Quick look notes for LADCP processing in IX

1. Make sure the raw file is on legdata: 
   cd /cruise/data/ladcp/raw
   ls ld rawdata/* (see files on legdata) 
   ls ld * (see files on fola)
   The latest station should have a name like rawdata/JR15003 002m.000.
2. Run unix script lad_linkscript_ix. This will find any files in 
   legdata that aren’t on fola, copy them across to the correct place 
   on fola using rsync, and create links in the IX processing tree so 
   that IX is aware of the raw files: ladcp/ix/data/raw/002/002DL000.000→
   ../rawdata/JR15003 002m.000 and so on. This script can be run from 
   anywhere, and will echo to the screen the identity of any files copied 
   and any links made. Check again using step 1 if you wish.
3. Run unix script ladctd_linkscript_ix. If the CTD 1-Hz ASCII file is 
   available, this will make a link in the IX processing tree so that 
   IX is aware of the CTD data:
   ladcp/ix/data/CTD/1Hz/ctd_jr15003_nnn_1hz.txt→ctd/ctd_jr15003_nnn_ 
   1hz.txt. IX can be run without CTD data for first-look checking, but 
   it will produce an error in calculating the magnetic variation, 
   because position is unknown and is found in the CTD 1-Hz file. If 
   you know the CTD file is not available, skip this step.
4. If you intend to run process cast v3 to use VMADCP data, check that 
   ladcp/ix/data/SADCP/os75_jr15003_ctd_028.mat is available.
5. Run the IX process:
   cd ladcp/ix/data or cd /cruise/data/ix (an abbreviation: ix→ladcp/ix/ 
   data) matlab &
   >> ixpath
   >> process_cast(nnn), where nnn is the station number.
6. Repeat steps 3, 4 and 5 as CTD and VMADCP data become available.
7. Note that on jr15003 there are three versions of process cast 
   available.
   process_cast_v5 calls set_cast_params_v5, and processes data into 
   DL_GPS/. Navigation is used but no BT or VMADCP constraint.
   process_cast_v4 calls set_cast_params_4, and processes data into 
   DL_BT. Navigation and BT are used but no VMADCP constraint.
   process_cast_v3 calls set_cast_params_v3, and processes data into 
   DL_BT_GPS. Navigation, BT, and VMADCP are all used.



8.5  References
   
Kawano, Takeshi, Michio Aoyama, Terry Joyce, Hiroshi Uchida, Yasushi 
    Takatsuki, and Masao Fuka- sawa, 2006, J. Oceanogr., 62, 777-792.




Figure 2: Calibrated temperature on SR1b, with bottle firings 
          (corresponding to SBE35 samples) shown by black circles 
          and float deployment stations by squares.

Figure 3: Calibrated salinity on SR1b, with bottle salinity 
          samples shown by black circles and float deployment stations 
          by squares.

Figure 4: Calibrated dissolved oxygen on SR1b, with bottle 
          oxygen samples shown by black circles and float deployment 
          stations by squares.

Figure 5: Profiles of zonal (top) and meridional (bottom) velocity from 
          LADCP at each station in Drake Passage, offset to the latitude 
          of that station, with dashed zero lines. Right hand panels show    
          northern profiles including the Subantarctic Front jet, with a 
          common zero line.






9  SOCCOM (SOUTHERN OCEAN CARBON AND CLIMATE OBSERVATIONS AND MODELING) 
   FLOAT DEPLOYMENTS AND CTD STATIONS
   Daniel Schuller

   
The SOCCOM (Southern Ocean Carbon and Climate Observations and 
Modelling) project implements sustained observations of the carbon cycle, 
together with mesoscale eddying models linked to    the observations. 180 
to 200 autonomous profiling floats with biogeochemical sensors (oxygen, 
nitrate, pH and optical sensors in addition to temperature/salinity) and 
sea-ice avoidance software will be deployed throughout the Southern Ocean 
during this project. These floats will extend current seasonally limited 
observations of biogeochemical properties into nearly continuous coverage 
in time, with horizontal spatial coverage over the entire Southern Ocean 
and vertical coverage to 2000 m. These float deployments must take place 
from research ships with CTD/rosette sampling in order to collect water 
samples (to be analysed for oxygen, nutrients, pH, alkalinity, HPLC, POC) 
for float profile calibration. This is the 2nd year of the project; 
multiple floats have been deployed from foreign and domestic re-  search 
vessels including Nathaniel B Palmer, Polarstern, and James Clark Ross. 
All floats deployed are operating well as of the end of the cruise, with 
data reported in near real-time and publicly available from:  
http://www.mbari.org/chemsensor/floatviz.htm.
   
The pH sensor technology, which was developed recently, is proving to 
be very robust. The T/S data are part of the Argo float data set.
   
The USA National Science Foundation (NSF) funds all measurements and 
calibration measurements, with the exception of the optical measurements. 
Optical measurements included in this plan have been proposed to NASA.
   
The 4 floats deployed from JCR will contribute to the international 
Southern Ocean Observing System (SOOS) and the Argo database.



9.1  Float Deployments

4 SOCCOM floats deployed on JR15003 according to Table 4:

Table 4: SOCCOM floats with deployment times and positions. I = ice 
         enabled; O = oxygen sensor; N = nitrate sensor; F = fluorometer 
         (WetLabs FLBB); p = pH sensor.

  Float ID    Sensors  CTD    Deploy.   Deploy.    Lat         Lon      Deployer
                       stn     date      time                             name
------------  -------  ---  ----------  ------  ----------  ----------  --------
1, 9652 Apex   IONpF   009  7 Jan 2016   0335Z  60.66637 S  54.82753 W  Schuller
2, 9657 Apex   IONpF   012  7 Jan 2016   1732Z  59.66695 S  55.44552 W  Schuller
3, 9655 Apex   IONp    016  8 Jan 2016   1743Z  58.05023 S  56.44734 W  Schuller
4, 9662 Apex   IONp    020  9 Jan 2016   1502Z  56.46764 S  57.40497 W  Schuller



9.2  CTD/Rosette Sampling
   
CTD casts were completed at each SOCCOM float deployment location for a 
total of 4 profiles.    Full water column bottle samples were taken for 
dissolved oxygen, pH/alkalinity, dissolved inorganic nutrients, salinity, 
HPLC and POC at each station in that order. Dissolved oxygen was analysed 
on  board. NOCS sampled and analysed water samples for salinity at these 
locations.



9.3  Dissolved Oxygen
Samples were analyzed for oxygen at 4 SOCCOM stations and 11 additional 
stations.



9.4  Sampling and Data Processing
   
Samples were collected for dissolved oxygen analyses as the first sample 
after the rosette was brought on board. Using a Tygon drawing tube, nominal 
125ml volume-calibrated iodine flasks were rinsed three times then filled 
and allowed to overflow for approximately three flask volumes. The sample 
draw temperature was measured with a small thermometer embedded in the 
drawing tube. Reagents (MnCl2 and NaOH/NaI) were added to fix the oxygen 
before stoppering. The flasks were shaken twice to assure thorough 
dispersion of the precipitate, once immediately after drawing, and then 
again after about 20 minutes. The samples were usually analyzed within 
several hours of collection. Thiosulfate normalities were calculated from 
each standardization and corrected to 20C. The 20C normalities and the 
blanks were plotted versus time and were reviewed for possible problems. 
Oxygens were converted from milliliters  per liter to micromoles per 
kilogram using the sampling draw temperature and the samples salinity.



9.5  Equipment and Techniques
   
Dissolved oxygen analyses were performed with an ODF-designed automated 
oxygen titrator using photometric end-point detection based on the 
absorption of 365nm wavelength ultra-violet light. The titration of the 
samples and the data logging were controlled by LabView software. 
Thiosulfate was dispensed by a Dosimat 665 buret driver fitted with a 1.0 
ml buret. The ODF method used a whole-   bottle modified-Winkler titration 
following the technique of Carpenter (1965) with modifications by Culberson 
(1991), but with higher concentrations of potassium iodate standard 
(approximately 0.012N) and thiosulfate solution (55 g/l). Standard KIO3 
solutions prepared ashore were run at the beginning of each run. Reagent 
and distilled water blanks were determined, to account for presence of 
oxidizing or reducing materials.




9.6  Volumetric Calibration
   
Oxygen flask volumes were determined gravimetrically with degassed 
deionized water to determine flask volumes at ODFs chemistry laboratory. 
This was done once before using flasks for the first time  and periodically 
thereafter when a suspect bottle volume was detected. The volumetric flasks 
used in preparing standards were volume-calibrated by the same method, as 
was the 10 ml Dosimat buret used   to dispense standard iodate solution.



9.7  Standards
   
Potassium iodate was obtained from Johnson Matthey Chemical Co. and was 
reported by the supplier to be >99.4% pure.



9.8  pH/Alkalinity
   
Samples were taken from 4 SOCCOM stations and 1 additional station. 
Approximately 10% of samples were duplicates. Nominal 500 mL samples were 
drawn from the Niskin bottles, preserved with mercury (II) chloride and 
packed for shipping via air freight back for analysis at Scripps 
Institution of Oceanography.



9.9  Nutrients
   
Samples were taken from 4 SOCCOM stations. Nominal 30 mL samples were 
drawn from the Niskin bottles into rinsed centrifuge tubes. They were 
immediately frozen in -20C freezer. Upon JCRs return   to UK the nutrient 
samples will be shipped on dry ice via air freight for analysis at Scripps 
Institution of Oceanography.



9.10  Salinity
   
Salinity samples were collected at all depths from the 4 SOCCOM CTD 
stations. Samples were analyzed shipboard by NOCS using JCRs Guildline 
8400B autosal.



9.11  HPLC and POC
   
HPLC/POC samples were taken from 4 SOCCOM stations and 6 additional 
stations. Samples were taken from the surface and cholorophyll maximum 
Niskin bottles. A duplicate sample was taken alter- nating between surface 
and chlorophyll maximum depths at each station as well. 1 L of seawater was 
filtered in the dark through glass fiber filters. Filters were immediately 
stored in aluminium foil packages in a dewar of liquid nitrogen. Filters 
and aluminium foil packets were pre-combusted for POC samples. Samples were 
moved to -80C freezer at the conclusion of the cruise. Upon JCRs return to 
UK samples will be shipped in a dry shipper back to Scripps Institution of 
Oceanography for analysis.



9.12  References
   
Carpenter, J. H., “The Chesapeake Bay Institute technique for the Winkler 
    dissolved oxygen method,” Limnology and Oceanography, 10, pp. 141-143 
    (1965).
Culberson, C. H., Knapp, G., Stalcup, M., Williams, R.T., and Zemlyak, 
    F., “A comparison of meth-  ods for the determination of dissolved oxygen in 
    seawater,” Report WHPO 91-2, WOCE Hydrographic Programme Office (Aug 1991).





10  UNDERWAY DATA COLLECTION AND PROCESSING


10.1  Computing and SCS data processing

10.1.1  Configuration of linux workstation ’fola’
   
The NOC MPOC OCP group brought a linux workstation (fola), which was 
the primary platform for data analysis during the cruise. The jcr 
cruise data directory was made available by mounting on fola.  That 
directory includes SCS data streams, data from other sources such as 
CTD, LADCP, VMADCP, and the legwork directory. The network data 
directory was mounted on fola so that /mnt/data/cruise/jcr was the 
parent directory of the individual cruise data directories identified 
by date. Cruise jr15003 was current → 20151217.
   
A link was made on fola in /local/users/pstar/cruise/data so that 
data/jcrfs → /mnt/data/cruise/jcr. This enabled access to 
the legdata directory as well as the legwork part of it. Since the 
current/ cruise directory sits below /mnt/data/cruise/jcr, useful 
directories could be accessed using the following example links: 

data/ctd/ASCII FILES/jcrfs_ctd → ../../jcrfs/current/ctd/JR15003
data/legwork → jcrfs/current/work 
data/vmadcp/jcrfs_adcp75 → ../jcrfs/current/adcp 
data/scs_raw_ship → jcrfs/current/scs/Compress
   
Workstation fola was backed up on a daily basis. A complete dump of 
cruise data and software was copied using rsync from fola to one of two 
Transcend portable hard drives. These drives were used to carry data 
back to NOC at the end of the cruise, including a final identical 
backup of fola on two drives.


10.1.2  SCS data streams
   
The SCS data streams (ashtech [nav/ash], ea600 [sim], anemometer 
[met/surfmet], oceanlogger [ocl], emlog-vhw [chf], gyro [nav/gyros], 
seatex-gll [nav/seapos], em122 [em122], seatex-hdt [nav/seahead]) were 
processed on fola during the cruise. Most were processed in 24-hour 
segments, using m_jr15003_daily processing.m, with cleaning and appending 
as required. Winch data were processed   by CTD station as part of 
standard CTD processing (ctd_all_part2.m).


10.1.3  Access to SCS data
   
SCS data are stored in *.ACO files, which are plain text. However, 
non-numeric characters make these slow to parse in Matlab. An ad hoc 
but fairly robust and quick-running system has evolved to make these 
data more easily readable for mexec processing.

  1. Parse the ACO files with linux sed, to remove non-numerical 
     characters. Input SCS files are in data/scs raw. On the ship and 
     during the cruise, data/scs raw → scs_raw_ship, 
     data/scs_raw_ship → jcrfs/current/scs/Compress. At the end of the 
     cruise, the contents of scs_raw_ship are copied to
     a local directory, data/sca_raw_postcruise. Then the link 
     is changed so data/scs raw scs_raw_postcruise, so that 
     raw SCS files can be accessed after the cruise.

     The sed parsing allows continually-filling SCS files to be 
     continually edited into data/scs sed/. Parsing is started and 
     stopped with linux commands sedexec_startall and sedexec_stopall. 
     If there is a problem with any aspect of sed processing, the 
     safest action is to delete all of scs_sed/*ACO and stop and 
     restart sedexec processing.

     The sedexec scripts live in data/exec/jcr. sedexec_startall needs a 
     list of ACO files to parse. This can be generated by a Matlab 
     script, data/exec/jcr/make list for sedexec_startall.m. This will 
     make list_jr15003, linked to by data/exec/jcr/list.

  SCS files note 1  The SCS data consist of .ACO files and .TPL files. The TPL 
                    files contain lists of variables. When a cruise begins, the 
                    data/scs_raw/*.TPL should be copied to data/scs sed. oceanlog- 
                    ger.TPL needs to be manually edited, as oceanlogger.ACO has 
                    time information for which  the number of fields changes 
                    when parsed through sed. The original oceanlogger.TPL begins 
                    thus:
  
                    126,oceanlogger-sampletime,YYY DDD HH:MM:SS 
                    127,oceanlogger-airtemp1,celsius
                    128,oceanlogger-humidity1, 
                    129,oceanlogger-par1,umol/S.m2
                    so the first line must be replaced with 3 lines thus: 
                    126,oceanlogger-sampletimeyyyy,YYYY 
                    126,oceanlogger-sampletimeddd,DDD 
                    126,oceanlogger-sampletimehhmmss,HH:MM:SS 
                    127,oceanlogger-airtemp1,celsius 
                    128,oceanlogger-humidity1,
                    129,oceanlogger-par1,umol/S.m2
  
  SCS files note 2  The default SCS variable names include the name of the 
                    data stream for each variable. e.g. oceanlogger-humidity1. 
                    The daily processing of SCS files removes the extra part of 
                    the variable name. The new names need to be in lookup 
                    template .csv files in data/templates. For example the first 
                    few lines of the oceanlogger template,
                    data/templates/scs jr15003 renamelist 
                    oceanlogger.csv, are oceanlogger 
                    sampletimeyyyy,sampletimeyyyy,YYYY 
                    oceanlogger_sampletimeddd,sampletimeddd,DDD
                    oceanlogger_sampletimehhmmss,sampletimehhmmss,HH:MM:SS 
                    oceanlogger_airtemp1,airtemp1,celsius
                    oceanlogger_humidity1,humidity1,
                    The set of required template files can be made in Matlab 
                    with ms_generate_varname_translation_all.m, which makes 
                    successive calls to ms_generate_varname_translation(stream). 
                    If this script fails, templates can be copied from a 
                    previous cruise. The template contents will be unchanged 
                    unless the variables in the SCS file have changed, e.g. a 
                    new sensor in the oceanlogger stream.

  2. Convert ACO text files to Matlab.
     Even the clean and numeric ACO files are too slow to routinely read 
     into Matlab to access data ’on demand’. Therefore a process is run 
     in which Matlab versions of the SCS data are accumulated into 
     data/scs mat/. In a Matlab window, the command ms update aco to 
     mat(’ea600’) will read data from data/scs sed/ea600.ACO and save 
     the data in data/scs mat/ea600.mat. This process also notes the 
     number of bytes of the ACO file converted. Next time the process is 
     run, those bytes are skipped so that only new data are converted.
     
     The command update allmat will update all the SCS streams with 
     multiple calls to
     
     ms update aco to mat. update allmat will need to be edited to add 
     new streams if new SCS streams are required, otherwise it does not 
     require any modification at the start of a cruise. Some Matlab 
     scripts (eg mday 00.m) that read data ’up to the present’ call the 
     update script before  loading data. Sometimes it is necessary to 
     run the update script manually from the command prompt, to ensure 
     all ACO data are available to following scripts.
     
     If the scs sed files have got into a mess and been regenerated or 
     scs sed parsing restarted, the   safest course of action is to 
     delete the contents of scs mat and run update allmat. This takes a   
     few minutes at the start of a cruise and rather longer, maybe up to 
     half an hour, if 30 or 40 days  data are waiting to be parsed. This 
     is necessary because the scs mat file keeps a count of the  number 
     of bytes of the ACO file parsed. If the ACO file has been altered 
     before that byte count,  the ms update aco to mat process may fail 
     to copy the data correctly, but may not give an error.

10.1.4  The mscs source directory
   
The mscs source directory cruise/sw/mexec v2/source/mscs contains 
the scripts for accessing the SCS data either directly or via scs 
mat. Some of the scripts, e.g. scs to mstar2.m are called by wrapper
scripts such as mday 00.m. Some of the scripts can provide quick access to 
SCS data that have not yet been processed into mexec files. Examples 
include: msgaps, mslast, mslistit, msload, mslookd (usually run as mslookd 
f), msnames, msposinfo, msposinfo noup (quick version for finding ship 
position at earlier time so not necessary to update scs mat/ first), 
msvars. See help mscs for further information.   The techsas equivalent 
library has help mtechsas which has extra documentation and help.



10.2  Underway surface water sampling

10.2.1  Underway surface thermosalinograph

The list of oceanlogger variables is as follows:


mexec directory  mexec short  mexec         mexec file  variables
                 name         directory     root
                              abbreviation
---------------  -----------  ------------  ----------  --------------
ocl              oceanlogger  M_OCL         ocl         tstemp
                                                        conductivity
                                                        salinity
                                                        sound velocity
                                                        chlorophyll
                                                        sampletemp
                                                        flowrate
                                                        sstemp
                                                        trans
                                                        sstemp2

Note the alternative temperatures: sstemp and sstemp2 for seawater intake, 
sampletemp for fluorometer sample temperature, tstemp for the SBE housing 
temperature for calculation of salinity.
   
A total of 41 underway samples were analysed for oceanlogger salinity 
calibration. Samples were drawn from the underway supply in the Prep Lab 
as often as every 4 hours during science time in ice- free areas, following 
the same procedure as for Niskin bottle samples, and the time noted in a 
logsheet to the nearest minute. Samples were analysed following the 
procedure described for CTD salinity samples. 

Data were read in as part of the daily processing. Data were set to absent at any 
time that the pumps were known to be off, either close to port, in ice, or where 
the flowrate indicated there was little or fluctuating supply. Relatively 
simple cleaning has been applied to the appended dataset using mtsg medav 
clean cal and mtsg findbad. Based on comparison with the bottle salinities 
an offset  of 0.06 psu was applied to the oceanlogger salinity record using mtsg apply salcal.



10.3  Surface water sampling for Nd isotope analysis
   
In Bransfield Strait and Drake Passage, several samples from the pumped 
surface water supply were taken in 10 L cubitainers, acidified, and stored 
for Nd isotope analysis ashore.



10.4  Daily processing of SCS streams
   
As part of the regular watchkeeping logging every 4 hours, we checked 
that the SCS streams were up- dating with reasonable values. Data were 
transferred from the onboard logging system (SCS) to fola daily using mday 
00 get all.m. This script also appends daily data files for streams other 
than bathymetry (see below).


Table 5: Times (from log sheet) and locations (from ship track) of surface 
         water samples for Nd isotope analysis

Sample Name  Date        Time   Latitude (S)  Longitude (W)  Sampler
-----------  ----------  -----  ------------  -------------  -------
Surface-01   23.12.2015  1600Z  61027.77’     52001.62’      TC
Surface-02   24.12.2015  0215Z  62020.27’     55055.86’      TC
Surface-03   24.12.2015  1145Z  63006.69’     59008.58’      TC
Surface-04   06.01.2016  1249Z  60050.94’     54042.45’      YF
Surface-05   07.01.2016  0354Z  60037.84’     54051.05’      YF
Surface-06   07.01.2016  0822Z  60019.08’     55002.44’      CdL
Surface-07   07.01.2016  1249Z  60000.07’     55013.92’      CdL
Surface-08   09.01.2016  0428Z  57015.50’     56056.27’      DB


10.4.1  Navigation
   
The list of navigation streams processed from SCS was given in Section 
10.1.2. After daily process- ing of SCS streams, navigation processing 
steps can be completed on the appended xxx jr15003 01.nc files. The 
steps are combined into a single wrapper mbest all.m. This script 
performs tasks such as subsampling to 30-second intervals, adding ship 
speed and course over ground, and merging on ship heading. Ship headings 
are properly vector averaged when subsampled. A best navigation file, 
data/nav/seapos/bst jr15003 01.nc, is the final output.



10.4.2  Surface meteorological sampling (SURFMET)
   
RRS James Clark Ross is equipped with a variety of meteorological 
sensors to measure air tem- perature and humidity, atmospheric pressure, 
total irradiance, photosynthetically active radiation, wind speed and 
wind direction throughout the cruise. The radiation and pressure 
variables were logged in data/met/surflight/. The remaining data were 
logged in /met/surfmet. The raw data files have extensions of the form  
jr15003 dNNN raw.nc, where NNN represents the day number.
   
Once the best navigation file is available, mtruew 01.m is run to 
combine ship navigation data with relative data from the anemometer to 
produce absolute and relative winds averaged to 1-minute resolution. 
As with best navigation, all headings are properly vector averaged, and 
the final product is the file data/met/surfmet/ met_jr15003_trueav.nc.


10.4.3  Bathymetry
   
The EM122 swath echosounder was turned off for the SR1b section (along 
which bathymetry has been measured on many previous cruises) in an 
attempt to improve the noisy VMADCP data (see below).
   
The raw data files have extensions of the form jr15003 dNNN.nc where 
NNN is the number of the Julian day. msim 01.m was run to remove data 
outside a tolerated range and apply a 5-minute median despiking, 
outputting the file sim jr15003 dNNN smooth.nc. msim plot.m copied the 
smoothed sim  data to the file sim jr15003 dNNN edited.nc and called 
mplxyed to allow a manual removal of the remaining spikes in sim data; 
mem122 plot.m was run to do the same for the em122 data (note that   
each script must be used to edit the correct data type; sim must be 
edited in msim plot and em122 in mem122 plot).
   
Two bathymetry streams are available via SCS: the ea600 single-beam echo 
sounder, and the centre   beam of the em122 multibeam (swath) system. Data 
are read in by the daily processing (mday 00 get all.m); for day number 014 
(for instance), ea600 and em122 data are read into sim/sim jr15003 d014.nc 
and em122/em122 jr15003 d014.nc, respectively. For streams other than 
bathymetry, daily processing ap-  pends each day onto a growing appended 
file, but the bathymetry records require manual editing before    they can 
be appended, so there is no append action for sim or em122 in the daily 
processing.  After editing (see below) they are appended using mday 02.

The bathymetry streams inevitably contain bad data where the automatic 
digital determination of  depth has failed to correctly infer depth from 
the analog signals. As the original analog records are not generally 
available to the person doing data editing/cleanup, some judgement is 
required to decide what  are good or bad data. In order to aid this 
process, there is a display of both of the two data streams, along with an 
estimate of bathymetry from satellite gravity data. Thus the ea600 data 
are edited by reference   to em122 data, and vice versa. There is a 
symmetric set of scripts for cleaning the two data streams.
   
The first step is to do some automated cleanup of both the ea600 and 
em122 streams, with msim 01 and mem122 01. Both must be run before 
proceeding with manual graphical editing.


10.4.4  EA600

For ea600, the process is as follows: 
 • msim 01
   reads raw data for the day (from e.g. sim_jr15003_d014_raw.nc);
   picks data in the depth range 5 to 10000, to discard zeros;
   takes the median depth over 300-second bins, to discard noise (example output  
   file: sim_jr15003-d014_smooth.nc)
   makes duplicate file in sim_jr15003-d014_edited.nc 

 • msim 02
   merges on swath centre beam data for the day (if available) to be used 
   in cleaning. Note that mem122_01.m must be run before this step.

 • msim plot
   calls mplxyed for manual removal of bad data. Note that the files are 
   set up so this file is used to edit bad data in the ea600 file. The 
   equivalent file in the em122 sequence should be used to edit bad data in the 
   em122 stream.msim_plot displays an extra window with the full ea600 data, to 
   guide the use of mplxyed. EA600 data quality: data editing was 
   done somewhat conservatively, so the cleaned records likely still 
   contain noise.

 • After cleaning in mplxyed, daily files were appended into a single 
   file, sim jr15003 01.nc, by running mday 02 (see mday 02 run all). At 
   this stage, the em122 depths used for data quality checking are 
   discarded.

 • Next, using the script mmerge_sim_nav_jr15003, navigation was added, 
   in sim_jr15003_01_nav.nc, and a Carter area correction applied, using 
   mcalc, in sim_jr15003_01_nav_cordep.nc. This last file is therefore 
   the master EA600 file, containing corrected bottom depths in 5 minute 
   bins.

10.4.5  EM122
   
Em122 centre beam depths were logged in SCS and downloaded in daily 
files to em122/. Two scripts are used to reduce and edit EM122 data, based 
on the scripts for EA600:
 • mem120_01
   reads raw data (from e.g. em122_jr15003_d014_raw.nc), 
   runs mdatpik to require depth > 20 m,
   runs mavmed to take the median over 300-s bins, producing 
   em122_jr15003_d014_smooth.nc,  and
   copies the file to an ’edited’ version (em122_jr15003_d014_edited.nc) ready for 
   manual editing. 

 • mem120 02
   merges on ea600 for display in mplxyed for QC.

 • mem120 plot
   plots data for editing: if all the relevant files exist, displays the 
   Matlab window with EM120, EA600 and satellite bathymetry, then enters 
   mplxyed on the edited file. This step can be repeated as often as 
   required. The Matlab plot window displays the data as found in the 
   most recently updated ’edited’ file. The cleaned data are then 
   appended using mday 02 (see above).

10.4.6  Chernikeef EM log
   
Chernikeef EM log data were recorded and downloaded daily. Besides 
appending the files, no further processing was carried out and the 
calibration of the EM log was not checked.



10.5  Vessel Mounted ADCP
   
A vessel-mounted 75-kHz Teledyne RD Instruments (RDI) OceanSurveyor 
Acoustic Doppler Cur-  rent Profiler (ADCP) was run throughout the cruise 
to measure horizontal velocity from 30 m to approxi- mately 400-800 m. The 
depth of the transducer is 5 m. The phased-array transducer should be 
insensitive to sound speed (temperature) changes (but see discussion 
below). The data may be particularly affected by bubbles under a certain 
range of ship heading relative to the seas, which appears to have 
dramatically reduced data quality at a few of the CTD stations. 
Coordinating pinging with the EM122 was not successful in deeper water 
(see below), and in some cases there appeared to be intereference from or 
with the bathymetric echosounders. The data quality is generally 
uncertain and the data will be reprocessed, edited, and evaluated ashore.

10.5.1  Real-time data acquisition and VMDAS files
   
The data from the instrument were acquired using the RDI VMDAS software 
package version 1.42, installed on a PC in the main laboratory. The 
software allows data acquisition in a number of configurable formats and 
performs preliminary screening and transformation of the data from beam to 
Earth coordinates. A perl script to subsample ship navigation data, 
NavigationRepeater, must be run on the same machine throughout data 
collection. VMDAS was run using a selection of preset configuration files 
(selected under “edit data options”) which allowed the instrument to be 
promptly switched between bottom tracking and water tracking; set for 
different depth ranges; and self-triggered or triggered by the K-sync unit 
(see below) so as not to interfere with other acoustic measurements. More 
detail on settings   is given below. Data collection was typically stopped 
and restarted, generating a new file segment num- ber, daily during the 
cruise, to facilitate incremental processing. Files were automatically 
placed on the network legdata/adcp directory and rsynced to fola daily 
using vmadcp linkscript.
   
The files produced have names of the form JR15003 os75nnn mmmm.ext, where 
nnn is the file sequence number, mmmm is the number of the segment file 
within the sequence and ext is the extension. A new segment file is 
automatically started when one of the file types reaches a size of 10 Mb. 
VmDas automatically increments the file segment number every time data 
collection is stopped and restarted.
   
The ’R’, ’S’ and ’L’ tabs on the VmDas menu bar allow the user to swap 
between graphical output from the .ENR, .STA and .LTA files. When in ’R’ 
mode, the default upper left hand display in VmDas is the raw velocity 
parallel to each beam, while ’S’ (short-term average) and ’L’ (long-term 
average) modes display currents averaged over 2 or 10 minutes, in Earth 
coordinates. Various display options   are available but data were 
generally monitored in either raw or short-term average form, and checked    
in more detail following daily processing. During the every-4-hours regular 
watchkeeping tasks the VMADCP ensemble number was checked to ensure the 
expected amount of data recording. As on previous cruise JR306, the 
ensemble number reset itself at various points, for unknown reasons (i.e., 
not wrapping over at any obvious or consistent number). We did not check if 
this led to any missed pings; 5-minute ensemble averages did not appear to 
be affected.

10.5.2 Settings
   
The VMADCP was run in single-ping mode, with an 8-m pulse, 100 8-m bins, 
and an 8-m blanking distance. In shallow water (<500 m generally), the 
instrument was run in bottom track mode to obtain phase and amplitude 
calibrations, and set to have fewer bins (reduced depth range) to enable 
more- frequent pinging. In deeper water the instrument was switched to 
watertrack mode, and watertrack calibration data were obtained during CTD 
station-keeping. The island stops on this cruise resulted in a number of 
potential bottom track segments.

For some of the cruise the VMADCP was set to be triggered by the K-sync 
system in order not to interfere with the bathymetric echosounders.
   
In deeper water (in Drake Passage) the EM122 triggered so infrequently 
that the ADCP repeatedly timed out while waiting for a ping command, 
resulting in resetting, and collecting little to no data. When the EM122 
was set to ping at a set interval, with the ADCP pinging in between, data 
quality of both instruments degraded. Where possible, therefore, we turned 
off the EM122 (for instance along SR1b, where swath bathymetry has been 
collected on the identical track many times before). K-sync settings were 
modified as follows (saved as physics800):
disable EM122 in uncheck “echo sounder is master” 
enable EA600, OS75
set fixed periods: EA600 1 s, OS75 3.5 s (necessary interval for 800 m range) 
trigger groups 1, 2, 3: OS75
trigger group 4: EA600

At times there also seemed to be interference in the EA600, which was 
attributed to the OS75, although it is unclear whether this was actually 
the cause. Since bathymetry data were most wanted outside Drake Passage 
(where the tracks we followed have been covered multiple times already), we 
switched   off the VMADCP for those segments.






11  INSTRUMENTATION, EXTRACTED FROM AME REPORT
    Paul Morgan

Table 6: Lab instruments used

         Instrument  S/N Used  Comments
         ----------  --------  --------
         Autosal     63360


Table 7: Acoustic instruments used

         Instrument                      S/N Used  Comments
         ------------------------------  --------  --------
         ADCP                            Y
         EM122                           Y
         TOPAS                           Y
         EK80                            Y
         10kHz IOS pinger
         Benthos 12kHz pinger + bracket  1316


Table 8: Oceanlogger
       
         Instrument                 S/N Used  Comments
         -------------------------  --------  -----------
         Barometer1(UIC)            5002    
         Barometer1(UIC)            5003    
         Foremast Sensors        
         Air humidity & temp1       3898    
         Air humidity & temp2       3896    
         TIR1 sensor (pyranometer)  2993      Not working
         TIR2 sensor (pyranometer)  2992      Not working
         PAR1 sensor                0127    
         PAR2 sensor                0126    
         prep lab        
         Thermosalinograph SBE45    0016    
         Transmissometer            396    
         Fluorometer                1100243    
         Flow meter                 811950    
         Seawater temp 1 SBE38      0601    
         Seawater temp 2 SBE38      0599    


Table 9: CTD

         Instrument                        S/N Used     Comments
         --------------------------------  -----------  ------------------------
         Deck unit 1 SBE11plus             0458
         Underwater unit SBE9plus          0707
         Temp1 sensor SBE3plus             2705
         Temp2 sensor SBE3plus             5766
         Cond1 sensor SBE 4C               2248
         Cond2 sensor SBE 4C               4471
         Pump1 SBE5T                       1807
         Pump2 SBE5T                       7606
         Standards Thermometer SBE35 0024
         Transmissometer C-Star            846
         Oxygen sensor SBE43               0676
         PAR sensor                        7274
         Fluorometer Aquatracka            088-249
         Altimeter PA200                   163162
         LADCP                             15060/14897  Changed to 14897 due to 
                                                        loss of beam intensity
         CTD swivel linkage                             Changed due to damage 
                                                        when CTD stowed away
         Pylon SBE32                       0636


Table 10: AME unsupported instruments logged

          Instrument  S/N Used  Comments
          ----------  --------  --------
          EA600       Y    
          Anemometer  Y    
          Gyro        Y    
          DopplerLog  Y    
          EMLog       Y    





12  Acknowledgments
   
We are sincerely grateful to the Master, officers, and crew, who were 
enthusiastic, helpful, and ac- commodating throughout the cruise. We would 
like to thank volunteers Lucie Cassarino, Tianyu Chen, Damien Desbruyeres, 
Casimir de Lavergne, David Byrne, Jennifer Mecking for their tireless work 
throughout the cruise, and Daniel Schuller for his assistance and advice 
with SR1b water sampling and calibration in addition to his float duties.













CCHDO Data Processing Notes


•  File Online Carolina Berys
74JC20151217.exc.csv (download) #7aca5
Date: 2016-09-12
Current Status: unprocessed



•  File Submission Robert M. Key
74JC20151217.exc.csv (download) #7aca5
Date: 2016-09-08
Current Status: unprocessed
Notes
Update:
Shore based nutrients added
shore based alk and pH added
header edited



•  File Online Carolina Berys
NOC_CR_38.pdf (download) #ebcfd
Date: 2016-07-18
Current Status: unprocessed



•  File Submission Yvonne Firing
NOC_CR_38.pdf (download) #ebcfd
Date: 2016-07-15
Current Status: unprocessed



•  File Online Carolina Berys
sr1b_74JC20151217_hy.csv (download) #d6318
Date: 2016-07-11
Current Status: unprocessed



•  File Online Carolina Berys
sr1b_74JC20151217_ct1.tar.gz (download) #34ca5
Date: 2016-07-11
Current Status: unprocessed



•  File Submission Yvonne Firing
sr1b_74JC20151217_ct1.tar.gz (download) #34ca5
Date: 2016-07-07
Current Status: unprocessed
Notes
Cruise JR15003, 17 December 2015 - 13 January 2016, including GO-SHIP line SR1b 
(SR01).  Temperature, salinity, and oxygen are calibrated, other variables 
uncalibrated.



•  File Submission Yvonne Firing
sr1b_74JC20151217_hy.csv (download) #d6318
Date: 2016-07-07
Current Status: unprocessed
Notes
Cruise JR15003, 17 December 2015 - 13 January 2016, including GO-SHIP line SR1b 
(SR01). 

