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CRUISE REPORT: P15S 
(Updated AUG 2009)



A.  HIGHLIGHTS

A.1.  CRUISE SUMMARY INFORMATION

               Section designation  P15S 
 Expedition designation (ExpoCode)  09FA20010524
                   Chief Scientist  Susan E. Wijffels / CSIRO 
                             Dates  24 MAY 2001 - 8 JUL 2001
                              Ship  R/V Franklin
                     Ports of call  Wellington, New Zealand
                                    Nuku'alofa, Tonga
                                    Apia, Western Samoa

                                                 0°
             Geographic boundaries  180°                    170° W
                                               49.5° S
                          Stations  129
      Floats and drifters deployed  0
    Moorings deployed or recovered  0
     Chief Scientist Contact Info.  Susan E. Wijffels
                                    CSIRO Marine Research - GPO 1538
                                    Hobart, Tasmania 7000 Australia
                                    Phone: 03 6232 5450 Fax: 03 6232 5123
                                    e-mail: Susan.Wijffels@marine.csiro.au











FRANKLIN VOYAGE SUMMARY NO. FR05/2001 

Title 

Monitoring ocean climate change around Australia: the Deep-Ocean Time-Series 
Sections (DOTSS). 


ITINERARY 

Leg 1:
Departed Wellington (New Zealand) 0915hrs Thursday 24 May 2001
Arrived Nuku'alofa (Tonga) 0830hrs Saturday 16 June 2001 

Leg 2:
Departed Nuku'alofa (Tonga) 2200hrs Saturday 16 June 2001
Arrived Apia (Western Samoa) 1000hrs Saturday 7 July 2001 local (8 July 2001 
AEST) 


PRINCIPAL INVESTIGATORS 

Susan E. Wijffels (Chief Scientist)
CSIRO Marine Research
GPO 1538
Hobart, Tasmania 7000 Australia
Phone: 03 6232 5450 Fax: 03 6232 5123
e-mail: Susan.Wijffels@marine.csiro.au 

John Church, Bronte Tilbrook and Steve Rintoul
Antarctic CRC and CSIRO Marine Research 

Nathan Bindoff
Antarctic Co-operative Research Centre, University of Tasmania 

Mark Warner and Chris Sabine
University of Washington, Seattle, USA 

John Bullister
NOAA-PMEL, Seattle, USA 


SCIENTIFIC OBJECTIVES 

• Establish a time series of full-depth repeat ocean measurements capable of 
  resolving decadal and longer time-scale changes in the structure and carbon 
  storage of the oceans around Australia, from Antarctica to the equator.  
• Use these data to test climate model predictions and to determine whether and 
  how fast climate is changing due to the Greenhouse Effect and/or natural 
  decadal variability.  


CRUISE TRACK 

Starting in Wellington, Franklin steamed into deep water south of the Chatham 
Rise and a test station was completed. Franklin then steamed directly to 170° 
W, 50° S where the meridional survey began. From there, Franklin worked 
northwards and westwards to near Chatham Island crossing a deep western boundary 
current (see Figure 1). From there, the track was northeastward recrossing the 
boundary current back to 170° W, then along 170° W, until interrupted for an 
exchange of personnel in Tonga. 

On Leg 2, near 17° S, the meridional line was interrupted in order to complete 
an additional crossing of the deep boundary currents found between 170° W and 
the Tonga-Kermadec Ridge. After completing this short zonal line, the 170° W 
meridional line was resumed until interrupted again near 10° S for a section 
across the deep Samoa Passage. From here the meridional line was completed to 
the equator along 168° 45'W. 


RESULTS 

A total of 129 CTD casts were completed. Four of these were test casts of 
various types but the rest of the casts were mostly to within 15m (or more 
usually 10m) of the bottom. The casts were made along 3 sections (Figures 1): 
along roughly 170° W from 50° S to the equator (a partial repeat of WOCE 
section P15S), along 17.5° S from 170° W across the deep western boundary 
current east of the Tonga-Kermadec Ridge (a partial repeat of WOCE section P21) 
and across the Samoa Passage (a partial repeat of WOCE section P31) which is the 
main pathway of deep water from the South to the North Pacific Ocean. 

On all casts a 24-bottle rosette system (10 litre bottles) was used to collect 
samples throughout the water column. Samples were collected for salinity, oxygen 
and nutrients (nitrate, phosphate and silicate) on all casts. On about half of 
the casts samples were also collected for dissolved inorganic carbon, alkalinity 
and CFCs (Freon 11, Freon 12) and on some casts carbon tetrachloride. The ship 
mounted acoustic Doppler current profiler, precision depth recorder and other 
underway instrumentation were run throughout the cruise.  

At 6 stations, samples were also collected for John Lupton (NOAA-PMEL, Seattle, 
USA) for helium analysis. 

The sections clearly show the major features expected - the northward 
penetration of Southern Ocean water masses (Sub-Antarctic Mode Water, Antarctic 
Intermediate Water, Circumpolar Deep Water and Antarctic Bottom Water) and the 
southward penetration of North Pacific water masses.  

Initial analysis on board indicate the data are mostly of high quality.  A post 
CTD calibration comparison indicates an rms difference between the bottle and 
CTD salinity of 0.0012 for bottles deeper than 1000 m (over 1300 comparisons).  
The bottle oxygen data also appears to be of high quality.  Initial calibrations 
of the CTD oxygen sensor look promising with an rms difference between the 
bottle and CTD oxygen data of 5-6 _ mole/litre.  However, even after the 
calibration, the times when the CTD oxygen sensor was changed can be seen, 
implying a need for further work on the calibrations.  The nutrient profiles 
look promising but there is some station to station noise in the data and some 
apparent jumps in deep nutrients.  Some of the later stations are being rerun 
because of growth in the auto-analyser sample line.  The station to station 
noise and the apparent jumps should decrease after the samples have been rerun 
and corrections from the standard reference material have been applied.   

On the last part of the first leg of the cruise and all of the second leg of the 
cruise, there was a contamination problem with the CFC samples, in particular 
with CFC-12.  This was finally tracked down to the eucalyptus oil injected into 
the air-conditioning system.  It appears that the oil settles on the Niskin 
bottles in the wet lab and then absorbs CFCs from the air before releasing it 
into the water samples.  The CFC signals in the upper part of the water column 
and in the deep boundary currents are clear but the ability to determine CFC 
ages may be compromised (at least for depths of 1000 db to 4000 db).  A full 
report on the CFC data collection and analysis in included as an Appendix.   

The sections clearly show the major features expected - the northward 
penetration of Southern Ocean water masses (Sub-Antarctic Mode Water, Antarctic 
Intermediate Water, Circumpolar Deep Water and Antarctic Bottom Water) and the 
southward penetration of North Pacific water masses.  The temperature and 
salinity sections along 170°W are shown in Figures 2 and 3.  In the deep zonal 
sections at 17.5°S and across the Samoan Passage, the northward flowing 
boundary currents are clear.  At both sections, there has been an increase in 
CFC concentration since these sections were last occupied.  However, no 
quantitative comparison with previous data has yet been undertaken.  

Samples were analysed for dissolved inorganic carbon (TCO2) and seawater 
alkalinity (TA). The TCO2 values were measured by coulometry using a SOMMA 
system. TA values were measured by potentiometric titration on a closed cell. 
For carbon parameters, full profiles (24 Niskin bottles) were taken every other 
CTD station along the cruise track, with surface and some fill-in samples (up to 
14) collected at other CTD stations. Where possible, carbon analyses were made 
at stations that coincided with locations that had been analysed for carbon 
during WOCE on sections P15S, P15N, P21 and P6. 

Data quality for both TCO2 and TA was monitored during the cruise using 
duplicate samples and by analysing Batch 52 Certified Reference Material (CRM) 
provided by Dr. Andrew G. Dickson, Scripps Institution of Oceanography. The data 
quality were good for both legs of the cruise. At each 24-bottle cast for 
carbon, three depths were sampled in duplicate. The duplicates were interspersed 
with the other samples from the cast and analysed. The measured CRM titration 
alkalinity values were used to calibrate the potentiometric titration cell 
volume. For 37 samples the calculated CRM alkalinity on both legs of the cruise 
the cruise was 2224.72 ± 1.03 mmoles/kg. Duplicate analyses for alkalinity 
showed an absolute difference between duplicates of 1.03 ± 0.91 mmol/kg (1 
s.d.; n=150).  TCO2 results for CRM samples 2005.45 ± 0.83 mmol/kg  (1 s.d.; 
n=66), and the absolute difference between duplicates was 1.08 ± 0.74 mmol/kg 
(1 s.d.; n=200).  

Surface DIC values followed expected trends with gradually decreasing 
concentrations to the north, a minimum occurring at station 73, at ~17.5°S, 
before increasing again. The bottom water, below 5000 db, showed a very 
consistent value of 2257 +/- 2 umoles/kg until station 112, at ~8°S, when the 
concentration started to increase reaching values of 2277 umoles/kg at station 
128, at the equator. A mid-depth maximum was very apparent on Leg II and 
increased in concentration as the track proceeded north. 

Continuous measurements of the fugacity of carbon dioxide (fCO2) in surface 
waters were also made along the cruise track. The fCO2 measuring system is based 
on a "Weiss" type equilibrator and a LICOR 6252 Infrared Gas Analyser (IR). 
During a six hour cycle three CO2-in-air standards, clean outside air, and air 
equilibrated with surface waters are analysed. The three standards and the air 
sample are analysed for eight minutes each at the beginning of the six hour 
cycle. Measurements are made in surface waters for the remainder of the cycle. 
Data are recorded as one minute averages of readings taken every second. The 
CO2-in-air standards are referenced to the WMO molar scale and were prepared and 
calibrated by Dr. P. Steele, CSIRO Atmospheric Research, Melbourne. During leg 
1, the underway seawater line does not appear to have been flushed sufficiently 
rapidly, resulting in warming of about 1° C between the seawater intake and 
equilibrator. The large warming and the low flushing rates through the water 
lines are likely to result in poor fCO2 data quality for leg 1. The flushing 
problem was corrected but not eliminated on leg 2, and the data quality for this 
leg is expected to have improved. 

 

CRUISE NARRATIVE 

Leg 1 

We left Wellington at 0915 on Thursday the 24th of May, 2001 and started heading 
South-East as soon as we were clear of the harbour.  The first station, a bottle 
test station was done on the afternoon of the 25th of May at 44° 26'S, 179° 
57'E.  We then proceeded to the first station on the WOCE P15 section at 49° 
30'S, 170° 00'W.  We reached this station in the early afternoon of the 27th of 
May.  We had had moderate following conditions all the way from Wellington.  As 
we approached this station the weather obligingly swung around to the South, 
giving us moderate following conditions for the first part of the section. 

When we reached the station at 45° 57'S it seemed that our luck with the 
weather had run out - the station had to be abandoned with the CTD at 4,000 
metres due to rapidly worsening conditions.  Once conditions improved we were 
able to start work again, having lost about 12 hours (29 and 30 May). 

The weather then continued to moderate and we were once again able to make good 
progress until early on the 3rd of June, when we were at 39°S, 172°W.  
Conditions worsened rapidly, culminating in winds gusting above 60 knots.  We 
only lost about a day here as, after about 12 hours, conditions started to 
moderate and we were able to begin work again in another 12 hours or so. 

After that we continued to work in conditions varying between very light (winds 
less than 5 knots) and moderate (average winds in the low twenties, gusting to 
the high twenties) for several days.  Mostly we had following conditions, 
enabling us to make good time between stations.   

Late on the 12th the weather degenerated again, resulting in the loss of nearly 
half a day.  Once we were able to start CTDs again we continued, completing the 
CTD at 20° 30'S late on the 14th of June before heading for Tonga. 

We reached Tonga at 0830 on the 16th of June, having completed 66 CTD stations, 
two further along the section than had been planned.  At three places along the 
section we had replaced two stations with one half-way between to help make up 
time lost for bad weather. 

 
Leg 2 

We departed Tonga at 10 PM Saturday June 16 and steamed east to recommence the 
170°W CTD section.  En-route we had a Muster, a safety briefing and a cruise 
briefing on Sunday June 17.  We also did a test CTD station.  After reaching 
170°W, we continued the CTD section northward.  At 17° 30'S, we completed a 
CTD section westward across the deep western boundary current near the Tonga-
Kermadec Trench.  Through much of this period, winds were light.  After 
completing the section across the Tonga-Kermadec Trench, we steamed eastward to 
return to the 170°W section.  By this time, the winds had increased to 25 kts 
from the southeast and the eastward steam was slow.  We completed an additional 
trial CTD station, firing all bottles at 2500 m to do a blank test for CFC-12.  
We then continued the 170°W CTD section northward in decreasing winds, 
completed a section across the Samoan passage, and then continued the CTD 
section north along 168°W to the equator.  Winds remained light to moderate for 
the rest of the cruise.  A final test CTD station, firing all bottles at 2000 m, 
for a blank test for CFC-12 was completed.  We then steamed to Samoa, docking at 
Apia at 1000 hours Saturday July 7, 2001.  Enroute, the ship lost power on 
Wednesday July 4.  Because the main UPS did not function, many of the 
instruments in the labs had to be restarted to complete the analyses of samples 
and the processing of data.  


Bottom Depth  

One unexpected feature observed on the PDR was a previously uncharted sea-mount 
at about 2° 3.36'S, 168° 45.098'W. The sea-mount rose from the ocean floor at 
about 5300 m to 1400 m over a distance of about 10 km.  The bottom topography 
data bases derived from satellite altimeter data should be checked to see if 
this sea-mount has been previously identified.  We moved the location of one of 
the CTD stations about 10 nm from above the steep slopes of the sea-mount.   


SUMMARY 

There were many more samples collected than is usual for the small number of 
scientists that can be accommodated on board Franklin.  As a result, the cruise 
was a heavy work load for all the scientific party on board.  The available 12 
berths limits the National Facility's capabilities.  However, the cruise was 
successful.  Virtually all of the stations were completed and an excellent data 
set collected.  This data set should be a sound basis for detection of changes 
compared with previous observations.   


PROBLEMS AND RECOMMENDATIONS 

The main UPS did not work for the whole of this cruise.  As a result many of the 
instruments in the labs had to be restarted when the ship lost power on 
Wednesday July 4.  Fortunately, this was after completion of all of the CTD 
stations but many of the analyses were still being undertaken.  The UPS should 
be fixed as soon as possible. 

There are a limited number of spares on board.  We would have liked the ability 
to change the oxygen sensor but there were no further spares.  Also there was no 
spare sounder display.   

The University of Washington Niskin bottles were used throughout much of the 
cruise in an effort to minimise CFC contamination problems.  While these bottles 
gave good salinity results, the valves and spigots were difficult to operate and 
there were numerous comments on the CTD log sheets about leaks from the end 
caps.   

The bow thruster caused some problems as it can drop out when used at 100% 
power.  This was not a major problem for this cruise, but could lead to losing 
more time to bad weather on a cruise where the weather was generally worse. 

The Franklin should have a second MATLAB licence.  This software is used 
extensively for user analysis functions, and is now also used heavily by ORV 
personnel for processing of data.  The single licence leads to inefficiency in 
processing and analysing of cruise results. 

On all of the deep CTD casts wire tension was very high.  This necessitated 
hauling of the deep portion of casts at speeds as low as 20 m/minute to stay 
within recommended working tensions of the wire.  Similarly, winch speeds were 
low at the start of the casts when lowering the CTD in moderate and rough 
weather.  This is a result of not being able to put enough weight on the rosette 
package (so as not to load the wire excessively during the deep portion of the 
casts) to make it sink more rapidly.  If winch speeds could be kept at 60 

m/minute then the order of two days of ship time could have been saved.  It is 
recommended that as soon as an opportunity arises that a thicker wire should be 
used.  This would have the advantages of increasing the safety margin, saving 
ship time and increasing the payload thus expanding the National Facility's 
capability by allowing additional instrumentation to be placed on the CTD 
package.   


PERSONNEL 

Scientific participants on Leg 1

Neil White           CMR                       Cruise Leader
Ming Feng            CMR                       Watch Leader
Don McKenzie         CMR                       CTD 
Lindsay Pender       CMR                       Computing
Steve Thomas         CMR                       Electronics
David Terhell        CMR                       Hydrochemistry
Val Latham           CMR                       Hydrochemistry
Neale Johnston       CMR                       Hydrochemistry
Fred Menzia          University of Washington  CFC
Regina Cesario       University of Washington  CFC
George Anderson      University of Washington  Carbon
Mark Pretty          CMR  Carbon
    

Scientific participants on Leg 2

John Church          CMR                       Cruise Leader
Mark Rosenberg       ACRC                      Watch Leader
Bob Beattie          CMR                       Computing
Lindsay MacDonald    CMR                       Electronics
Kautu Temaki         Kiribati                  Observer  CTD
Gary Critchley       CMR                       Hydrochemistry
Kate Berry           CMR                       Hydrochemistry
Neale Johnston       CMR                       Hydrochemistry
Fred Menzia          University of Washington  CFC
Regina Cesario       University of Washington  CFC
George Anderson      University of Washington  Carbon
Jeanette O'Sullivan  CMR                       Carbon

 

ACKNOWLEDGEMENTS 

We received excellent support from the Ship's officers and crew, the scientific 
staff and Franklin Operations officers. We thank them and the shore based 
support staff for ensuring the success of the cruise. 

This cruise is a contribution to CSIRO's Climate Change Research Program, with 
partial funding provided by Australia's National Greenhouse Research Program. 
The CFC and US CO2 programs were supported by funds from the National Science 
Foundation, award OCE-0095960. 

Neil White,
Chief Scientist Leg 1,  

John Church
Chief Scientist Leg 2 

 
Original CSIRO Report can be found at:  
http://www.marine.csiro.au/marlin/rvdata1.htm
 
Figure 1.  Cruise Track from Wellington to Tonga to Apia, Samoa. The CTD station 
           locations are indicated by the dots. 


UNDERWAY DATA

Data processing completed by 
Bernadette Heaney, July 2001 
 

1.  VOYAGE DETAILS  

"Monitoring ocean climate change around Australia" 

 
1.1  Principal Investigators  

Susan Wijffels, CSIRO Division of Marine Research John Church, Bronte Tilbrook 
and Steve Rintoul, Antarctic CRC and CSIRO Marine Reserach Nathan Bindoff, 
Antarctic CRC, University of Tasmania Mark Warner, University of Washing, 
Seattle, USA John Bullister and Chris Sabine, NOAA-PMEL, Seattle, USA  

 
2.  GENERAL UNDERWAY DATA PROCESSING PROCEDURES  

A set of standard "underway" instruments are logged onboard the research vessel 
"Franklin"; this data is displayed in real-time onboard to assist with voyage 
planning and watch keeping; some of the data is subsequently processed onshore 
to produce a set of standard underway data.  

The data is logged to hourly ﬁles; the naming convention is explained in Section 
7.1 on page 12; (these are referred to as "raw" data ﬁles.  


                                                               UNDERWAY DATA PROCESSING



The standard underway data set is 5 minute values of ship position (latitude and 
longitude), water depth, sea surface temperature and sea surface salinity; air 
temperature, wind speed and direction, humidity, barometric pressure, solar 
radiation; corrected wind speed and wind direction, ship direction and speed and 
gust.  

All times in this report are UTC.  

A data format guide can be found at 
http://www.marine.csiro.au/datacentre/process/formats/uwy.htm  

 

3.  POSITION  

3.1  Instrument  

Ashtech G12 sensor - installed on Franklin July 2000.  


3.2  Raw Data  

3.2.1  vvyydddmss.gpoc ﬁles  

5 byte records of integer values of:time in integer seconds since 1970 (nb whole 
seconds, ie per second)latitude and longitude in signed microdegreessigned u and 
v components of velocity in mm/s 

3.2.2  vvyydddmss.gpo ﬁles  

A date and time string -gps date and time and system date and time at the start 
of each hourly ﬁle.  

full resolution NMEA VTG and GGA strings (5 per each second)  

 
3.3  Data Processing Procedures  

3.3.1  *.gpoc ﬁles  

One minute position values have been decided using the *.gpoc ﬁles; these are 
loaded into the navigation archive and available in the "underway" data set  



                                                               UNDERWAY DATA PROCESSING


3.3.2  *.gpo ﬁles  

10 second position data has been extracted from the NMEA GGA string. This is 
available in netcdf format and was used for correcting positions in CTD 
processing - this data will be added to the "Data Warehouse".  

 
3.4  Data Coverage  

Start 23-May-2001 21:31 
End 07-Jul-2001 14:17 
Tonga - port call 15-jun-2001 15:36 - 16-Jun-2001 09:06 
 

3.5  Data Quality  

The accuracy of non-differential data from the G12 is sub 5 metres; differential 
correction can increase the accuracy to 1 metre.  

From 22 June - 6 Jul there were unexplained gaps in the data of about 3-4 
minutes occuring around 0700 utc daily. We are continuing to investigate whether 
this is caused by an incorrect instrument setting or a fault with the 
instrument. Similar gaps were also noted on leg 2 of FR 9/2000.  



4.  WATER DEPTH  

4.1  Instrument  

Continuously logged data from the Simrad EA 500 Scientiﬁc echo sounder.  

 
4.2  Raw Data  

4.2.1  vvyydddmss.pdr  

date and time (UTC)
data indicator
depth in metres (depth below surface)
 





                                                               UNDERWAY DATA PROCESSING


4.2.2  yyyymmdd-hhmmss.ek5  

Sonar data echogram ﬁles.  

 
4.3  Data Processing Procedures  

Using *.pdr ﬁles, obviously bad depths are rejected. Depths are calculated for 
each whole minute by doing a linear regression through the data points within + 
30 seconds of each minute and removing any outliers, then re-ﬁtting until the 
standard error is acceptable.  



4.4  Data Coverage  

start 23-May-2001 21:49
End 07-Jul-2001 18:01
 
Tonga - port call 15-jun-2001 15:36 - 16-Jun-2001 09:00.The instrument was not 
working after the port call until 18-Jun-2001 09:50. 

 
4.5  Data Quality  

Standard error less than square root { (depth x .005) + 10 )}, ie less than 6.3 
metres in water 6000 metres deep, or less than 3.2 metres in water 100 metres 
deep. The sound speed is set to 1500 m/s and no corrections are made for true 
sound speed.  

The sounder incorrectly computed the bottom due to the maximum or minimum ranges 
being incorrectly set on several occasions so there is no data for these times 
(15-Jun-2001 03:58 07:40; 20-Jun-2001 05:21 - 06:50; 24-Jun-2001 09:43 - 10:11).  

Because of increased bow thruster activity on stations 6, 9 and 10 the bottom 
could not be correctly determined and this data has been deleleted.  

There was no echogram data for 5-Jul-2001 00:10 - 07:34 and 7-Jul-2001 03:46 - 
18:01. So these data could not be veriﬁed against plots.  

 





                                                               UNDERWAY DATA PROCESSING


5.  SEA SURFACE TEMPERATURE AND SALINITY  

5.1  Instrument  

Seabird thermosalinograph  

 
5.2  Raw data  

One minute averages  
date and time UTC  

quality indicator mean temperature at the inlet mean temperature at the probe 
mean conductivity mean salinity turner ﬂuorometer outputs (2) and spare channels 
(2) number of samples for the current minute  

 
5.3  Data Processing Procedures  

Surface values of sea temperature and salinity for each CTD station are compared 
with the thermosalinograph values. An offset is then applied to the sea surface 
temperature and salinity.  

 
5.4  Data Coverage  

TABLE 1. Data rejected 
      ___________________________________________________________________
      
               start  end       temperature    
       Date    time   time   salinity or both  comments
       ------  -----  -----  ----------------  -------------------------
       23-May  22:04  22:15          b         
       29-May  23:28  23:54          b         
       02-Jun  01:17  01:56          b         
       04-Jun  20:22  23:59          b         instrument being repaired
       05-Jun  00:00  23:35          b         instrument being repaired
       17-Jun  05:17  05:45          b         
      ___________________________________________________________________
      
 





                                                               UNDERWAY DATA PROCESSING


5.5  Data Quality  

There were many "spikes" in the salinity data up till the instrument was 
repaired.  

The CTD salinity values should be within .003 resolution, and the CTD 
temperature within .003 degrees ; the thermosalinograph only records to the 
second decimal place so the best pre-cision would be within .01 psu for salinity 
and .01 degrees for temperature.  

An offset offset was added to the salinity data of 0.004 and -.019 for 
temperature.  

Fluorometer data is not a standard product.  

Temperature and salinity data for this voyage compares well with CTD temperature 
and salinity data.  

 
6.  Meteorology data  

6.1  Instruments  

The vvyynnnhmm.met ﬁles contain values from the following selected instruments, 
as shown in the .metcal ﬁles. The meterorological station is mounted 17 m above 
sea level.  

 
TABLE 2.  vvyynnnhmm.met  

Instrument name 
AD590 solid state temperature      air temperature 
Vaisala solid state probe          humidity 
3 cup anemometer                   wind speed 
vane driving a potentiometer       wind direction 
licor LI-192SB                     radiation 
rain guage                         cummulative rain 
and values of                      ship speed and heading(from the doppler log 
and gyro) corrected 
                                   wind speed and wind direction
                                   max wind speed and wind direction
                                   max corrected wind speed and associated wind direction



                                                               UNDERWAY DATA PROCESSING


The Vaisala Digital Barometer is mounted 9 metres above sea level inside the 
bridge. 


TABLE 3.  vvyynnnhmm.vdb 
vaisala PA 11 A digital barometer  bartometric pressure and the 3 hourly trend



6.2  Raw data  

6.2.1  vvyydddhmm.metcal  

calibration and channel option ﬁle for Franklin meteorological ﬁle  

 

6.2.2  vvyydddhmm.met  

date and time (UTC) T/F to indicate if ship speed and direction data were 
available 1 minute averages of values for each channel as selected in the metcal 
ﬁle (usually air temperature, humidity, wind speed, wind direction, licor)  

1 minute psuedo channels (ship speed and heading, corrected windspeed and wind 
direction, maximum corrected wind speed and associated wind direction) 

each channel and psuedo channel has a quality indicator
 
6.2.3  vvyydddhmm.vdb  

Date and time UTC quality ﬂag barometric pressure in mBar three hourly trend 
quality ﬂags  

 
6.3  Data Processing Procedures  

Bad data is ﬂagged; 5 minute averages are produced and stored in the met data 
archive.  

 






                                                               UNDERWAY DATA PROCESSING


6.4  Data Coverage  

Start 23-May-2001 21:29 
End 07-Jul-2001 18:21 
Tonga - port call 15-jun-2001 15:36 - 16-Jun-2001 09:06 
 

6.5  Processed data  

A rise in air temperature noticed 09-Jun-2001 08:47 -09:24 when the vessel was 
on station and in light winds; this may be due to the superstructure heating 
and/or air from the smoke stack wafting over the sensor.  

The processed data has been loaded into the meteorology data archive; and the 
resultant eleven columns available for each 5 minute value are  

TABLE 4. Processed Meteorlogical data  

air temperature             uncorrected wind speed 
uncorrected wind direction  humidity 
barometric pressure         solar radiation 
corrected wind speed        corrected wind direction 
ship direction              ship speed 
gust 



7. OTHER 

7.1 Hourly ﬁle naming convention  

eg fr01079a00.gpoc vvyynnnhmm.int  

where vv is vessel where fr - franklin yy - year ddd - day through year a - hour 
through day a- 00; b 01 ... x 23 mm - 00 minute at start of ﬁle - usually ﬁles 
are started every hour - but if logging is restarted minute of restart .int - 
instrument gpo - gps gpoc - compressed gps pdr - precision depth recorder met - 
meteorological data vdb - barometer tsg - thermosalinograph  

 
7.2 Printed material  

Printed materials created during the processing are available from the Data 
Centre (Terry Byrne).  

 
ADCP

Data processing completed by 
Bernadette Heaney, September 2001 
 

1.  VOYAGE DETAILS  

"Monitoring ocean climate change around Australia"  

 
1.1  Principal Investigators  

Susan Wijffels, CSIRO Division of Marine Research 
John Church, Bronte Tilbrook and Steve Rintoul, Antarctic CRC and CSIRO Marine 
Research 
Nathan Bindoff, Antarctic CRC, University of Tasmania 
Mark Warner, University of Washing , Seattle, USA 
John Bullister and Chris Sabine, NOAA-PMEL, Seattle, USA 
 

2.  PROCESSING NOTES  

2.1  Features of this voyage  

In good weather conditions the depth range of the ADCP was good (350 m at 
maximum speed, 03-Jul-2001 10:47). There was very little bottom track data.  

 
2.2  Special processing for this voyage  

3 minute *.adp ﬁles returned from the ship were processed to produce a set of 
data corrected with 3DF heading. As it had been reported that the 3DF-GPS was 
not logging at some times during the voyage and also some concern that the ADCP 
logging also "hung" the data was also processed using heading from the gyro 
compass.  

The raw ping by ping ADCP data ﬁles (*.rawdp) were processed using the program, 
rawdp2adp which was run combining raw ADCP ping data with gyro compass heading 
to pro-duce 3 minute *.adp ﬁles which were then processed in the usual manner to 
produce the stand-ard processed data set. Reference layer averaging for the 
production of *.adp ﬁles was over bins 2 to 8.  

A subsequent examination of 10 reported gaps showed that during 7 of these gaps 
there was no gyro corrercted ADCP data as well indicating that the ADCP logging 
had "hung" as well at these times - this will be investigated further.  

 


                                                                   ADCP PROCESSING 


2.3  Proﬁles produced  

2.3.1  3DF GPS heading used  

Best available correction (bottom track preferred to direct GPS ship velocities, 
preferred to position-derived GPS velocities). No reference layer averaging in 
ﬁnal integration:
 
fr0105_3df.any: 3095 20 minute proﬁles.

fr0105_3df_60.any: 1037 60 minute proﬁles.


Bottom track corrected, no reference layer averaging in ﬁnal integration:
fr0105_3df.abt: 7 20 minute proﬁlesNon-integrated proﬁles (3 minute ensembles):

e_f0105_3df.any: 20634 3 minute proﬁles. All possible ensembles with best 
available correction (bottom track preferred to direct GPS velocities, preferred 
to position-derived GPS velocities).

GPS corrected (direct GPS ship velocities preferred to position-derived GPS 
velocities) the following *agp ﬁles were integrated using reference layer 
averaging over bins 2 to 8, then mergedwith ﬁles which were integrated using no 
reference layer averaging.

fr0105_3df.agp: 3095 20 minute proﬁles. 

fr0105_3df_60.agp: 1037 60 minute proﬁles. 
 


2.3.2  Gyrocompass heading used  

Best available correction (bottom track preferred to direct GPS ship velocities, 
preferred toposition-derived GPS velocities). No reference layer averaging in 
ﬁnal integration: 

fr0105.any: 3098 20 minute proﬁles. 

fr0105_60.any: 1038 60 minute proﬁles. 

Bottom track corrected, no reference layer averaging in ﬁnal 
integration:fr0105.abt: 7 20 minute proﬁles 



                                                                   ADCP PROCESSING 



Non-integrated proﬁles (3 minute ensembles):e_f0105.any: 20630 3 minute proﬁles. 
All possible ensembles with best available correction(bottom track preferred to 
direct GPS velocities, preferred to position-derived GPS velocities). 

GPS corrected (direct GPS ship velocities preferred to position-derived GPS 
velocities) the following *agp ﬁles were integrated using reference layer 
averaging over bins 2 to 8, then merged with ﬁles which were integrated using no 
reference layer averaging.  

fr0105.agp: 3098 20 minute proﬁles.  

fr0105_60.agp: 1038 60 minute proﬁles.  


2.4  Data Rejections  

2.4.1  Data ﬁles using 3DF GPS heading  

Out of a total of 20668 three minute ensembles, 20637 made it through to the 
processed ﬁle stage, with 575399 total good bins.  

Bin 1 rejections: 385  

Number of bins rejected due solely to:  

    %Good < 20%: 291641 
    %Good < 50% where RLA was bad and no acceleration: 4471 
    %Good < 70% where RLA was bad and there was acceleration: 168 
    Vertical velocity > 0.40 m/s: 153 
    S.D. of error velocity > 0.15 m/s: 1161
    Isolates : 0
    Absolute velocity > 2 m/s: 0
    dv/dz shear per metre in upper 200 m > 0.035 m/s: 0
    dv/dz sites: 37

Number of bins rejected due to multiple tests: 159260 

2.4.2  Data ﬁles using gyro compass heading  

Out of a total of 20665 three minute ensembles, 20636 made it through to the 
processed ﬁle stage, with 580305 total good bins.  

Bin 1 rejections: 367  


                                                                   ADCP PROCESSING 


Number of bins rejected due solely to:  

    %Good < 20%: 284629 
    %Good < 50% where RLA was bad and no acceleration: 3653 
    %Good < 70% where RLA was bad and there was acceleration: 129 
    Vertical velocity > 0.40 m/s: 281 
    S.D. of error velocity > 0.15 m/s: 1119
    Isolates : 0
    Absolute velocity > 2 m/s: 0
    dv/dz shear per metre in upper 200 m > 0.035 m/s: 0
    dv/dz sites: 43

Number of bins rejected due to multiple tests: 161162  


3.  CALIBRATION  

ADCP water proﬁle vectors (measured relative to the ship) are calibrated by 
being rotated through an angle alpha and multiplied by scaling factor 1 + beta. 
The rotational calibration pri-marily corrects for misalignment of the 
transducer with respect to the ship, of the ship with respect to the gyrocompass 
(or 3DF GPS), and the error in the gyrocompass (or 3DF GPS). The scaling 
multiplier primarily corrects biases arising from the proﬁler itself. Both of 
these calibrations make a large difference to the resultant currents, 
particularly because they are both applied to the usually large ship-relative 
currents. For example, a scaling mulitplier of 0.01 applied when the water 
velocity with respect to the ship is 6 m/s alter the measured absolute currents 
by 6 cm/s.  

The following calibrations were chosen for this voyage.  

 
3.1  Files using the 3DF GPS ship's heading:  

alpha = 0.987 +/- 0.3  

1 + beta = 1.012 +/- 0.006  

 
3.2  Files using the Gyrocompass ship's heading:  

alpha = 0.957 +/- 0.3  

1 + beta = 1.0099 +/- 0.006  

 
                                                                   ADCP PROCESSING 


4.  ERRORS  

The data provided should not be taken as absolutely true and accurate. There are 
many sources of error, some of which are very hard to quantify. Often the 
largest error is that of determining the ship's actual velocity.  

 
4.1  Accuracy of water velocity relative to the ship  

The theoretical approximate short-term velocity error for our 150 KHz narrow-
band ADCP is  

sigma =1/(pulse length X square root of pings per average)  

For a 3 minute ensemble with say 170 pings, using 8 m pulse, this gives a 
theoretical error of 1 cm/s for each value (that is, independently for each 
bin).  

For 20 minute proﬁles, with say 1150 pings averaged, the error in measuring the 
velocity of the water relative to the ship is probably reduced to the long term 
systematic bias. Of this bias, RDI says,  

"Internal bias is typically less than 1 cm/s, depending on several factors 
including tempera-ture, mean current speed, signal/noise ratio, beam geometry 
errors, etc. It is not yet possible to measure ADCP bias and to calibrate or 
remove it in post-processing."  

In addition, there are the transducer alignment and attitude sensor errors, 
which aminly cancel out where bottom-track ship velocities are used (Section 4.2 
on page 8). For GPS ship velocity corrected currents, the transducer alignment 
and attitude sensor errors probably have a residual effect after calibrating of 
roughly:  

0.3 cm/s per m/s of ship speed, due to, say, 0.3 degree uncertainty and 
variation in alignment angle.  

0.6 cm/s per m/s of ship speed, due to, say, 0.006 uncertainty and variation in 
scaling factor.  

This gives us, say, 0.67 cm/s error per m/s of ship speed, or 4.1 cm/s at 12 
knots.  

Other sources of bias might be the real-time and post-processing data screening, 
and depth-dependent bias.  

 
                                                                   ADCP PROCESSING 



4.2  Bottom track proﬁles  

Firstly note that errors in current speed arising from transducer alignment and 
attitude sensor limitations will substantially cancel out. Normally, the 
accuracy of screened bottom track data appears to be of the same accuracy as 
non-SA GPS, that is, about 2 -3 cm/s for a 20 minute proﬁle. However, the error 
in the current direction is at least the error in alpha.  

 




































HYDROLOGY PROCESSING

Data processing completed by 
Rebecca Cowley 8 November, 2001 
 

  

1  SUMMARY  

These notes relate to the production of calibrated hydrology data for the RV 
Franklin voyage Fr05/2001.  

Salinity, dissolved oxygen and nutrient data was processed. 128 deployments were 
completed, of which 128 have valid data.  

 

2  VOYAGE DETAILS  

The following information is taken from Voyage Summary Fr05/2001.  

 

2.1  Chief scientist  

Susan E. Wijffels (Chief Scientist) 
CSIRO Marine Research GPO Box 1538
Hobart Tasmania 7000 Australia
Tel: 03 6232 5450 Fax: 03 6232 5000 
Email: Susan.Wijffels@marine.csiro.au

John A. Church, Steve R. Rintoul, Bronte Tilbrook 
CSIRO Marine Research  

Nathan Bindoff 
Antarctic Co-operative Research Center 
University of Tasmania 
 
Mark Warner and Chris Sabine
University of Washington, Seattle, USA 
 
John Bullister 
NOAA-PMEL, Seattle, USA 
 





                                                                    HYDROLOGY PROCESSING 



2.2  Voyage objectives  

Establish a time series of full-depth repeat ocean measurements capable of 
resolving decadal and longer time-scale changes in the structure and carbon 
storage of the oceans around Australia, from Antarctica to the equator. Use 
these data to test climate model predictions and to,determine whether and how 
fast climate is changing due tothe Greenhouse Effect and/or natural decadal 
variability.  


2.3  Area of operation  

See Figure 1.  

 

3  PROCESSING NOTES  

3.1  Introduction  

The hydrology data was processed according to the procedures outlined in 
"Hydrology data processing procedures", First edition, Rebecca Cowley.  

Hydrology data is collected on the upcast of a CTD deployment, and salinity data 
is compared to calibrated CTD upcast burst data. Erroneous values are deleted 
from the dataset. Dissolved oxygen and nutrient data are compared deployment to 
deployment, with obvious outliers deleted from the dataset.  

CTD unit #20 was used on this voyage and 128 deployments were completed, of 
which 128 contain hydrology data. Salinity, dissolved oxygen and nutrient data 
were collected.  

 
3.2 Salinity  

Salinity data deleted from the dataset are shown in Table 1. All deletions were 
due to a bad sample or analysis. Many outliers were retained and can be 
attributed to the surface water structure which leads to anomolies between the 
CTD and hydrology data. The area of sampling had surface water with steep 
haloclines. The final CTD salinity - Hydro salinity offset plot is shown in 
Figure 2.  




                                                                    HYDROLOGY PROCESSING 


Table 1:  Salinity measurements deleted from hydrology dataset.  
            _______________________________________
                                        CTD-
             Deploy-  Rosette   Niskin  Hydro 
             ment     Position  bottle  salinity 
                                        difference
             -------  --------  ------  ----------
                 2        5      1107    -0.015
                 2       11      1210     0.075
                 7       18      1261    
                12       19      1231    -0.009
                12       22      1302     0.009
                19       10      1266    -0.014
                25       21      1104    -0.015
                38       21      1104    -0.011
                47        6      1227    -0.197
                51        5      1107     0.073
                53       21      1104    -0.053
                54       23      1114    -0.014
                60       22      1101     0.156
                64        1      1233     0.036
                64       13      1004     0.200
                70       21      1204    -0.020
                71       21      1204    -0.027
                72       22      1231    -0.015
                73        9      1027    -0.014
                73       22      1266    -0.012
                74       21      1204    -0.016
                75       23      1114    -0.024
                78       20      1221    -0.012
                82       12      1217     0.013
                85       18      1261     0.012
                86       22      1266    -0.017
                87       21      1204    -0.015
                90       19      1215     0.013
                93       17      1260    -0.011
               100       20      1114     0.011
               115       19      1266    -0.264
               121       21      1037    -0.023
               124       16      1251    -0.020
               124       19      1266    -0.111
              




                                                                    HYDROLOGY PROCESSING 
               


               125        9      1264    -0.012
               125       22      1010    -0.012
               126       24      1006    -0.012
            _______________________________________

 
Figure 2  CTD salinity - Hydro salinity final offset plot.  


3.2.1  Data Quality  

Results in the first leg (deployments 1 to 65) have less scatter than the second 
leg. This may be due to several factors or a combination of them:  

• Most of the scatter in figure 1 is in the top 200m of the deployments and may 
  indicate a different water structure in the surface layers of the second leg 
  compared to the first leg.  
• Different analysts and samplers.  
• Different climatic conditions.  


3.3  Dissolved oxygen  

Only one data point was deleted from the dataset (deployment 40, rosette 
position 11, bottle 1264), as the result appeared incorrect and was marked as a 
possible leaker in the CTD sheets. The corresponding nutrient and salinity 
results for this sample were not deleted as they appeared to be acceptable.  

The results for station 40 were added to the dataset post-voyage and an edited 
oxygen file (f0105040a.scp) was saved with the original oxygen files.  

3.3.1  Data Quality  

The dissolved oxygen data quality for this voyage is good.  

 
3.4  Nutrients  

All nutrient results were retained.  

3.4.1  Data Quality  




                                                                    HYDROLOGY PROCESSING 



Generally, the data appears to be of good quality, however there is no quality 
control report available for this voyage as yet.  





4  OTHER  

Niskin bottle numbers were altered from the 4-digit number to a three digit 
number for archiving purposes. The bottle numbers originally ranged from 1000 to 
1400, and were a mixture of NOAA and CSIRO bottles. In the archive, the bottle 
numbers have had the first digit removed. Users are advised to refer to the CTD 
sheets to confirm the original numbers. Copies of the CTD sheets are available 
from Terry Byrne at the Data Centre.  

Copies of printed materials and further information can be obtained from the 
Data Centre (Terry Byrne or Rebecca Cowley).  

Processing completed by Rebecca Cowley on 8 November, 2001. 
Rebecca.Cowley@csiro.au  



CTD PROCESSING

Data processing completed by 
Bob Beattie, October 2001  


1.  SUMMARY  

These notes relate to the production of QC'ed, calibrated CTD data from R V 
Franklin voyage Fr 05/2001 (24th may - 7th July, 2001)  

Data for 129 deployments was acquired using a Seabird SBE911 CTD unit ﬁtted with 
a 24 bot-tle rosette sampler. Pressures and preliminary conductivity values were 
computed using the Seabird-supplied calibration factors and calibrations 
provided by the CSIRO Marine Research Calibration Facility were used to compute 
the water temperatures. The data was subjected to automated QC to remove spikes  

The ﬁnal conductivity calibration was based on a single, whole-of-voyage 
deployment, all sample depths, sample grouping. This calibration had standard 
deviation of 0.00216 p.s.u.  

                                                                    CTD PROCESSING 



Dissolved Oxygen was calibrated by ﬁtting the data to an Owens and Millard 
(1985) model of the Beckman-style oxygen sensor. It is apparent that this model 
does not quantify all factors affecting the sensor output, which means that the 
CTD oxygen values should only be used for qualitative interpretation.  

 


2.  VOYAGE DETAILS  

2.1  Title  

Monitoring Ocean Climate Change around Australia. The Deep Ocean Time-series 
Sections  

 
2.2  Principal Investigators  

Susan E Wijffels, CSIRO Marine Research, Hobart  

John Church, Bronte Tilbrook and Steve Rintoul, Antarctic CRC and CSIRO Marine 
    Research, Hobart  
Nathan Bindoff, Antarctic CRC, University of Tasmania, Hobart,  
Mark Warner & Chris Sabine, University of Washington, Seattle, USA  

 

CTD PROCESSING NOTES  

John Bullister, NOAA-PMEL, Seattle, USA  


2.3 Voyage objectives  

According to the voyage summary, these were to:  

• Establish a time series of full-depth, repeat ocean measurements capable of 
  resolving decadal and longer time-scale changes in the structure and carbon 
  storage of the oceans around Australia, from Antarctica to the Equator.  
• Use these data to test climate model predictions and to determine whether, and 
  how fast cli-mate is changing due to the Greenhouse Effect and/or natural 
  decadal variability.  
 


                                                                    CTD PROCESSING 



For further details, refer to the Voyage Summary Report 
(http://www.marine.csiro.au/franklin/plans/2001/fr0900s.html).  

 
2.4  Area of operation  

Figure 1 Fr 5/01 CTD stations 




3.  PROCESSING NOTES  

3.1  Background Information  

The data was acquired with CSIRO's CTD unit #20, a Seabird SBE911 with dual 
conductivity and temperature sensors, an SBE13B, 'Beckman' dissolved oxygen 
sensor and a 24-bottle rosette.  

 
CTD Processing Notes  

The raw CTD data was converted to scientiﬁc units and written to netCDF format 
ﬁles for processing using the matlab-based, procCTD package. procCTD is 
described in the procCTD User's Manual.  

procCTD applies automated QC and preliminary processing to the data. This 
includes spike removal, identiﬁcation of water entry and exit, conductivity 
sensor lag corrections and the determination of the pressure offsets. It also 
loads the hydrology data and computes the match-ing CTD sample burst data.  

The bottle sample data was used to compute ﬁnal conductivity and dissolved 
oxygen calibra-tions. These were applied to the data and the ﬁles of binned, 
averaged data were produced.  


3.2  Pressure and temperature calibration  

Pressures were computed using the Seabird-supplied calibrations. The temperature 
sensors were calibrated on 8th May 2001 at the CSIRO Marine Research Calibration 
Facility. (Calibra-tion reports 159T and 160T.)  




                                                                    CTD PROCESSING 



An additional pressure offset correction was computed for each deployment by 
assuming a lin-ear drift between the pre and post-deployment, out-of-water 
pressures. The pressure offsets for the voyage are plotted in Figure 2, below. 
The pressure sensor shows slight hysteresis in its response, with the out-of-
water offsets for the deeper deployments being about 0.4 dB greater than the in-
water offsets.  


Figure 2:  Pressure Offsets, deployments 1-129 


The temperature sensors stayed in calibration during the voyage, as the mean 
outputs of the primary and secondary temperature sensors generally agree within 
+/- 0.2 mDeg C (Fig 3)  

 
Figure 3 Mean (Primary-Secondary) temperature, P >1000 dB 

 
3.3  Conductivity calibration  

The procCTD conductivity calibration procedures differs from our old (pre 
procCTD) procedures in that  

The calibration is applied in addition to the base (Manufacturer's0 calibration, 
rather than being applied to the raw data.  
 
No allowance is made for inter-deployment drift.  
 
It was decided to produce a single calibration, based on the sample data for all 
the deploy-ments, rather than break up the voyage into two, or more deployment 
groups. I consider this to be justiﬁed, as  

1.  There is no obvious deployment grouping in the in the plot of calibrated 
    (CTD - Bottle) conductivity Figure 4.  

 Figure 4:  Callibrated (CTD - Bottle) Conductivity 








                                                                    CTD PROCESSING 



Note:  

There is a suggestion that there is slightly greater scatter in the data for 
deployment 67 onwards. This can also be seen if these deployment groups are 
calibrated separately. The pre-67 (Leg 1) deployments give a calibration ﬁt 
standard deviation (SD) of 0.00179 psu and the post-67 (Leg 2) group an SD of 
0.00245 psu. The cause of this effect is not known, but it is presumably due to 
a difference in the sampling or analytical procedures used on the two legs of 
the voyage  

 
2.  The plot of uncalibrated (Primary - Secondary) conductivity for pressures > 
    1000 dB (Fig-ure 5) conﬁrms that there were no major shifts in the 
    calibration during the voyage.  


Figure 5:  Mean (Primary - Secondary) Conductivity, P > 1000 dB


There was about 2.0E-04 S/m relative drift between the sensors, between 
deployments 20 and 64. The secondary cell failed during deployment 65 and was 
replaced before deploy-ment 88. The relative drift from deployment 88 onwards 
was 1.0E-04 S/m.  

We have no way of telling which sensor was drifting, but no drifts of this 
magnitude are evi-dent for the primary sensor data (Figure 4). 2.0e-04 S/m 
translates to 0.0025 psu at 1.07 deg C, which is similar to the measurement 
precision that we are trying to achieve. This sug-gests that future versions of 
procCTD should include a drift component in the calibration.  

The all-deployment data results in a calibration of 

    Scale Factor (a1)       1.0003232    w.r.t. M/facturer's calibration 
    Offset (a0)            -2.12262E-04  ditto 
    Calibration S.D. (Sal)  0.00216 psu 

This is based on all the samples, apart from those excluded by procCTD's Remove 
Outliers option, and a small number of gross outliers that had been manually 
ﬂagged as 'bad'.  

The above calibration factors were applied to all deployments.  

 


                                                                    CTD PROCESSING 



3.4 Dissolved Oxygen Sensor Calibration  

3.4.1 Data Quality  

The oxygen data generally appears to be of good quality, but some problems were 
experienced, which resulted in the sensor being changed several times during the 
voyage (Thomas, 2001; MacDonald, 2001) 

 ____________________________________________________________________________

  Date    Deployment  Reported Problem  Action 
  ------  ----------  ----------------  ------------------------------------
            1-33                        Sensor S/N 130527 
  5 June     34       Steps in trace    Installed sensor S/N 130526 
             67       Steps in trace?   Swapped pump 
  29 June   109       Steps in trace    Re-installed original sensor (130527) 
  ____________________________________________________________________________


Note         
It is likely that the steps in the oxygen were due to contact problems, as 
similar problems have been rectiﬁed in the past by screwing in the sensor to 
increase the contact pressure.  

The following table lists deployments that appear to be affected by the above 
problems. It was compiled after a brief, visual inspection of the deeper, less 
rapidly varying segments of the oxygen proﬁles on the procCTD multi-parameter 
plots. No attempt has been made to correct or edit out the suspect data from the 
averaged ﬁles. 

 














                                                                    CTD PROCESSING 



______________________________________________________________________________

  Deployment  Problem 
  ----------  ----------------------------------------------------------------
      26?     Small spike at 2500 dB 
      28      'Steppy spikes', 2800 - 3000 dB 
      29      Bad step at 4500 dB 
      30      Bad step at 4000 dB 
      31      Bad step at 3500 dB 
      33      Small step at 3000 dB 
      40,     41?  Possible, small steps vic. 2100-3600 dB (both) & 3700 (40) 
      66      Many bad steps, esp 2300 -3300 & 4000 -5700 dB 
      68      Bad steps 4400 - 5400 dB 
      77      Small +ve spike at 4500 dB 
      79      Small -ve step, 4500 - 4700 dB 
     104      Small -ve spike, 4500 dB 
     107      Steppy proﬁle 1400- 2100 dB(?), Small, +ve spikes 3400 - 3700 dB 
     108      Very steppy proﬁle below 2000 dB 
______________________________________________________________________________


The above list is not exhaustive.  


3.4.2 Calibration procedure  

Our model for the response of the Dissolved Oxygen sensor is based on Owens and 
Millard (1985). It uses an iterated, 6-parameter ﬁt for the parameters:  

    Oxygen Current Slope (gain)
    Oxygen Current Bias
    Sensor Lag
    Activation Energy
    Reaction Volume
    Temperature weight

In principle, the last 4 factors should be constant for the sensor type and 
geometry, with only the Slope and Bias changing, as the sensor becomes depleted. 
In practice, we iterate some or all of the other components, as we have not yet 
determined the ideal default values.  





                                                                    CTD PROCESSING NOTES



In addition, there seems to be a hysteresis effect that is not included in the 
sensor model. This means that it is not possible to produce a good ﬁt of both 
the downcast and upcast sensor out-puts to the bottle data. (The 'downcast 
samples' are the downcast values for the same pressures as the 'Upcast sample 
bursts.)  

The data from the two sensors used during the voyage was calibrated separately.  

Reaction Volume and Temperature Weight were left at the default values of -29.6 
and 0.9 resp.  

Deployments 1 - 33; 109 - 129 (Sensor s/n 130527)  

1.  The iteration would not converge when I attempted to use all the deployments 
    to compute the Sensor Lag and the Activation Energy, so these were computed 
    using deployments 1-33 and were applied to both groups of deployments 
          Sensor Lag 15.223
          Activation Energy 4692.4 

2  The samples were calibrated against the downcast 'sample burst' data to 
   determine the Slope and Bias. 

   Deployment grouping  Current Slope  Current Bias  Fit S.D. (uMole/l)
   -------------------  -------------  ------------  ------------------
          1 - 33          3.303E-04     8.1388E-04        3.7635    
        109 - 129         3.663E-04     1.0965E-02        6.5826


Deployments 34 - 108 (Sensor s/n 130526)  

1.  All the deployments were used to compute the Lag and Activation Energy 
          Sensor Lag		40.145 
          Activation Energy	4385.1  


The lag is much higher than that for sensor 130527. I initially tried to use the 
value from this sensor, but this caused the down and upcast data to plot as 
separate populations.  
 






                                                                    CTD PROCESSING NOTES



2.  The deployments were arbitrarily divided into 3 groups of sequential 
    deployments, to reduce the effect of sensor depletion, and the bottle data 
    were calibrated against the down-cast 'sample bursts' to compute the Slope 
    and Bias. 

   Deployment grouping  Current Slope  Current Bias  Fit S.D. (uMole/l)
   -------------------  -------------  ------------  ------------------
         34-54           7.1586E-04    -9.666E-03         7.834
         55-74           6.9137E-04    -1.1903E-02        6.318
         75-108          7.0061E-04    -1.0964E-02        8.481
 

3.4.3 Discussion  

The sensor lags of 15.223 and 40.145 are higher than Seabird's suggested normal 
values of around 7.0. Lindsay Pender (pers. comm.) thinks that, because we are 
not accounting for the hysteresis, it is being expressed in the lag.  

There is a reasonable agreement between the bottle data and the downcast 
proﬁles, but it is by no means perfect. Figure 6 illustrates two typical 
examples  

 
Figure 6:  Downcast CTD oxygen + bottle oxygen (o) & upcast CTD oxygen (x) 
           (uMole/l) 


The calibrated oxygen data should only be used for qualitative and semi-
quantitative work. It is as good a ﬁt as can be expected, given the limitations 
of our current understanding of the oxygen sensor model.  

 
3.5  Other sensors  

No other CTD sensors were logged during this voyage.  










                                                                    CTD PROCESSING 



3.6  Binned data ﬁles  

The calibrated data was 'ﬁltered' to remove pressure reversals and binned into 
2dB averaged netCDF ﬁles. The binned values were calculated by applying a 
linear, least-squares ﬁt to the bin data and using this to interpolate the value 
for the bin mid-point. This is more accurate than simply taking the mean of the 
data.  

Each binned parameter in each bin is assigned a QC ﬂag. Our ﬂagging scheme is 
described in 
http://www.marine.csiro.au/datacentre/ext_docs/DataQualityControlFlags.pdf.  

The QC Flag for each bin is estimated from the values for the bin components. 
(We haven't yet documented this. For the moment, refer to the comments in matlab 
function matlab/tool-box/local/dpg/util/@QCFlag/estimate.m (or 'help 
estimate').) The QC Flag for derived quantities, such as Salinity and Dissolved 
Oxygen is taken to the worst of the estimates for the parameters from which they 
are derived.  

 

4.  References  

Beattie, R.D., in prep, procCTD CTD Processing Procedures Manual. FrameMaker 
    document /net/fdcs/opt/fdcs/src/ctd/doc/procCTD.fm  

Owens, W.B, and J.C. Millard Jr., 1985: A new algorithm for CTD oxygen 
    calibration. J. Phys-ical Oceanography., 15, 621-631.  

MacDonald, L, 2001, Marine Instrumentation Voyage Report for R V Franklin Voyage 
    Fr05B/2001, 16 June - 8 July, 2001 (unpub.).  

Pender, L., 2000: Data Quality Control Flags. 
    http://www.csiro.marine.au/datacentre/ext_docs/Data QualityControlFlags.pdf  

Thomas, S., 2001, Marine Instrumentation Voyage Report for R V Franklin Voyage 
    Fr05A/2001, 24 May - 16 June, 2001 (unpub.).  

 







HYDROCHEMISTRY, LEG 1
(Val Latham, Neale Johnston and Dave Terhell)

SUMMARY 

The voyage principal investigator was Susan Wijffels 

66 CTD stations were completed. 

Analyses carried out:

                 Nitrate/nitrite                          1467
                 Phosphate                                1467
                 Silicate                                 1467
                 Salinity (Guildline salinometer)         1448
                 Dissolved Oxygen (automated  titration)  1429


Rosette and CTD 

CTD #20 (new seabird) was used with the new 24 bottle.


Niskin bottles 

10L NOAA bottles. 


Salinity Offset 

For those taking a preliminary look at the CTD data, the CTD was reading about 
0.017psu low.


Detailed Report (Hydrochemistry)
ALPKEM 

The Alpkem A/D box experienced problems on the first day Steve Thomas determined 
that the chip controlling data output to the computer was faulty. He modified 
this chip and the A/D box worked until the power was switched off to the unit 
when the same problem occurred. He replaced the chip with a different chip which 
was modified which is currently working.

The A/D box and the detectors have all been earthed as it was noted that 
touching any part of the Alpkem caused the baselines to shift.
The back pressure on the 3 channels was modified to optimise the system as was 
the wetting agent.


                                                                          HYDROCHEMISTRY



Towards the end of the cruise the Nitrate standard calibration started to fall 
below the origin and give low SRM recoveries. This is being checked.


DISSOLVED OXYGEN 

The dissolved oxygen equipment worked well with no failures. A problem with the 
flasks is that some are getting chipped and have dangerously sharp edges which 
can be sanded blunt. Unfortunately there are not enough spare bottles to easily 
replace the chipped ones. 

The data when compared to WOCE data showed an offset at depth due to different 
units. The units were corrected and the data was then in agreement. The 
correction was to multiply the oxygen units in micromol/litre by 1000/rho where 
rho is the potential density of the water sample (at zero pressure) using the 
full potential density (~1026 or so kg m-3) not just the density anomoly.  

Oxy/kg = oxy/litre * 1000 / (potential density at zero pressure)


SALINITY 

On startup the salinometer 62547 was found to have a blockage in the air tube 
above the 2nd bottom arm of the cell. This was cleared by pushing water, then 
air down the thick plastic tubing attached to the 4 air tubes. It was found that 
it was only necessary to use air.

The optimum settings for the lab airconditioner were found to be:

          Parameter  Setting
          ---------  -----------------------------------------------
          Mode       Heat
          Temp       22 degrees
          Fan        High (showing fan icon with 3 sets of brackets)
          Flap       Fixed straight out

The above settings result in a Lab temperature approx 23 degrees..


 





HYDROCHEMISTRY, LEG 2
(Gary Critchley, Neale Johnston and Kate Berry)

Summary

The voyage principal investigator was Susan Wijffels 

63 CTD stations were completed (129 for legs A plus B) 

Analyses carried out : 
                                             Leg B  Leg A  Total in data set
    ---------------------------------------  -----  -----  -----------------
    Nitrate/nitrite                          1389   1467   2856
    Phosphate                                1389   1467   2856
    Silicate                                 1389   1467   2856
    Salinity (Guildline salinometer)         1437+  1448   2885 +
    Dissolved Oxygen (automated  titration)  1387+  1429   2816 +


Rosette and CTD
CTD #20 (new seabird) was used with the new 24 bottle rosette.


Niskin bottles
10L NOAA bottles. 

Salinity Offset
For those taking a preliminary look at the CTD data, the CTD was reading about 
0.017psu low.

Data

Some preliminary editing of salinity values, whilst not all necessarily wrong 
because of disagreement with CTD burst data, were removed in order to get a 
"cleaner" look at the comparative plots of sample versus CTD values. This was 
only completed up to station 108. Some dissolved oxygen data was edited, as 
necessary. Check data present indicates the data set is quite complete for 
stations 67 -129. Unfortunately, all the paperwork from Leg A was removed from 
the vessel at Tonga, which meant we were unable to verify the 
presence/absence/errors of data from leg A. There is also the chance that 
inadvertently, some leg B data was written over leg A data.









                                                                          HYDROCHEMISTRY



Detailed Report (Hydrochemistry)

ALPKEM 

The Alpkem A/D box worked for the duration after being repaired on the first 
leg. The Phosphate detector became unstable during the cruise and was replaced 
by the spare. On being checked by lindsay no fault could be found. The spare 
Phosphate detector lost power to the Lamp which was discovered to have been 
caused by a leak shorting out the remote control board in the back of the 
detector. The original detector was put back into service and was stable for 
several days and then again became unstable. The repaired spare was put back 
into the system. Again no problem could be found with the unstable detector. 
Feeling is either it's breaking down when gets overheated or else there's a bad 
connection  

The Nitrate standard calibration fell below the origin and gave low SRM 
recoveries. The problem was discovered to be a growth in the sample line, this 
was cleaned out and all the duplicate samples are being run. The two results 
will be compared back in Hobart and a final data set prepared. 

There was very little drift in any channel. A cooling coil was placed into the 
Phosphate line which has stabilised the chemistry so there is no drift with lab 
temperature changes. 

The cadmium is now stored under Nitrogen gas as it is thought that storage in 
the air in the lab deteriorated the cadmium. One of the lengths of Cadmium gave 
poor columns with a lot of trouble getting a regular bubble flow out of the 3 
coils made from it. 

On a whole the system is running very well. 


DISSOLVED OXYGEN 

The dissolved oxygen system performed very well, with good quality data being 
achieved. 

An incorrect determination of the bi-iodate normality was made (0.0091150N) and 
this was used for stations 76 - 92. The correct normality was determined as 
being (0.0100015N). The dissolved oxygen for these stations in the hydro 
program, micromoles per litre, were all multiplied by (0.0100015/0.0091150) to 
correct the effected oxygen data. 



                                                                          HYDROCHEMISTRY



SALINITY 

Salinometer 62 021 was used for all of leg B, set at a bath temperature of 24, 
and was found to be extremely reliable and stable for the whole voyage. 

Due to some overfilling of the bottles on some casts, it was quite difficult to 
obtain any consistent readings for some samples due to the inability to fully 
shake and mix the sample prior to analysis. 

After preliminary calibration of the CTD using the analysed salinities, a 
standard deviation of 0.0027 psu was achieved for full water column data. Below 
1000 metres, the standard deviation achieved was 0.0012 psu. The upper 1000 
metres had a lot of structure and some very steep gradients. 


The optimum settings for the lab air conditioner were found to be:

           Parameter  Setting
           ---------  -----------------------------------------------
           Mode       Heat
           Temp       21 degrees
           Fan        High (showing fan icon with 3 sets of brackets)
           Flap       Fixed straight out

The above settings result in a Lab temperature approx 24 degrees, with the small 
desk fans on, to move the air around the salinometer work area. 

TO DO 

Seawater lines on Port side sink and top fresh water tap on Starboard sink have 
very low pressure. Scheduled for next port period. (att ships working group) 

Look at using stills for water production for Milli-Q system as seemsd to be 
some problems with feed water quality from vap system. 

Look at using pinch valves rather than solenoid valves in the second system. 

SUPPLIES REQUIRED 

Thermometers for DO samples. 

Computers to replace the Octec computers. 



                                                                          HYDROCHEMISTRY



NUTRIENTS    
Rebecca Cowley, Susan Wijffels, December, 2008.  

This is an abridged version of the original report which contains more detail on 
the correction methods investigated. For the full version, contact 
Rebecca.Cowley@csiro.au.  


Introduction:  

Data was collected in the Southern Pacific Ocean along P15S during 2001. The 
nutrient data from the voyage was known to have large errors associated with it, 
particularly with nitrate and phosphate. The data has been reviewed and re-
processed, comparing it to the DISCO 1996 voyage along the same section. This 
report discusses the reprocessing method and results. All final results are 
reported in umol/kg. Nitrate concentrations refer to nitrate+nitrite.   



Procedure:  
1.  Re-calculate concentrations: From about run 40 to near the end of the 
    voyage, it was clear there was an issue with the Alpkem in both the nitrate 
    and phosphate channels. It was discovered at the end of the voyage that 
    there was a growth in both flow cells. This resulted in depressed peak 
    heights (see figures below - 'first set/second set' refers to the first and 
    second set of calibrants in each run).   

    The re-calibration method uses the f values for each level of calibrant, and 
    the sample results were calculated based on the f values from the next-
    highest calibrant.   

2.  Final plots to flag outliers: The final results were plotted against ctd 
    pressure and theta to identify outliers. The outliers were flagged as 'bad' 
    (with a 4 according to WOCE standards). Any results where pressure was 
    missing were flagged with a 4 and any where oxygen and salinity were missing 
    were flagged with a 3 (questionable).


Corrections to Nitrate/nitrite data   

1.  Use an average refractive index and blank value. In place of the actual 
    refractive index and blank values for each run, an average value from all 
    the runs was calculated and used in the peak height correction for each run. 
    This made some improvement in the precision of the results between runs. 

2.  Recalculation of data with sensitivity factors from the next highest 
    calibrant. Closer evaluation of the WOCE method (looking at actual OSU runs) 
    showed that OSU only utilised one standard when calculating the sensitivity 
    factors. This makes sense when the system is completely linear and the 
    sample concentrations are close to the calibrant concentration used. For 
    this data, the next highest calibrant from the sample concentration was used 
    to calculate the concentration. 


Corrections to Phosphate data   

1.  Mean RI and blank values subtracted from peak heights: The mean RI and blank 
    values for all runs was subtracted from the peak heights during the 
    calculations, rather than the individual run's values. 

2.  Recalculation of data with sensitivity factors from the next highest 
    calibrant. Closer evaluation of the WOCE method (looking at actual OSU runs) 
    showed that OSU only utilised one standard when calculating the sensitivity 
    factors. This makes sense when the system is completely linear and the 
    sample concentrations are close to the calibrant concentration used. For 
    this data, the next highest calibrant from the sample concentration was used 
    to calculate the concentration.


Corrections to Silicate data   

1.  Mean RI and blank values subtracted from peak heights: The mean RI and blank 
    values for all runs was subtracted from the peak heights during the 
    calculations, rather than the individual run's values. 

2.  Recalculation of data with sensitivity factors from the closest calibrant. 
    Closer evaluation of the WOCE method (looking at actual OSU runs) showed 
    that OSU only utilised one standard when calculating the sensitivity 
    factors. This makes sense when the system is completely linear and the 
    sample concentrations are close to the calibrant concentration used. For 
    this data, the next highest calibrant from the sample concentration was used 
    to calculate the concentration. 


Conclusions   

The data from this voyage is very noisy. The analysis for nitrate and phosphate 
was flawed, and the results difficult to repair. The bias in the nitrate and 
phosphate results was very much improved by calibration of the results using the 
f value of the next-highest calibrant, and the noise between runs was improved 
by using a mean refractive index and reagent blank value. Sensitivity (f-value) 
is calculated as   

                                          CA
                              f= (AC - A2)    

Where Ca is the calibrant concentration, AC is the absorbance of the calibrant 
and A2 is the absorbance of the matrix (or zero calibrant). To calculate the 
concentration of a sample, the peak height is multiplied by its regressed f 
value.   

The source of the bias in the results may be attributed to one or all of the following:   
• Poor performance of the instrument at the time of analysis was not addressed 
  immediately, and this is the main source of the bias. In particular, not 
  cleaning the system regularly seems to be the main problem.  
• Post-run analysis - positioning of the baseline markers during post-run 
  analysis could result in an offset.  
• Errors during calibrant make-up. The source of the inter-run noise may be 
  attributed to one or all of the following:  
• Instrumental noise - the Alpkem system was notoriously noisy.  • Errors during 
  calibrant make-up.  
• Contamination of samples during sampling/analysis.    

Estimation of error in the results   

Using the final method of calibration, the coefficient of variation in the 
results was  calculated (based on a pooled standard deviation of the QC samples 
that were run  through the entire voyage). Below are the coefficient of 
variation results for the final  results.  The average coefficient of variation 
for the results is:  Nitrate/Nitrite: 1.64%  Silicate: 1.35%  Phosphate: 5.3% 


References   

WOCE Operations Manual, Volume 3. WHP Office Report WHPO 91-1. WOCE Report No. 
    68/91. November 1994, Revision 1.  

CSIRO Hydrochemistry Operations Manual (1999). Cowley, R., Critchley, G., 
    Eriksen, R., Latham, V., Plascke, R., Rayner, M., Terhell, D  



CHLOROFLUOROCARBONS (CFCs) 

Principal Investigators Mark Warner and John Bullister
Sample collection and analysis provided by Frederick Menzia, and Regina Cesario 

Specially designed 10-l water sample bottles were used on the cruise to help 
reduce CFC contamination during R/V Franklin cruise FR0105 Between 50 S and the 
equator nominally along 170 W. 

Samples for the analysis of dissolved CFC-11, CFC-12 and  CFC-113  were drawn 
from approximately 1900 of the water samples collected during the expedition.  
Samples for carbon tetrachloride (CCl4 or CFC-10) analysis were drawn from 
approximately one quarter of the samples.  When taken, water samples for CFC 
analysis were usually the first samples drawn from the 10-l bottles. Care was 
taken to co-ordinate the sampling of CFCs with other samples to minimize the 
time between the initial opening of each bottle and the completion of sample 
drawing. In most cases, dissolved oxygen, DIC, and alkalinity were collected 
within several minutes of the initial opening of  each bottle. To minimize 
contact with air, the CFC samples were drawn directly through the stopcocks of 
the 10-l bottles into 100-ml precision glass syringes equipped with 2-way metal 
stopcocks. The syringes were immersed in a holding tank of clean seawater until 
analyzed.  

To reduce the possibility of contamination from high levels of CFCs frequently 
present in the air inside research vessels, the CFC extraction/analysis system 
and syringe holding tank were housed in a modified 20' laboratory van on the aft 
deck of the ship.  

For air sampling, a 45 meter length of 3/8" OD Dekaron tubing was run from the 
CFC lab van to the bow of the ship. A flow of air was drawn through this line 
into the CFC van using an Air Cadet® pump. The air was compressed in the pump, 
with the downstream pressure held at 1.5 atm using a back-pressure regulator. A 
tee allowed a flow (100 cc min-1) of the compressed air to be directed to the 
gas sample valves, while the bulk flow of the air (>7 l min-1) was vented 
through the back pressure regulator. Air samples were only analyzed when the 
relative wind direction was within 60 degrees of the bow of the ship to reduce 
the possibility of shipboard contamination. The Air Cadet pump was run for at 
least 60 minutes prior to analyzing each batch of air samples to insure that the 
air inlet lines and pump were thoroughly flushed  























                                                                          HYDROCHEMISTRY



Concentrations of CFC-11, CFC-12 and CFC-113 in air samples, seawater and gas 
standards on the cruise were measured by shipboard electron capture gas 
chromatography (EC-GC), using techniques similar to those described by Bullister 
and Weiss (1988). For seawater analyses, a 35-ml aliquot of seawater from the 
glass syringe was transferred into the glass sparging chamber. The dissolved 
CFCs in the seawater sample were extracted by passing a supply of CFC-free purge 
gas through the sparging chamber for a period of 4 minutes at 70 cc min-1. Water 
vapor was removed from the purge gas during passage through an 18 cm long x 3/8 
inch diameter glass tube packed with the desiccant magnesium perchlorate. The 
sample gases were concentrated on a cold-trap consisting of a 1/8 inch OD  
stainless steel tube with an  ~7 cm section packed tightly with Porapak N (60-80 
mesh). To cool the trap, isopropanol cooled by a Neslab Cryocool® refrigeration 
system was forced from a reservoir beneath the trap to a level above the packing 
with a stream of compressed nitrogen. After quickly bringing the isopropanol to 
the top of the trap, a low flow of nitrogen was bubbled through the bath to 
reduce gradients and maintained a temperature of -20oC. After 4 minutes of 
purging the seawater sample, the sparging chamber was closed and the trap was 
held open for an additional 1 minute to allow nitrous oxide (N20) to pass 
through the trap and thereby minimize its interference with CFC-12. The trap was 
isolated, the cold isopropanol in the bath was drained, and the trap was heated 
electrically to 125oC. The sample gases held in the trap were then injected onto 
a precolumn (30 cm of 1/8 inch O.D. stainless steel tubing packed with 80-100 
mesh Porasil C, held at 90oC), for the initial separation of the CFCs and other 
rapidly eluting gases from the more slowly eluting compounds. The CFCs then 
passed into the main analytical column (~183 cm of 1/8 inch OD stainless steel 
tubing packed with Carbograph 1AC, 80-100 mesh, held at 90oC) for final 
separation, and into the EC detector for quantification.  

The analysis of carbon tetrachloride was made on a separate, but nearly 
identical apparatus to the electron capture-gas chromatography system used in 
the analysis of CFC-11, CFC-12 and CFC-113 (Bullister and Weiss, 1988).  Samples 
were drawn in the same type of syringes used for the CFC analysis.  In the CCl4 
system, the sample injection port was flushed with 30-40 ml of sample before 
injecting sample into a calibrated loop (~30 ml).  After filling, an additional 
30 ml of water was pushed through the loop and allowed to overflow.  For 
analysis, a valve was switched and  the water sample held in the loop was pushed 
into the stripper with the same CCl4 free nitrogen that was used to strip the 
sample.  The gases removed from the sample were dried while passing through an 
~18 cm x 3/8 inch OD tube of magnesium perchlorate and concentrated on a  trap 
packed with four inches of Porapak N and held at -30oC during trapping.  At the 
conclusion of stripping, the trap was heated electrically and the contents swept 
onto the precolumn (0.53mm I. D. x 30 meters, DB624 capillary column, 45oC)) 



                                                                          HYDROCHEMISTRY



with clean nitrogen.  The desired gases passed on to the main analytical column 
(0.53mm I. D. x 30 meters, DB624 capillary column, 45oC), before the precolumn 
vented the later peaks.  All other aspects of the analysis were the same as the 
CFC analysis.   

Both of the analytical systems were calibrated frequently using a standard gas 
of known CFC composition. Gas sample loops of known volume were thoroughly 
flushed with standard gas and injected into the system. The temperature and 
pressure were recorded so that the amount of gas injected could be calculated. 
The procedures used to transfer the standard gas to the trap, precolumn, main 
chromatographic column and EC detector were similar to those used for analyzing 
water samples. Two sizes of gas sample loops were present in the CFC analytical 
system, while four calibrated sample loops were used in the CCl4 system. 
Multiple injections of these loop volumes could be made to allow the system to 
be calibrated over a relatively wide range of concentrations. Air samples and 
system blanks (injections of loops of CFC-free gas) were injected and analyzed 
in a similar manner. The typical analysis time for a seawater, air, standard or 
blank sample was 15 minutes on the CFC system and 20 minutes on the CCl4 system. 

Concentrations of the CFCs and CCl4 in air, seawater samples and gas standards 
are reported relative to the SIO93 calibration scale (Cunnold, et. al., 1994). 
Concentrations in air and standard gas are reported in units of mole fraction 
CFC in dry gas, and are typically in the parts-per-trillion (ppt) range. 
Dissolved CFC and CCl4 concentrations are given in units of picomoles per kg 
seawater (pmol kg-1). CFC and CCl4 concentrations in air and seawater samples 
were determined by fitting their chromatographic peak areas to multi-point 
calibration curves, generated by injecting multiple sample loops of gas from a 
working standard (PMEL cylinder 33790 for CFC-11, CFC-12 and CFC-113;  PMEL 
cylinder 33780 for CCl4) into the analytical instrument. The concentrations of 
CFC-11 and CFC-12 in this working standard were calibrated before and after the 
cruise versus a primary standard (36743) (Bullister, 1984). No measurable drift 
in the concentrations of CFC-11 and CFC-12 in the working standard could be 
detected during this interval. Full range calibration curves were run at 
intervals of  3 days during the cruise. Single injections of a fixed volume of 
standard gas at one atmosphere were run at intervals of 1 to 2 hours to monitor 
short term changes in detector sensitivity.  

Extremely low (<0.01 pmol kg-1) CFC concentrations were measured in water 
between 2000 and 3000 meters at the Northern end of the section between 15 ºS 
and 45 ºS along this section. Based on the median of CFC concentration 
measurements at these  depths, which is believed to be nearly CFC-free, blank 
corrections will be applied to the data set. If the measured CFC concentration 



                                                                          HYDROCHEMISTRY



for a sample is very low, subtracting a blank can result in a very small 
negative number reported.  Blank corrections will be applied to the CCl4 data if 
necessary. 

On this expedition, we estimate precision (1 standard deviation) of 1-2% or 
0.005 pmol kg-1 (whichever is greater) for dissolved CFC-11, 2% or 0.005 pmol 
kg-1 (whichever is greater) for dissolved CFC-12 measurements.  F-113 and CCl4 
precision is yet to be determined as there was F113 contamination for most of 
the cruise. 

A number of water samples had clearly anomalous concentrations relative to 

adjacent samples for one or more of the trace gases. These anomalous samples 
appeared to occur more or less randomly during the cruise although more 
frequently for F12 and F-113, and were not clearly associated with other 
features in the water column (e.g. elevated oxygen concentrations, salinity or 
temperature features, etc.). This suggests that the high values were due to 
individual, isolated low to moderate level CFC contamination events. The source 
of the contamination was eventually tracked down to eucalyptus oil that is 
regularly injected into the ships air conditioning unit.  It appears that some 
of the oil was collecting on the bottles and absorbing CFCs.  Measured 
concentrations for all samples will be included in subsequent reports, but those 
showing contamination will be given a quality flag of either 3 (questionable 
measurement) or 4 (bad measurement). 

 



















APPENDIX A -- MARINE INSTURMENTATION 
(Lindsay MacDonald)

 
CTD  

The Seabird 911 CTD # 20 itself performed very reliably throughout this leg of 
the cruise however some problems were encountered with some of the sensors. 


CONDUCTIVITY SENSORS 

The secondary conductivity sensor had failed on the final cast of the first leg. 
It  had cracked at pressure and no longer tracked the primary cell which agreed 
with the bottle data. 

It was swapped with serial # 042234 from the spare CTD # 19. 

However when this cast was plotted the following day it was found that this cell 
had tracked the primary to 1000m and then started producing spurious data and 
eventually no output. 

The remaining sensor # 042235 from the spare CTD was swapped for this unit. It 
worked perfectly for the remainder of the cruise. 


D.O. SENSOR 

There seemed to be the occasional voltage jumps or steps displaying in the 
dissolved oxygen sensor early in leg2. This sensor along with its electronics 
package had been swapped from the spare unit on leg 1 of this cruise. 

Data from the altimeter, which uses another of the analogue input channels on 
the CTD, were checked on the same casts as the problem oxygen data but no 
correlation was found. The D.O. data plot then seemed to settle down. On 29/6/01 
the D.O. sensor showed very unstable readings. The D.O. sensor was removed from 
its package and swapped with that on the spare CTD. It had been used on leg 1 
prior to the swap. New oil and O rings were used. The D.O. output then gave good 
stable readings, which seemed to follow that of the WOCE cruise data a few years 
prior to this cruise. 


BOTTLE FIRING FAILURES 

Bottle # 18 failed several times. It was thought that there maybe some foreign 
matter lodged in the mechanism. It was tested several times using random firing 
procedures by sending the appropriate commands to the annex port. Rubber bands 
were used to simulate a bottle lanyard but with a lot lower tension in air. 


                                                    APPENDIX A -- MARINE INSTURMENTATION



It was discovered that the lanyard from bottle # 18 was most likely catching on 
a cable tie on the seacable going to the load cell. The cable ties were changed 
to a different position and some electrical tape was used to cover the cables 
and the problem did not re-emerge. 

The lanyard from Bottle position # 19 also began catching but this time in the 
gap left at the top of the rosette frame join. This should be filled with epoxy 
or similar to prevent this occuring again. 


CABLE 

At the end of the cruise the CTD cable was inspected for kinks and corrosion. 
The only corrosion evident was the usual surface rust. The secondary clamps on 
the rosette termination were opened up and inspected and found to be near new 
condition. A re-termination of the cable was deemed unnecessary at this stage. 
This should most likely be carried out in Brisbane prior to Fr0701. 


WINCH MONITORING SYSTEM 

On the initial CTD test cast at the start of leg 2 there was no data output from 
the CTD winch monitoring PCB. This required the top to taken off the box and the 
connector supplying power and the backup battery removed and then re-installed 
to reset the firmware. The first time this was done carried out data was being 
transmitted but it was corrupted. A second reset fixed the problem. It is not 
very good practise to do this. There is a breaker on the ships office level that 
can be reset to achieve the same result. 

The following night I was called from sleep to perform this once more. After 
this the problem did not reoccur for the remainder of the cruise. 

On 21/6/01 large spikes were evident on the CTD tension continuous plot when the 
CTD was on board with no load on the strain gauge. This had disappeared by the 
next day. 


EA500 SCIENTIFIC SOUNDER 

At the beginning of leg 2 the display on the EA500 appeared very noisy. 
Adjustments were carried out to try and improve this. Problems were encountered 
locking onto the bottom once the ship was in depths over 3000 metres. Eventually 



                                                    APPENDIX A -- MARINE INSTURMENTATION



on the 3rd day of leg 2 the bottom could not be found and the display was 
extremely noisy. The transmit pulse could not be heard in the lower decks of the 
ship so the EA500 was opened up and investigated. The High Voltage Led was not 
illuminating. The power supply board appeared difficult to remove so a decision 
was made to install the spare EA500 from the Electronics Lab but keep the same 
transceivers. This required swapping most of the boards to the spare frame. 
However on power up there was no video output from this unit. The display and 
ethernet card was then swapped but still no display. 

The power supply board was then removed from the spare unit and the original 
configuration with the new power supply was put together. This rectified the 
problem and the sounder was back in business. The problem was traced to an open 
circuit power resistor. Some replacements for this have been ordered from Hobart 
to repair the spare card on Fr06/01. 

Unfortunately on the 30/6/01 the EA500 Video display stopped working. There 
appeared to be no EHT voltage. There are no circuits provided with this monitor 
and no parts kept on board which could possibly fix the problem. An old NEC 
Multisync monitor was found in a box in the laundry store and connected to the 
EA500 output. It produced a very poor display of the video output but sufficient 
to see the bottom and change settings. This only lasted about 1 hour before 
completely losing sync, vertical height and illumination. 

A spare NEC multisync from Hobart will be used for Fr06 and the EA500 monitor 
hopefully repaired between Fr06 and 07. 

 
SATELLITE COMMUNICATIONS 

On the first day of leg 2 there were problems using email on both Inmarsat B and 
Minisat M.  

The former reported a busy signal on every attempt for the first few days. The 
Minisat could be used for voice communication but not data. Resetting the annex 
port for the Minisat however, rectified this problem. 

After approximately 4 days the Inmarsat B system began working again. The 
problem was most likely with ship based equipment. The fax machine however would 
not work on this system. The fax machine for the Optus mobilesat system which 
was out of range for this cruise was connected up to the Minisat system and 
worked successfully for the cruise. 




                                                    APPENDIX A -- MARINE INSTURMENTATION



U.P.S. 

A load test was carried out on the U.P.S. battery bank as the U.P.S. has not 
been holding up when the ships power failed since the ship left Hobart. 

A piece of timber with three 24volt lamps wired in series was used for the load. 
This load  drew 6.5 amps from a well charged battery. 

All batteries produced a similar result with a voltage reading across the 
battery of approximately 12.4 volts with the load applied, except for 2. The 
battery on the middle shelf at the front on the RHS dropped to about 1.2 volts 
under load. The battery on the top shelf, front , LHS dropped voltage faster 
than the others and eventually after 30 or 40 seconds was down to 9.5 volts. 

These batteries will be replaced when the ship gets to Brisbane at the end of 
Fr06/01. A spare should also be kept on the ship under trickle charge. 

On the 4/7/01 on the return journey the ships engine stopped causing a power 
blackout. The UPS did not hold up as had been the case in May. The ships 
Engineers tell me that on blackout the UPS throws the inverter input from the 
ships mains to the battery bank but approximately 30 seconds after the blackout 
that the battery isolation breaker trips as the batteries cannot hold the load 
on the inverter. This should all be checked out again when the batteries are 
replaced during the 1 month port period in Brisbane at the end of Fr06. 


ALPKEM 510 NUTRIENT DETECTORS 

Two Nutrient Detectors used by the chemists had problems during this leg.  

One stopped working altogether. The lamp was not operational. This was traced to 
be no lamp ground being switched to the lamp filament. The cause of this was 
found to be some liquid which had managed to flow into the rear of the unit and 
get under a ribbon connector on the remote control PCB. This caused a 400 ohm 
leakage path between 2 pins on the connector which was sufficient to pull a 
normally logic high state down to a low. This flowed on through some logic 
circuitry and eventually preventing a transistor from switching the lamp ground. 

All care should be taken to prevent chemicals spilling into electronic 
equipment. 





                                                    APPENDIX A -- MARINE INSTURMENTATION



The other Nutrient detector has an intermittent noise problem. All power 
supplies check out ok. Each time this unit was brought into the Electronics the 
fault seemed to disappear. 

     ___________________________________________________________________

                                            Required 
                                    Used    Attention  Further 
                                    On      During     Action   
      Equipment/Systems             Cruise  Cruise     Required  Action
      ----------------------------  ------  ---------  --------  ------
      Ctd Mkiiib #2                                       
      Ctd Mkiiic #8                             
      Ctd Mkiiic #10                             
      Rosette Go 12bottle                             
      Rosette Go 24 Bottle #1                             
      Rosette Go 24 Bottle #2                             
      Eg&G 1401 Deck Unit #1                             
      Eg&G 1401 Deck Unit #2                             
      Rosette Frame 12 Bottle                             
      Rosette Frame 24 Bottle 2.5l                             
      Rosette Frame 24 Bottle 10l                             
      Seabird Frame 24 X 2.5 Litre                             
      Seabird Frame 24 X 10 Litre     X                        
      Altimeter #162                             
      Altimeter #163                  X                        
      Pinger  #1190                             
      Pinger  #1266                             
      Seabird Ctd #19                             
      Seabird Ctd #20                 X         X               
      Ctd Sliprings/Cable             X                        
      Fluorometer Seatech  142s                             
      Chelsea Transmissometer                             
      Seatech Transmissometer                             
      Licor U/W Light Sensors                             
      Adcp                            X                        
      Moon Pool Trolley               X                        
      Ea500                           X         X               
      Ashtech 3d Gps                  X         X               
      Ashtech G12 Gps                 X                        
      Fugro Dgps Receiver                             
      Winch Monitoring System         X         X               
      


                                                    APPENDIX A -- MARINE INSTURMENTATION



      Vaisala Balloon Receiver                             
      Vaisala Data Converter                             
      Met Station                     X                        
      Synchro/Digital Converter       X         X               
      Doppler Log Interface           X                        
      Pa System                       X                        
      Seabird Tsg                     X                        
      Fluorometer (Wetlabs)           X         X               
      Ez Net                    
      Datataker Gp Lab                             
      Datataker Spare Elec W/Shp)                             
      Scintillation Counter                             
      Radiation Monitor                             
      Westinghouse Mobilsat                             
      Ctd Display Pc (Big Ctd)        X                        
      Xbt Display Pc                             
      Ctd Display Pc                  X                        
      Op's Room Pc (Pc-1)             X                        
      Op's Room Pc (Pc-4)             X                        
      Winch Control Area Pc           X                        
      Winch Display Pc                X                        
      Electronics Workshop Pc         X                        
      Critec Ups (Computer Room)      X         X          X     
      Fdcs-Log-1                      X                        
      Fdcs-Log-2                      X                        
      Fdcs-User                       X                        
      Xwindows Monitors               X                        
      Delp Monitors                   X                        
      Video Camera System             X                        
___________________________________________________________________















APPENDIX B - COMPUTING REPORT FOR FRANKLIN VOYAGE FR05B/2001
(Bob Beattie)


1.   WORK DONE

1.1   System management

1. Lindsay Pender complained of very slow network traffic to fdcs-log-1 during 
   the latter part of 5A. Communications eventually failed completely. Re-
   seating fdcs-log-1's UTP connector seemed to fix the problem. e.g., I was 
   able to transfer a 31.5Mb file between fdcs-log-1 & fdcs-user in under 44 
   secs (approx. 700 Kb/s).

2. The password on the Computer Room Remote Annex 2000 had been set to a non-
   standard value when the unit was replaced during Fr01/01. I reset the 
   password to the 'normal' setting.
3. Email was used more heavily than ever. 2.18 Mb of messages were sent and 3.25 
   Mb were received for the 21 day leg, which translates to approx. 260 Kb/day. 

   The email system played an important part in the research. e.g. the CFC team 
   were in regular contact with their colleagues in the US, both to supply them 
   with data updates or to seek assistance with solving the several instrumental 
   and sampling problems that they encountered during the voyage

   On two occasions, the NEXUS password server in Hobart failed over a weekend 
   and I had to phone Al Blake to ask him to restart it. We are indebted to him 
   for his efforts.

4. INMARSAT B
   When making email transfers, I usually tried to make at least one attempt 
   with the 'B', before I switched to the Mini M. Of the 91 attempts that I 
   logged, 38 succeeded, 27 failed to connect because the line was reputedly 
   'BUSY' and on 26 occasions it dropped out after the connection was 
   established.

   I could see no obvious pattern to the failures, except on one occasion, when 
   it dropped out 3 times while the vessel was turning slowly to come onto 
   station. The success rate did seem to improve in the last week of the voyage.

   In contrast to the 'B', the 'M' behaved almost flawlessly, with only one or 
   two drop-outs for the entire voyage.


1.2  Data acquisition and acquisition software

1. The way program now handles way-points in the Western hemisphere. DELP now 
   displays Western hemisphere positions correctly.


                                                          APPENDIX B -- COMPUTING REPORT


2. There was no provision for monitoring VOY-LOG or WLOG on DELP. These now 
   publish data on sms and were added to the DELP options file.

3. Data backups are taking an increasingly long time. It took 5.25 hrs to do the 
   final, 14Gb /data backup of fdcs-log-2 and even longer on fdcs-log-1, which 
   was slowed down by the data collection system.

   I adopted a different strategy this voyage to try to spped things up. The 
   /data backups were (meant to be) made well ahead of time and any new files 
   were picked up in a final daily_cpio.

   We will have to re-think our backup strategies. I tried using tar, intead of 
   cpio, in the hope of being able to achieve higher blocking factors, to reduce 
   tape usage, but it seemed to store about the same amount of data as a cpio 
   backup & could not handle continuation tapes.

   The backup scripts now return the time of completion, so we know how long 
   they took.

4. Early in the voyage, we engaged in email correspondence with Jeff Dunn & 
   Bernie re the quality of the ADCP data. Jeff suspected that the pitch & roll 
   corrections were being applied incorrectly. We did not pursue the matter any 
   further, as we presume that Jeff will be investigating the problem. 



3.  

1.3   CTD data collection and processing

This took up a large part of my time during the voyage 

1. There were two failures of the secondary Seabird conductivity sensors during 
   the voyage. On both occasions, the failures were detected using procCTD 
   plots. The replacement sensor has been very reliable, tracking to within 
   0.0011 - 0.0021 S/m of the primary sensor for the remainder of the voyage.

   The calibration of the secondary conductivity sensor was modified in the 
   readCrw configuration file each time the sensor was changed. (It would be 
   useful if the configuration editor had a 'cut and paste' facility to copy a 
   calibration from one configuration file to another.)

2. Gary Carol's CTD notes were converted to Frame & updated to reflect our 
   current procedures.
3. The procCTD manual was updated.


                                                          APPENDIX B -- COMPUTING REPORT


4. Several minor modifications were made to procCTD
   • The 'head-room' in procCTDGetBurstData was increased from 2 to 6 minutes 
     after it complained that there was no data for 10 of the 24 bottles on a 
     deep test station. (The CTD had 'drifted' deeper after sampling had 
     started, putting the missing samples in the downcast.)
   • procCTDApplyCondCal now gives the correct indication of 'deployment 
     progress' 


1.4  Analysis & display software

I spent some time debugging & developing Gary Carol's CTD sectioning and 
profiling programs. Further work needs to be done. There are still a few bugs 
and a GUI user interface would be useful. I almost completed one for the 
profiling programs, but I didn't have time to adapt Lindsay's deployment 
selection GUI. 

John Church found the programs to be very useful for monitoring data quality, 
especially for highlighting problems with the hydro data. The rapid feedback 
meant that the problems could be rectified when things were fresh in peoples' 
minds. It is very difficult to remember what was done when you are trying to 
rectify a problem several months down the track. 

1.5   Miscellaneous
Mark Rosenberg, Lindsay Macdonald & I carried out tests with the new CSIRO xbt 
system, in response to a request from Lindsay Pender & Alex Papij. The results 
were emailed to Hobart. 


2.   Problems & recommendations

1. Several procCTD suggestions & problems have already been communicated to 
   Lindsay by email and are not dealt with here.

2. procCTD's automated bad data detection does not reject steps in the 
   conductivity due to cell contamination. This would best be done using an 
   interactive, graphical procedure.

3. fdcs-log-1's console went blank early in the voyage, but the computer 
   continued to run OK, so I did nothing about it until a power failure forced a 
   reboot. The screen still didn't come up until I re- seated the keyboard 
   cable.



                                                          APPENDIX B -- COMPUTING REPORT



4. fdcs-user experienced problems twice, one of them requiring a reboot. It is 
   suspected that /tmp filled up due to the large number of plots being spooled 
   from the pc's. We need a mechanism for periodically flushing /tmp or for 
   deleting the print files after the jobs have completed.

5. The DELP nav output is periodically being corrupted. I suspect that this is 
   due to a process over- writing the GPO sms latitude & longitude.

6. The Ashtec 3DF continues to hang periodically and has to be restarted, either 
   by power cycling or by stopping and starting the logging software several 
   times until it acknowledges the RESET command sent by the logging software. 
   This has to be a firmware problem, and we should continue to make 
   representations to Ashtec until it is solved.

7. The ADCP software hangs periodically - it seems to happen when 3DF data has 
   been unavailable for some time. The ADCP logging & display processes have to 
   be killed and restarted, usually twice, before logging will resume.

8. The Doppler Log logging controller reported bad data on a number of 
   occasions. I did not have sufficient free time to investigate this further.

























DATA PROCESSING NOTES

Date        Contact   Data      Action         Summary
----------  --------  --------  -------------  ---------------------------------
2004-10-29  Kozy      CO2       DQE            Begun
            I have a file with all hydrographic, CFCs and Carbon data from P15S 
            section from Australian scientists. I have put SR3 sign for this 
            section instead and could not understand why I cannot find P15S. I 
            have also a cruise report. Do you have all hydrographic data for 
            this section and non of the carbon-related and CFC measurements?

            I will make all necessary QA-QC work as usual and reformat these 
            data to WHPO format and send the file to Steve.

2004-12-10  Kozyr     CFCs        Submitted    exchange file, includes all parameters
            I received the hydrographic and CO2 measurements from Susan E. 
            Wijffels(CSIRO), made all QA-QC and sent the data to CCHDO on 
            12/10/2004. 

            From: KOZYR, ALEX
            Email address: kozyra@ornl.gov
            Institution: CDIAC/ORNL
            Country: USA 
            
            The file:
                fr0501_woce_exchange_cfc.txt - 827435 bytes
            has been saved as:
                20041210.131553_KOZYR_P15S_SR03_fr0501_woce_exchange_cfc.txt
            in the directory:
                20041210.131553_KOZYR_P15S_SR03
            The data disposition is:
                Public
            The bottle file has the following parameters:
                SALNTY, SALNTY_FLAG_W, CTDOXY, CTDOXY_FLAG_W, OXYGEN, 
                OXYGEN_FLAG_W, SILCAT, SILCAT_FLAG_W, NITRAT, NITRAT_FLAG_W, 
                PHSPHT, PHSPHT_FLAG_W, CFC-11, CFC-11_FLAG_W, CFC-12, CFC-
                12_FLAG_W, CFC113, CFC113_FLAG_W, CCL4, CCL4_FLAG_W, TCARBN, 
                TCARBN_FLAG_W, ALKALI, ALKALI_FLAG_W
            The file format is:
                WHP Exchange
            The archive type is:
                NONE - Individual File
            The data type(s) is:
                Bottle Data (hyd)
            Documentation
                The file contains these water sample identifiers:
            Cast Number (CASTNO)
            Station Number (STATNO)
            Bottle Number (BTLNBR)
            Sample Number (SAMPNO) 
            
            KOZYR, ALEX would like the following action(s) taken on the data:
                 Place Data Online 
            
            Any additional notes are:
            This is an exchange formatted file I received from John Bullister 
            with all data para-meters measured during the Deep-Ocean Time-Series 
            Sections (DOTSS), Repeat Section P15S/SR03. I've made all QA-QC on 
            carbon-related measurements (TCARBN and TALK). I also include a 
            cruise report file for your information.

2004-12-10  Kozyr     TCARBN/ALK  Submitted    along w/ data report
            I have just submitted an exchange formatted file I received from 
            John Bullister with all data parameters measured during the Deep-
            Ocean Time-Series Sections (DOTSS), Repeat Section P15S/SR03. I've 
            made all QA-QC on carbon-related measurements (TCARBN and TALK). 
            There is only one file I could submit at once using your web page, 
            so I attached here a documentation file for P15S/SR03 cruise.

2004-12-13  Anderson  CO2         Submitted    Exchange file; to be put online
            Copied files submitted by A. Kozyr from INCOMING to
            .../p15s_2001a/original/20041210_KOZYR_P15S_2001. 

            Bullister gave this file to Kozyr. It is in exchange format and 
            contains all data parameters measured duringDeep-Ocean Time-Series  
            Sections (DOTSS). 

            These data need to be put online.

2005-01-04  Key       CO2         DQE Begun    will provide per S. Wijffels' OK
            Kozyr and I are currently working on a SR03, 2001, Franklin cruise. 
            The files include CFCs and carbon as well as the routine stuff. I've 
            contacted Susan Wijffels to try to clean up a few questions on flag 
            values for the routine measurements and to make sure iit is OK to 
            submit the results to you.

2005-01-04  Key       BTL         DQE Begu     will submit per S. Wijffels' OK
            Kozyr and I are currently working on a SR03, 2001, Franklin cruise. 
            The files include CFCs and carbon as well as the routine stuff. I've 
            contacted Susan Wijffels to try to clean up a few questions on flag 
            values for the routine measurements and to make sure iit is OK to 
            submit the results to you.

2007-01-10  Wijffels  BTL         Data Update  Date correction
            The date should be> 2000 9 27 23 53 15 

            That is 2000-09-27 @ 23:53GMT - add 12 hours to your date! I've 
            attached the julian/gregorian .m files we use. The other values look 
            correct. 

            I've attached ascii versions of the hydrology data which should be 
            pretty easy to figure out for checking date and location 
            translations. 

            I've also attached pdf's of the hydrology data processing. Please 
            add a caveat if possible, that the nutrient data are suspect on both 
            cruises - bottle salts and oxygens are good. 

            I'll send the CTD data processing reports along in another email. 

2007-01-10  Wijffels  Cruise Report  Submitted  CTD processing report


2007-04-10  Key       BTL            Submitted
            Metadata to accompany data submission of today. The version of the 
            data I started with originated with Alex Kozyr (12/22/04). Most 
            flags in that file were "1". I did primary QC on all parameters. 
            Some notes included in the README file attached. Bottom depths 
            estimated from global topography. All calculated parameters with my 
            functions (depth, theta, sigmax, aou). I have not tried to get 
            H3/He3 data from Lupton. Permission received from all PIs to 
            submit/post. I will notify them that I submitted to you and to 
            CDIAC. All units and flags WOCE standard. Place Data Online 

            1/25/05 Initialized README file for Franklin re-occupation of P15S
            S. Wijffels Ch. Sci.
            EXPOCODE: 09FA200105_1
            leg 1: 5/24/2001 Dpt Wellington, NZ
            6/16/2001 Arr. Tonga
            leg 2: 6/16/2001 Dpt Tonga
            7/7/2001 Arr Apia, Western Samoa
            24bottle X 10 liter rosette
            Splus name p15s2001a 

            Hydro: Who - Wijffels; Status - final; S Plus - up to date
                  Notes: File from Kozyr 12/22/04
                  Bottom depths estimated, bottle depths calculated
                  Flagged Salt: 76-1-14
                  See Johnson et al. 2007; Roemmich et al. 2007. 
            Nuts/O2: Who - ; Status - final(?); S Plus - up to date
                  Notes:
                  Deep nitrates are about 1umol/kg lower than NOAA 1996 occupation
                  Flagged NO3: 5-1-19,31-1-10,103-1-17,107-1-23,122-1-15
                  Deep phosphates are about .05 umol/kg lower than NOAA occupation
                  Flagged PO4: 1-1-24,5-1-19,96-1-20,103-1-17,109-1-8
                  Deep silicates are very similar to the NOAA occupation
                  Flagged Si: 5-1-9,53-1-5,64-1-1
                  Deep aou are very similar to the NOAA occupation
                  Flagged O2: 8-1-10,40-1-11,58-1-18,64-1-1,78-1-16,107-1-23
                  Note from Wijffels 4/10/07 - nuts still need more QC. 
            TCO2: Who - B. Tilbrook and C. Sabine; Status - final; S Plus - up to date
                  Notes: Batch 52 CRM

                  Shipboard value for 66 samples 2005.45+/-0.83
                  Deep tco2 are very similar to the NOAA 1996 occupation
                  Flagged: 10106 14105 24113 53105 78116 78115 107123 111101
                        113121 113110 115119 115107 128119 
            TA: Who - B. Tilbrook and C. Sabine; Status - final; S Plus - up to date
                  Notes: Batch 52 CRM
                  Shipboard value for 37 samples 2224.72+/- 1.03
                  Deep alk are very similar to the NOAA occupation
                  Flagged: 8108 10114 11115 12110 14107 14105 20107 28110 30103
                        37120 53105 58124 81124 91105 99104 106119 113110 116103 
            fCO2: Who - f; Status - not sampled; S Plus -
                  Notes: 
            pH25: Who - ; Status - not sampled; S Plus -
                  Notes: 
            CFC: Who - M. Warner and J. Bullister; Status - final; S Plus - up to date
                  Notes: full cfc-11&12 with partial CCl4 

            
            C-14: Who - ; Status - not sampled; S Plus -
                  Notes: 
            
            C-13: Who - ; Status - not sampled; S Plus -
                  Notes: 
            
            H-3/He-3: Who - J. Lupton; Status - no data yet ; S Plus -
                  Notes: 
            
            Other:
            References:
            Johnson, G. C., S. Mecking, B. M. Sloyan, and S. E. Wijffels. 2007. 
                Recent bottom water warming in the Pacific Ocean. Journal of 
                Climate, accepted.
            Roemmich, D., J. Gilson, R. Davis, P. Sutton, S. Wijffels and S. 
                Riser, 2006. Decadal Spin-up of the South Pacific Subtropical 
                Gyre. J. Phys. Oceanogr., in press

2008-12-04  Key       BTL             Submitted    NUTs data reprocessed
            Introduction:
            Data were collected in the Southern Pacific Ocean along P15S during 
            2001. The nutrient data from the voyage was known to have large 
            errors associated with it, particularly with nitrate and phosphate. 
            The data has been reviewed and re-processed, comparing it to the 
            DISCO 1996 voyage along the same section. This report discusses the 
            reprocessing method and results. All final results are reported in 
            umol/kg. Nitrate concentrations refer to nitrate+nitrite. 

            Procedure:
            1. Re-calculate concentrations: From about run 40 to near the end of 
               the voyage, it was clear there was an issue with the Alpkem in 
               both the nitrate and phosphate channels. It was discovered at the 
               end of the voyage that there was a growth in both flow cells. 
               This resulted in depressed peak heights (see figures below - 
               'first set/second set' refers to the first and second set of 
               calibrants in each run). The re-calibration method uses the f 
               values for each level of calibrant, and the sample results were 
               calculated based on the f values from the next-highest calibrant.
            2. Final plots to flag outliers: The final results were plotted 
               against ctd pressure and theta to identify outliers. The outliers 
               were flagged as 'bad' (with a 4 according to WOCE standards). Any 
               results where pressure was missing were flagged with a 4 and any 
               where oxygen and salinity were missing were flagged with a 3 
               (questionable). 

2008-12-16  Key        BTL            Submitted    NUTs/CO2/ALK/CFCs/He
            Status: public
            Action: Place Online 

            You will get another copy of this file when I submit the CARINA 
            tarball. I seriously doubt there will be any differences. If there 
            are, it will be reflected in the datestamp within the datafile. 


2009-08-18  Kappa      Cruise Report  Website Updated  New TXT report online
            New cruise report inludes:
            1) Original cruise report submitted by PI
            2) Data reports available at CSIRO website:          
               http://www.marine.csiro.au/marlin/rvdata1.htm
            3) Data processing notes 

2009-08-28  Kappa      Cruise Report  Website Updated  Nutrients report added 
            New cruise reports, both text and pdf versions, now contain a report 
            on Nutrient data processing, and are online.

