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DI258 cruise report

1. 0 T T 0 0 T T signal at bottom of mixed layer 500 spikes 7 500 500 4 1000 4 1000 1000 4 1500 F E 1500 1500 f o eo ks step 2000 f 4 2000 2000 4 2500 f 4 2500 2500 f 4 bottom reflection 3000 3000 I I I i 3000 1 L 110 105 d d 00 95 3 4 5 6 7 34 8 34 9 35 35 1 corrected backscatter temperature C salinity average of the four beams and 30 data ensembles for weab 1 ctd temperature w245 1 ctd salinity w245 1 0 T 0 T T T 0 signal from bottom of mixed layer 200 200 200 400 400 400 increase between 400 and 800m 600 f 4 600 600 E S 800 800 800 o o ks 1000 f 4 1000 1000 1200 f 1200 1200 increase at top f lower layer 1400 strong bottom 1400 1400 28 reflection 1600 1600 i L 1600 I 4 j 95 2 4 6 34 8 34 9 35 35 1 Fig 17 Backscatter temperature and salinity profiles for CTD14239 100 corrected backscatter temperature C salinity upper plots and for CTD14245 lower plots Text section 2 6 2 Fig 17 10 4 0 25 9 4 0 245 e S gJ 0 24 E F 7 10235 E 2 5 R 64 0 23 2 o T S8 54 0225 amp z 5 9 w 4 1022 8 2 E 2 o 2 3 0 215 E amp 24 021 a 14 0 205 0 T 1 T T T T 1 0 2 05 Nov 10 Nov 15 Nov 20 Nov 25 Nov 30 Nov 05 Dec 10 Dec 15 Dec Date Duplicate difference Thiosulphate titre Fig 18 Time series of the volume of thiosulphate req
2. 13 25 12 75 12 25 11 75 11 25 10 75 10 25 9 75 9 25 8 75 8 25 7 75 7 25 6 75 6 25 5 75 5 25 4 75 39 0 37 0 35 0 33 0 31 0 29 0 27 0 25 0 23 0 21 0 19 0 17 0 15 0 13 0 11 0 9 0 7 0 5 0 3 0 1 0 Fig 21 a TSG salinities for Discovery 258 Leg 1 35 2 T T T T T T Raw i Corrected x Bottle 35 1 35r 34 9 Salinity 34 8 34 7 312 314 316 318 320 322 324 326 328 330 Julian day b TSG salinities for Discovery 258 Leg 2 35 6 T T T T Raw elei eo Gee Ge oe Reo Corrected Pepe chee Mee cones cam pese eel v7 x Bottle l 35 4 Salinity Co 1 x 35 34 9 34 8 34 7 332 334 336 338 340 342 344 346 348 Julian day Fig 22 Calibration of thermosalinograph TSG salinity for leg 1 upper graph and leg 2 lower graph Text section 9 1 3 Fig 22 Leg 1 Leg 2 Po rer sepe d pee pao ejus totes eer et use 00 312 314 316 318 320 322 324 326 328 0 00 time JDAY 1 fluor ug l 2 ptir W m2 3 chla ug l o nh e ns gettin x ere nm 0 00 time JDAY 1 fluor 2 ptir 3 chla Fig 23 Underway time series of total solar irradiance ptir surface fluorescence fluor and chlorophyll concentration measured on samples collected from the ship s non toxic water supply chla Leg 1 upper graph and leg 2
3. c Mean std dev of corrected error at each station AS Conductivity correction factor 1 00004924535078 Fig 4 Salinity errors for first lowered Sea Bird CTD Text section 2 2 1 195 200 205 210 215 220 225 230 235 Discovery station number minus 14000 Fig 4 a Uncorrected error in S E r o ep e ILE UE 500r E nu c J S 1000 eee S ERR gt EEE p EPER AEEA EEE PPAR A AEEA EEE A E AEE 4 a s i KJ A 5 9 4500 PITE PP TETEY TEE Se VT PPP pcr Belt oh tech BRA PT 4 e 2 a 2000 s tt pte es 7 2500 F d H 3000 i i l i i 0 02 0 019 0 018 0 017 0 016 0 015 0 014 0 013 AS x 10 b Corrected error as fn of s d of pressure 4 T T T T T T T T BE hes ec og dedi niodo d cx ps E TT 2r E i 4 TM 2 S Mean abs error 0 00086927 ih n pO Mean error s d 9 41e 07 0 0011104 e sit Tee 4 wu A Orc Cae ZEE m VR qon pd uar E HEEL LLL Eine toe 4 1 F e T v oat w og 2 ee 2 l 3 i 2 i i i i i i 0 0 2 0 4 0 6 0 8 1 1 2 1 4 1 6 1 8 Std dev of P for period surrounding bottle fire x 10 c Mean std dev of corrected error at each station 3 T mj T T T T 2r ses I n 1 L a o Ll T t 4 B i B z 0 M wands ee ae a ee ae i ius 2j es DEP UR PAR
4. 2 2 1 Lowered Sea Bird CTD CTD measurements of salinity from around the time of bottle firings were compared with the salinity of water sampled from the bottles measured using the salinometer The CTD values were averaged over a period from 2 sec before to 5 sec after the bottle firing this period is set as a pair of parameters to the DatCnv stage of the Sea Bird processing on the PC discussed elsewhere Raw errors E Sopp Ssa are plotted against pressure in Fig 4 Only values from the primary conductivity sensor will be considered here Most of these errors are already small between 0 002 and 0 000 but the accuracy can be improved still further by using the salinometer values for calibration as follows As on earlier cruises the fundamental correction is applied to conductivity rather than salinity A slope correction only is applied with zero offset as recommended in the Sea Bird software manual 1 Calculate the conductivity C from the bottle salinities and CTD pressures and temperatures using either peos83 or the Matlab routine sal2cond m in data61 sjb394 like all other Matlab routines mentioned here CTD conductivites C orp are already present in the sam files 2 Calculate the average value K Cir Css of the ratio of the salinometer to the CTD conductivity Anomalous values are excluded from this calculation ad hoc in the present case stations where the raw error E in salinity was less than 0 004 or great
5. 2 63 2 42 1 78 4 06 6 29 6 61 10 93 15 55 17 68 19 83 22 67 53 56 52 40 52 39 53 28 30 04 32 03 34 02 36 22 42 70 36 83 49 68 58 81 7 57 18 44 20 22 20 32 19 69 21 45 25 91 30 36 46 27 2222222222222222222222222222222222222222222222222222222222225 14216 3 serial sampling nets only 2 pup 14222 trap problem 14224 trap problem 14232 trap problem 14240 DM worked OK BO 22 1 01 05 59 60 53 83 N 36 2 41 W EN 22 1 01 08 53 60 49 99 N 36 10 19 W G07 Float BO 22 1 01 12 00 61 2 91 N 37 2 59 W G07 14244 CTD BE 22 1 01 12 24 61 246 N 37 304 W BO 22 1 01 13 19 61 236 N 37 2 56 W EN 22 1 01 14 43 61 258 N 37 2 73 W Table 19 RRS Discovery 258 station list leg 2 MarProd Station no Instru Code Date Time GMT Latitude Longitude Comments position cast haul ment DD MM YY HH MM site F07 14245 CTD BE 28 11 01 13 28 65 15 068 N 29 29 551 W BO 28 11 01 14 03 65 15 147 N 29 29 168 W EN 28 11 01 15 05 65 15 405 N 29 28211 W F07 14246 ARIES BE 28 11 01 15 44 65 14 865 N 29 29 483 W BO 28 11 01 17 22 65 12 703 N 29 37 316 W EN 28 11 01 18 52 65 11 064 N 29 45 797 W F05 14249 CTD BE 29 11 01 04 14 64 20 111 N 31 59 586 W BO 29 11 01 05 06 64 20 215 N 31 59 342 W EN 29 11 01 06 43 64 20 441 N 31 58 932 W F05 14249 LEK BE 29 11 01 07 00 64 20 439 N 31 59 011 W BO 29 11 01 07 22 64 20 305 N 31 59 3322 W BU 29 11 01 07 55 64 20 136 N 32 0 333 W EN 29 11 01 08 15 64 20 083 N 32 1 305 W F05 14250
6. Deployment technique The method for deploying the frame evolved during the cruise and current best practice is to use a deck winch leading athwart ships to a large trawl block braced with bar and aft over the A frame To achieve this two 250 m lengths of wire were attached to the deck winch and joined with paired Hammerlock shackles Due to the loss of the Scanmar tow fish the birdcage hydrophone was used to receive the Scanmar signal and was deployed onto the lifting wire after the first 250m of wire had been run out It was generally recovered before lifting the frame and always well before the end of the first 250m of wire was recovered This deployment technique is not ideal as the frame is very vulnerable to damage between the deck and the water s surface and this problem is exacerbated by the extreme pitching motion experienced on the aft deck under all but the calmest sea conditions The experience on this cruise suggests that it is vital that the frame can be left in a position to receive mains power during start up and shut down operations as the power drawn provides the primary diagnostic tool for finding out what is going on within the Behemoth without opening the waterproof housing Also it is both simpler and safer if the battery pack can be charged whilst it remains in the frame In the future the frame should ideally be deployed from amidships to reduce the risk of damage to the equipment and increase the range of sea conditio
7. The main autoanalyser power supply was replaced early in the cruise after it fused a consequence of spray entering a poorly secured deadlight behind the instrument in heavy seas Following the port call a new set of pump tubes was fitted These were again renewed following the medevac approximately half way through leg 2 At this point the compressor controlled air injection on the phosphate line was converted to roller pump tube controlled injection in a bid to stop the phosphate baseline shifts that began to occur after the mid cruise port call The wash time was increased to 90 sec for leg 2 as the nitrate calibration curve was found to be non linear on the first station following the port call In hindsight this was probably caused by the new cadmium column bedding in and thus a mistake as it increased the run time by about 3096 and possibly contributed to the phosphate problems observed throughout leg 2 The minimum sample time with the current analyser configuration compatible with square N and Si peaks is 90 sec however 45 sec appears to be an adequate wash time to get acceptable resolution of N peaks when the cadmium column is bedded in nicely The computer that logged the data from the analyser stopped communicating with the instrument on 12 December and was replaced by the computer that controlled the oxygen instrument having taken the precaution of preloading the software onto both machines Data files were compressed using winzip a
8. 29 11 01 oP 64 21 22N 32 32 674 T 1 T 1 10 15 20 25 CALABUS C5 m 3 Discovery 258 02 12 014 orc 54 T 0 5 S Lr 1 15 20 25 T 10 CALABUS C5 m 3 T 0 5 PC ARIES 296 Discovery 258 12 12 01 o 56 52 34N 298 19 10w Ext n lesedasid m 0 5 10 15 20 25 CALABUS C5 m 3 Fig 24 pe 41 37 33 29 25 21 17 13 9 C 60 000 Calanus m C 30 000 Calanus m Sampled but no Calanus Fig 25 Winter abundance of Calanus finmarchicus stages C4 and C5 in the eastern North Atlantic Combined data 1991 2001 from ICOS TASC and other net samples yellow circles FRS Marine Laboratory Aberdeen black circles calibrated OPC and Discovery 258 red circles preliminary OPC data Note that definitive MarProd data will not be available until summer 2002 after samples have been sorted and actual counts made Text section 10 3 1 3 Ff 11 15 Fig 25 id 7 To AC 3 F i E SST C 4 6 8 10 12 14 Fig 26 Sea surface temperature composite image for 19 25 November 2001 upper with associated analysis of frontal features lower Text section 13 Fig 26 Fig 27 Examples of the photographic record of the cruise ARIES recovery above and zooplankton sorting right Text section 14 MUSTARD 01 Fig 27
9. 53 52 51 50 gt 4 q A 45 35 25 15 5 actual cast positions e CTD ARIES planned but not occupied Fig 1 Sampling sites for the first Marine Productivity cruise Discovery 258 and a few other planned stations Text section 1 3 Fig 1 53 52 51 50 4 45 35 25 15 5 MarProd Nov Dec 01 e CTD ARIES o Oceanus 369 Aug 01 Txx TASC Icelandic stns Fig 2 Combined figure of Discovery 258 sampling sites Oceanus 369 stations and Icelandic sites sampled during the TASC Trans Atlantic Study of Calanus project Text section 1 3 Fig 2 degrees lat 1000m oc allctds AA 50 0 Ss op Jor pp or TE dp ppp py Tor pap TT EE 50 40 30 20 10 lon degrees Fig 3 Map of potential temperature C at 1000 m gridded from Oceanus 369 and Discovery 258 stations shown as dots Ellipse of influence for gridding was 3 lon x 1 5 lat so beware extrapolation Text section 1 3 Fig 3 a Uncorrected error in S 500r _ 1000 bar 2 1500 2000 Pressure 2500 3000 K ee o ec Se gt oo oso tee o 3500 8 4 2 0 2 4 6 AS x10 b Corrected error as fn of s d of pressure AS 2r AL Mean abs error 0 00085991 a Mean error s d 6 0192e 06 0 0013908 ere 6 0 5 1 15 2 Std dev of P for period surrounding bottle fire
10. Then use ftp to transfer the btl files which are ASCII to data61 bottle the bottle directory Same technique as for CTD files step 4 10 samO This converts the ASCII btl file into the firing file fir14191 or similar It contains all the basic variables from the CTD master 24hz file excluding flag and also their standard deviations The firing file is written to the bottle directory and its permissions set to read only To avoid cluttering the bottle directory new conventions have been set up as follows At the start of the cruise mkdir sub directories to the bottle file with 3 character names matching those needed on the cruise e g fir sal chl oxy nut The relevant files will be held in each sub directory only sam and btl being in the bottle directory 11 sam1 This converts the fir file into the master sam file First derived variables salin salin2 potemp potemp2 are calculated by peos83 Then the file is copied to the sam file adding names from the sam names file all in the bottle directory sam names contains only those names that are NOT already in the fir file Thus the names in sam names are typically botsal botsalf nio2 3 sio3 po4 botoxy toxfix and chla A new variable is created for each of these names with the units and value given in the sam names file Two further variables are added at the start of the sam file namely sampnum and statnum The station number is statnum e g 14193 and the sampnum is
11. between 2230 and 0215 followed by the LEK between 0300 and 0530 using the same calibration equipment A 38 1 mm tungsten carbide standard target sphere was suspended approximately 10 m below each transducer in turn and data were collected using the usual logging systems for each echosounder A CTD cast immediately before the calibration gave an average sound speed of 1494 5 ms in the top 12 m of the water column which gave the following expected target strengths for the standard target taken from standard curves Foote 1990 J acoust Soc Am 88 1543 6 38 kHz transducers 42 34 dB 120 kHz transducers 39 52 dB 200 kHz transducers 39 15 dB Data were collected to calibrate both the integrator SV gain and the Target Strength TS gain for each transducer In most cases after the initial data collection at the standard gain setting 26 5 dB in all cases several further iterations of adjusting the gain to a new calculated value and collecting data were performed for each parameter for each transducer The final calculations of the calibrated gain values were made at a later date The final gain values were calculated solely from on axis pings where possible or in the case of the LEK 120 kHz transducer pings which were as near on axis as possible 0 18 off axis in one direction only In the case of the single beam transducers TEK 120 kHz and 200 kHz the position of the sphere relative to the transducer was taken fr
12. oxygen concentration between all the duplicate pairs sampled was 0 38 There is no indication of systematic changes in analytical precision with time Fig 18 Richard Sanders 7 2 Nutrients 7 2 1 Methods Concentrations of nitrate nitrite hereafter nitrate reactive orthophosphate hereafter phosphate and orthosilicic acid hereafter silicate were measured on unfiltered water samples using a Skalar Sanplus autoanalyser situated in the forward port corner of the Decklab This was unsatisfactory given the wildly fluctuating temperatures in this laboratory The proposed containerisation of chemistry on the second MarProd cruise Discovery 262 should assist in this respect Samples collected using the CTD were drawn directly from the Niskin bottles into brand new 40ml Coulter Counter vials Samples collected using ARIES were drawn through FRS supplied tube into brand new 40ml Coulter Counter vials Both sets of samples were stored at 4 C in darkness prior to analysis and analysed as soon as practicable Analysis generally took place within 12 hr but was on occasions delayed by as much as 24 hr The analytical methods followed those laid out by Kirkwood in the Skalar user manual with the following exception The flow rates of the two phosphate reagents were increased at the beginning of the cruise from 0 1ml min to 0 23 ml min and the flow rate of the phosphate sample was increased from 0 8 ml min to 2 ml min This was in order to alter the
13. probability of significant downtime due to weather However given the total lack of winter zooplankton data for most of the Irminger Basin and few measurements elsewhere it was considered that the cruise would be worthwhile even if only a small number of stations could be worked In the event while there were prolonged periods of downtime useful coverage of the Irminger Sea and southern Iceland Basin was achieved The split of time between major activities given below Table 1 based on statistics kept by the Master shows that there was 40 downtime in leg 1 and 29 in leg 2 Despite this 18 ARIES stations were worked in the third of the total cruise that was science time 11 of them also with Dual Methot net tows and 5 also with the Ocean Sampler In addition there were 27 lowered CTD stations 6 of them followed by lowered EK500 scientific echosounder LEK deployments Note also that 24 29 of the time was passage The passage time was actually longer because around two days were entered as downtime due to bad weather Thus there is a considerable penalty in working in the Irminger Sea or even the western Iceland Basin when the passage is from Southampton or even the Clyde Table 1 Time distribution between scientific and non scientific activities Science Passage Weather Other Manoeuvring downtime downtime Leg 1 hours 182 9 141 9 208 5 20 4 28 3 per cent 31 24 36 4 5 Leg2 hours 165 9 151 1 97 6 50 9 48 5 per cent 32 29
14. to find the next number to use Make sure you are on discovery6 Type dobackup lt number gt where lt number gt 1 2 3 4 or 5 Leave for a few hours Occasionally it will fail with a tape io error The only way round this I have found is to erase the tape and start again Use mt f dev rmt 0 erase The script dobackup is as follows if hostname discovery6 then echo need to be on discovery6 exit endif echo n enter tape number set tapenum lt set listname tape tapenum date m d list bin rm f listname touch listname bin cp VERS users nerc pstar shipexec set device dev rmt Oc set dirs data61 data62 data63 users nerc pstar users pexec set here pwd seti 0 while i lt dirs i i 1 echo n writing dirs i cd dirs i tar cf device 78 if status 0 then echo problem status status returned exit endif echo done echo n listing dirs i Q im1 i 1 if im1 0 mt f device n fsf im1 tar tvf device n gt gt here listname if status 0 then echo problem status status returned exit endif echo done cd here end A5 Zooplankton sorting procedures A5 1 Sampling on deck Always use safety clothing and safe working practices when on deck and in hangar area Keep clear of launch and recovery operations if not actively engaged Use seawater deck hose to wash down all sampling nets or wait un
15. 14283 14295 Table 5 Mean true and absolute differences for nitrate phosphate and silicate determinations Table 6 Nutrient analysis errors due to uncorrected instrument drift and to analytical imprecision Table 7 RMS deviations of phosphate data from best model II regression between nitrate and phosphate data from the entire cruise and for work periods within it Table 8 SF samples taken Table 9 Float deployments Table 10 Sensors for Surfmet and thermosalinograph Table 11 Comparison of port based positional accuracy determinations Table 12 Gaps in Ashtech 3DGPS coverage Table 13 ADCP files and their Pstar equivalents 3 Table 14 FRRF files Table 15 Net haul summary Table 16 Summary of data collected via level ABC logging Table 17 SST imagery for Irminger Sea and Iceland Basin Nov Dec 2001 Table 18 Station list leg 1 Table 19 Station list leg 2 Table 20 Gain values for TEK and SEK calibrations LIST OF FIGURES Fig 1 Sampling sites for Discovery 258 Fig 2 Combined figure of Discovery 258 sampling sites Oceanus 369 stations and TASC sites Fig 3 Potential temperature at 1000 m from Oceanus 369 and Discovery 258 stations Fig 4 Salinity errors for first lowered Sea Bird CTD Fig 5 Salinity errors for second lowered Sea Bird CTD Fig 6 Salinity errors for ARIES Sea Bird CTD Fig 7 CTD errors caused by trapped water in rosette Fig 8 CTD errors caused by trapped water in rosette continued Fig 9 Correlations of chlorophyll
16. 19 10 9 A detailed cruise diary is given in Appendices Al 1 A1 2 the sites occupied are shown in Fig 1 and a complete list of sites and stations gear casts is given in Appendix A1 3 An overview of sampling locations is appropriate here Note that the original cruise plan envisaged four lines A B C and D from north to south to be worked across the Irminger Basin To close the circulation a fifth line E was to be run along the Reykjanes Ridge Line D was deemed the highest priority to be completed on leg 1 if possible It soon became clear that these lines could not be achieved For one thing working northwestwards was into the prevailing wind and swell For another with weather windows often only a day or so it was more fruitful to work a site wherever we happened to be rather than to head for a line which might be reached just as conditions deteriorated again In the end line D was partly run line A was replaced by line F west from Iceland to Greenland and line G replaced lines B and C Line G was extended usefully into the Iceland Basin at the end of the cruise Line H consists of odd stations down the length of the Irminger Basin From a physics perspective it was always going to be impossible to occupy sufficient stations to map in detail the circulation of the Irminger Basin We were most fortunate therefore that Dr Robert Pickart of Woods Hole Oceanographic Institution had occupied over 150 CTD stations on RV Oceanu
17. 26 November Raymond Pollard 58 A1 2 Discovery 258 diary Leg 2 27 November 2001 Tuesday Julian day 331 After a two night mid cruise break in Reykjavik Discovery sailed for leg 2 at 15 48 Sailing was delayed from the planned morning departure because of strong winds down the west coast of Iceland However it was preferred to depart in daylight even if we needed to shelter later In the end this was not necessary and the PES fish was deployed at 20 10 and speed picked up 28 Nov Wednesday 332 The first intention was to work a line of four sites F7 F5 F3 and F1 from the Denmark Strait across to the Greenland Shelf By morning the wind had abated and good progress was made along the whole of line F F7 at the southern exit from the Denmark Strait was reached at 13 06 and CTD 14245 to 1540 m completed As expected a strong bottom boundary layer of Denmark Strait Overflow Water was found Immediately after the TEK was deployed and then ARIES 14246 7 8 from 15 44 to 18 52 29 Nov Thursday 333 Site F5 was reached at 03 53 This was a repeat of TASC station T13 previously occupied for Calanus finmarchicus by Icelandic researchers so a fairly full suite of measurements was made CTD 14249 was followed by LEK 14249 While the LEK data were recovered there was a problem with connectors believed to be a consequence of the LEK electronics having been designed for a quiet Autosub environment This will necessitate ope
18. 33 The floats may also experience an episode of deep convection which is suspected to take place during the winter in the Irminger Sea Table 9 Float deployments Float Argos ID Deployment time Latitude Longitude CTD station ddd hh mm N W Martec 33 D64A4 318 01 08 56 34 36 54 14231 Apex 434 A2F9E 325 17 45 60 39 34 18 14239 Apex 436 A3072 326 12 00 61 03 37 03 14244 Martec 34 D66C9 338 07 14 61 26 39 37 14275 The Apex floats manufactured by Webb Research Inc are easier to set up Apart from a desirable but optional test procedure which was carried out and which we strongly recommend all that is required is a reset of the float using a magnet a couple of checks that the float has activated properly and the replacement of a bung in the lower end of the float The Martec floats also have a test procedure which should be carried through because other users have experienced failures both at this stage and post deployment An inconvenient aspect of the test procedure is that the floats need to be in an upright position for the test of the hydraulic systems which presumably depend on gravity These floats also need to be programmed with the mission parameters This makes deployment more time consuming of order 45 min but gives more flexibility In particular one can decide at deployment time on the depth at which the floats are to drift an option not available with the Webb floats Another shortcoming of the Martec floats i
19. 4 bolts gone and a second loose A metal band held with a jubilee clip to fix the cylinder had also gone A bolt preventing the whole mounting from swinging 180 to allow the cylinder to be removed had also gone Clearly there is significant vibration Extra brackets were fitted to prevent motion and reduce vibration and banding renewed A SW swell prevented us from making the course 298 towards D16 so course was 283 passing about 10 nm to the south of D16 Thus the plan was to deploy the nets so that ARIES would reach maximum depth roughly when we were closest to D16 DM 14201 was deployed 22 25 01 24 10 Nov 3 hr in all 10 Nov Saturday 314 The modified PES fish failed to communicate with the DM on this deployment so the PES fish was recovered Cable damage was found also signs that the fish had struck the hull Beyond repair After several hours it was decided to continue with ARIES deployment using the characteristics of the first tow to fly blind to about 2000 m well short of the water depth ARIES 14202 3 4 was deployed 05 20 08 32 3 hr to about 2000 m On recovery it was found that the SB CTD had not operated as the new battery had run down very quickly Ocean Sampler not be deployed again until sea much calmer to prevent nets shredding again or some protection for the nets provided e g by putting old DM nets around them Thus work near D16 complete and course set for D15 at 09 04 After recovering the TEK CTD
20. For leg 2 the times for on station data were extracted from the start and end of CTD files pinq times in seconds after 20 010101 000000 and used to datpik the data from both of the master leg 2 ADCP files through the use of script do getstns Times of underway sections ARIES tows and Dual Methot tows were extracted manually and sections for ADCP data extracted with datpik using do getuway 9 2 7 On station profiles The on station data tends to be the best quality ADCP data penetrating deepest into the water column The on station data for the CTD stations were selected and averaged into u and v profiles for each ADCP The data were merged together and the differences in u and v calculated 75 minus 150 As on Discovery 253 the results were very encouraging suggesting the ADCPs agreed within the expected noise level of the instruments U east Mean 0 129 cm s sd 1 973 n 1356 V north Mean 0 167 cm s sd 2 161 n 1356 However it was clear from the good values that the 150 kHz data appeared considerably poorer This may be a result of the 4 m bin length chosen for the 150 kHz setup and sparse winter populations of zooplankton Certainly the good contour plots look like they show biological layering but only a thorough investigation of the amplitude backscatter will confirm this 9 2 8 Depth of penetration The main potential advantage of the 75 kHz ADCP is that the lower frequency means greater depth penetration though
21. In response to our queries John Wynar Bob Keogh and Steve Whittle investigated the problem The quarter turn valve in the bleed pipe was open however on closer inspection following the removal of the bleed pipe the valve was found to be blocked by scale build up The blockage was removed but did not solve the problem as the bleed pipe itself was blocked on the air side of the valve This was more difficult to clear as around 8 cm of the flexible pipe was scaled up However following drilling and poking this too was cleared This immediately solved the problem with ADCP data quality and was completed by the afternoon of Julian day 313 Subsequently Bob and Steve also investigated the gate valve in the large bore steel stand pipe to which the aforementioned bleed pipe connects The processing exec s used on the ADCP are adpexecO0 4 as given in Appendix A22 A calibration of the 150 kHz ADCP was achieved using the limited high quality bottom tracking data available from our departure across the southern Hebridean shelf As a result of the limited amount of good bottom track data available but the very low positional scatter in the Trimble GPS 4000 positions as determined earlier we experimented with a calibration based on standard two min ensemble profiles rather than the usual 10 or 20 min averages The data used were between 306 19 00 41 and 306 22 08 42 After removing outliers of 2 standard deviations this resulted in tang 1 1434 s d 0 01
22. P 6 6 6 8 7 7 2 7 4 7 6 b Rate of change of temperature C s 0 15 T T T T T T 0 05 0 1 O45 Ee iere a m j j j j 6 6 6 8 7 7 2 7 4 7 6 c Package downward acceleration dbar s 1 T 4 j 6 6 6 8 T7 7 2 7 4 7 6 Time into cast in minutes Fig 7 CTD errors caused by trapped water in rosette illustrated are the downward velocity a and acceleration c of the lowered CTD package and the time rate of change of the measured temperature b from a minute long section of a downcast when the package was passing through a thermocline region Text section 2 2 3 Fig 7 a Correlation of dT dt with speed 0 3 T T T 0 7 l j j j j 20 15 10 5 0 5 10 15 20 Lag in seconds ve where speed leads dT dt b Correlation of dT dt with acceleration 0 8 T T T 0 8 fi l 20 15 10 5 0 5 10 15 20 Lag in seconds ve where acceleration leads dT dt Fig 8 CTD errors caused by trapped water in rosette correlations of temperature change with a speed and b acceleration Text section 2 2 3 Fig 8 0 25 Convert fluor to chla from CTDs 14191 to 14263 0 22 Chl mg m3 0 028 2 812 x fluorctd 0 20 error bars span 0 05 mg m3 0 17 t t hry Ha 0 12 o 3 0 10 0 08 0 05 0 03 0 00 0 00 0 15 0 30 0 45 0 60 chla mg m3 0 25 Convert fluor to chla
23. W EN 03 12 01 15 14 61 38 346 N 40 39 342 W 64 G04 G04 G05 G05 G06 E16 E13 E13 E13 G12 E09 G13 G14 G14 G15 G16 G17 14269 14272 14275 14276 14279 14282 14283 14284 14287 14288 14289 14290 14293 14294 14295 14296 ARIES OS CTD Float ARIES ARIES CTD CTD ARIES CTD CTD CTD ARIES DM CTD CTD ARIES BE BO EN BE BO EN BE BO EN BO BE BO EN BE BO EN BE EN BE BO EN BE BO EN BE BO EN BE BO EN BE BO EN BE BO EN BE BO EN BE BO EN BE BO EN BE BO EN 03 12 01 03 12 01 03 12 01 03 12 01 03 12 01 03 12 01 04 12 01 04 12 01 04 12 01 04 12 01 04 12 01 04 12 01 04 12 01 08 12 01 08 12 01 08 12 01 09 12 01 09 12 01 09 12 01 09 12 01 09 12 01 09 12 01 09 12 01 09 12 01 10 12 01 10 12 01 10 12 01 10 12 01 10 12 01 10 12 01 11 12 01 11 12 01 11 12 01 11 12 01 11 12 01 11 12 01 11 12 01 11 12 01 11 12 01 11 12 01 11 12 01 11 12 01 12 12 01 12 12 01 12 12 01 12 12 01 12 12 01 12 12 01 16 06 17 35 18 57 20 03 20 32 21 03 04 47 05 38 07 08 07 14 13 28 15 45 18 10 11 48 13 07 14 25 07 10 07 41 08 30 09 01 10 23 11 28 12 37 13 46 15 15 15 47 16 42 22 07 22 45 23 58 04 19 04 51 05 53 11 12 13 12 15 11 16 12 16 50 17 30 21 21 22 03 23 14 04 14 05 02 06 23 11 10 13 09 15 43 61 61 61 61 61 61 61 61 61 61 6
24. Water track velocities written into sur file bottom track into sbt files if in bottom track mode Velocities were scaled to cm s and amplitude by 0 45 to db The time variable was corrected to GPS time by combining the PC clock time and the PC GPS offset The depth of each bin was determined from the user supplied information Output files sur258 raw sbt258 raw data edited according to status flags flag of 1 indicated bad data Velocity data replaced with absent data if variable 2 bmbad was greater than 25 of pings where gt l beam bad therefore no velocity computed Time of ensemble moved to the end of the ensemble period 120 sec added with pcalib Output files sur258 sbt258 this merged the ADCP data both files with the Ashtech a ghdg created by ashexec2 The ADCP velocities were converted to speed and direction so that the heading correction could be applied and then returned to east and north Note the renaming and ordering of variables Output files sur258 true sbt258 true applied the misalignment angle o and scaling factor A to both files Variables were renamed and re ordered to preserve the original raw data Output files sur258 cal sbt258 cal merged the ADCP data both files with the Trimble GPS 4000 navigation file gp42581 created by gp4execO and the bestnav navigation file abnv2581 created by navexecO Ship s velocity was calculated from 2 minute spot positions taken from the
25. ant ee REM ee te es x a s ae cue te Gosia sea eee X lll x 0 i ji 0 500 1000 1500 2000 2500 3000 3500 pressure dbar Fig 11 Difference in oxygen concentration between bottle samples botoxy and CTD sensors for SBE43_0086 casts 14191 14231 upper plot and for SBE43 0076 casts 14239 14275 lower plot plotted against pressure Text section 2 4 Fig 11 2 0 T T T T oxygen residuals after calibration 0 13 3 17 umol kg bot oxyc umol kg ll l I I ll 0 500 1000 1500 2000 2500 3000 3500 pressure dbar Fig 12 Oxygen residuals after calibration of the Sea Bird oxygen sensor oxyc against pressure Text section 2 4 Fig 12 bot oxy umol kg Bottle SeaBird oxygen differences 40 CTDs 14283 to 14295 17 0 2 4 30 J x x x x x x x E X J LA nom n mum SP es ti ee neice eee Na ei x x x x X X x X NU x x Perret rete eee eee eee eee ee eee I K x X x x 10 E x X 0 l l I l 0 500 1000 1500 2000 2500 3000 3500 pressure dbar Fig 13 Difference in oxygen concentration between bottle samples and CTD sensor bot oxy against pressure for casts 14283 14295 CTD SBE43 0076 following down time period during the second leg of the cruise Text section 2 4 Fig 13 w200 1 85 T T T T bin 8 i bin 6 I h UN bin 4 Sv 100 bin 2 110 l l 0 5
26. as G10 and the original C1 position By deploying only ARIES and the CTD at alternate sites with one DM tow it was hoped to be able to complete three ARIES casts before the weather broke ARIES was recovered at 13 57 and passage set for G9 where the TEK was recovered and a float deployed at 17 42 before heaving to As an alternative launch procedure the float was lowered over the starboard rail on a single string through a hole in the plastic flange around the float body This was not as satisfactory as the previous deployment as the potential for the ship to run over the float was greater and the string had to be cut when it tangled CTD 14239 was worked from 18 08 to 20 24 The case for the modified IOS transducer was pressure tested on this cast the end face having been ground flat to create a firm O ring seal The bottom ten rosette bottles were sampled for SFs which may have been transported from where it had been deployed in 1996 m the Greenland Sea This will done for as many casts as possible in the Irminger Basin After launching the TEK passage was resumed and DM 14240 deployed at 23 40 in the vicinity of G8 22 Nov Thursday 326 DM was recovered at 01 28 and the bar between the two nets found to have worked satisfactorily for the first time The nets had been re rigged on a different frame ARIES 14241 2 3 followed from 02 57 to 08 55 This deployment took longer than planned for the positive reason that the transducer had
27. at reduced vertical resolution 16m bins vs 4m During Discovery 258 the 75kHz ADCP managed to reach 700 750m on station and 400 500 m steaming In contrast typical maximum depths for the 150 kHz are 350 400 m under the same conditions It is noticeable though that the 75 kHz depth penetration during steaming suffered very readily with the onset of anything other than calm conditions It was postulated on Discovery 253 that the forward well is more prone to contamination by bubbles than the aft well and if the 75 kHz ADCP is to become the standard ADCP for Discovery it may be appropriate to move the 75 kHz to the aft well However the underway data during cruise 258 were generally poor as a result of poor weather and high steaming speeds when weather windows occasionally permitted them The mid depth spiking in the 75 kHz data at 330 m discussed on Discovery 253 was not obvious during cruise 258 however the small amount of good underway data available may make this observation unreliable John Allen Penny Holliday Paula Mcleod Ulrike Riemenschneider 9 3 FRRF Fast Repetition Rate Fluorometer The FRRF is an active fluorescence instrument which can be used to make rapid non destructive and in situ measurements of phytoplankton physiology Kolber ZS Prasil O amp Falkowski PG 1998 Biochemica et Biophysica Acta 1367 88 106 Such data can then be used in bio physical models to estimate the rate of phytoplankton photosynthesis at scales
28. but over the stern using the A frame The pallet truck is used to transfer it from the hangar to the stern The LEK was deployed from 15 24 15 43 and proved satisfactory Trials of the final vehicle the Ocean Sampler Ocean were not conducted Nor was there time to trial the Dual Methot net DM a two net system to be deployed to 800 m collecting samples in the ranges 0 400 m and 400 800 m After completion of trials the PES fish was recovered and course set for Ayr where four scientists and an engineer were put ashore using the Ayr pilot boat at 18 30 Thereafter the ship remained hove to overnight sheltered behind Arran This delay was necessitated by problems with the main winch which had cut out several times during the trials and is fundamental to the programme Because of the long hours worked it was deemed prudent for the UKORS mechanical engineers to investigate the problem in the evening before conducting trials the following day 3 Nov Saturday 307 08 00 Failed relay found in the winch system was replaced last night Need tests this morning to see if problem is solved 12 00 Tests satisfactory On passage toward first open ocean sampling site 14 00 Both battery chargers for LADCPs are u s Hopefully ingenuity will find a partial solution but it may not be possible to use both the 150kHz and 600kHz LADCPs on every CTD cast 14 20 Motor that drives the autoanalyser bubbles through the tubes has packed up Will try to
29. few remain These are removed by pmdian check that I have not set the limits too fine PAVRGE 1 second averaging followed by PHEADR to reset the sample rate in the header to 1 sec PINTRP on pressure is essential for later averaging on pressure PEOS83 is run twice to calculate salinity potemp and density Output file is ctd14nnn 1hz 7 ctd2 This exec extracts all data while the CTD was in the water into ctu and the down cast after 2db averaging into the file 2db Thus before this exec is run mlist should be used to find suitable data cycles for truncation While automatic ways of extracting suitable data cycles can be found my experience is that these can be fooled for example by spikes and I find mlist a quick way of checking the data quality at the same time Thus run MLIST with vars press temp cond salin Note the max pressure from the heading Scroll quickly through the list to find a the data cycle at which the CTD was nearest to the surface at the start the SB only switches on once in the water so is held at 5m then raised to the surface before starting the down cast b the data cycle at which the CTD reached its maximum depth c ditto when it came out of the water at the end The most reliable indicator of this is when the conductivity starts going to zero Pressure will be close to zero but might have a slight zero offset so is less reliable than conductivity Pick a data cycle just before conductivity sta
30. in the top 1000m of the water column both in conjunction with the various nets and on transects between stations The towed body is deployed on the starboard side of the ship aft of the winch cabin using a lifting wire and is towed from a boom deployed forward of the CTD gantry The boom must be stowed inboard during each CTD deployment so the towed body must be recovered before each CTD station and re deployed afterwards As with the LEK before any data were collected the equipment was calibrated to allow the correct integrator and target strength gain values to be applied during post processing see Appendix A3 Deployment diary Few problems were found in the use and deployment of the TEK towed body once the initial difficulties with the deployment were resolved see below After the loss of the Scanmar tow fish the Scanmar hydrophone was transferred to the towed body between CTD stations 14211 and 14215 and it provided a suitable platform for this use which did not appear in any way to affect its primary function as a platform for gathering acoustic data Between the first and second legs of the cruise between CTD stations 14244 and 14245 the aft lifting wire was replaced as was the shackle connecting the towing wires to the boom The lifting wire had to be replaced as it was showing significant deterioration This was probably due to it being fixed at both ends and the use of a swivel at the end of the replacement wire appeared to
31. is held in files in subdirectory casts Dsss cc scdb perl S domerge prl c0 sss cc The above is czero Here the data is filtered and despiked matlab plist sss cc do_abs Note the here in the cast ID This should produce plots of velocity and various other fields Copies are also written into subdirectory casts Dsss cc merge as postscript format plotthem Dsss cc outside matlab sends them to laser These steps produce velocity data with zero mean The processing up to the load step does not need to be repeated for the next stage However if it goes wrong note that there are various ASCII files in the proc directory which are appended to These are stations asc mag var tab proc dat and latlon asc If in doubt remove the entry in each file for the current station delete the directory Dsss cc under the casts directory and start again from the beginning Once the CTD data have been processed and navigation is up to date the absolute velocities for the 150 kHz can be calculated These steps have been incorporated into a script called ladcpproc They are cd proc cd Rctd Use mlist to create an ASCII listing of the CTD data mlist data61 ctd ctd14ccc ctu The output file should contain the four variables time press temp and salin Time should be in seconds vars 1 2 3 16 fmt time 10 1 DC 72 ascii list There should be no ASCII header and no record numbers Access MLIST ASCII and remove by hand mv MLIST ASCII ctd
32. laproc2 can be exited after this step On Discovery 258 svcalc3 m has been used since the data plot of backscatter has been changed The current structure on Discovery 258 for the 600 kHz uses an laproc2 m file which runs up to just before velocities are calculated when it creates a mat file containing all variables required for the backscatter calculation and then exits For cast 200_01 for example the following sequence can be used visbeck sss cc This creates a matlab procedure to get the LADCP data for an individual cast and make a mat file of the backscatter for future reference matlab v14ccc Run the procedure svcalc3 sss cc Calculating and range correcting backscatter svplot sss cc 1 This plots the backscatter in a number of bins as a function of depth and horizontal beam angle svavrge2 sss cc This generates and plots a simple mean of all the data ensemble forall four beams Useful for indicating steps and spikes in the data but very slow svavrge sss_cc 10 This averages the four beams into vertical profiles of backscatter Its only output at present is a plot 74 A2 3 4 Bottom track data The 150 kHz has been set up to emit bottom pings so bottom track velocities can be extracted The firing processing does not use them so in the past the bottom data has to be extracted from the binary rdi file on the PC using application BBLIST Visbeck extracts and uses the bottom data 1f requested in the demo m file so ma
33. lower graph Text section 9 1 3 Fig 23 Depth metres Depth metres Depth metres Depth metres Discovery 258 10 11 01 OPC ARIES 202 54 33 39N 31 37 25W Discovery 258 08 11 01 OPC ARIES 196 54 03 95N 28 45 79W 8 500 ri 1000 er i 10007 ag 1500 1500487 t 2000 pun 2500 25004 seabed 2606m 3000 4 SE 3026m i i 3000 i 0 6 10 15 20 25 0 5 10 15 20 25 CALABUS C5 m 3 CALABUS C5 m 3 Discovery 258 10 11 01 l Discovery 258 12 11 04 OPC ARIES 207 s7 10 37 M 3a za szw 55 36 57N 34 27 49W 0 E aieo 3 e u 4000 FFM P E 1500 k seabed 1500m t 20004 E 24004 3000 1 T T T T T T T T T T 0 5 10 15 20 25 0 5 10 15 20 25 CALABUS C5 m 3 CALIABNUS C5 m 3 Discovery 258 04 12 01 OPC ARIES 276 61 13 69N 38 31 83W OPC ARIES 269 Discovery 258 03 12 01 40 40 07w 61 38 46N x ogee Pid T 1000 AS dep sc T af c 1500 R9 5 7 seabed 1962m 2000 Depth metres seabed 2623m T T 0 5 10 CALABUS C5 m 3 Discovery 258 21 11 01 OP T T T T T 15 20 25 0 5 40 15 20 25 CALABUS C5 m 3 ARIES 279 62 39 23N 26 27 53W ee Mt sfJ a 1280m No seabed 1420m Depth metres DT T T T T 0 5 10 15 20 25 CALAMUS C5 m 3 T T T T 10 15 20 26 CALABUS C5 m 3 T 0 6 Fig 24 OPC Optical Plankton Counter estimat
34. of 8m The instrument is a narrow band phased array ADCP with 76 8 kHz frequency and a 30 beam angle The PC was running RDI software VmDAS v1 2 012 and WinADCP v1 1 0 Gyro heading and GPS Ashtech heading location and time were fed as NMEA messages into the software which was configured to use the Gyro heading for co ordinate transformation The software logs the PC clock time stamps the data start of each ensemble with that time and records the offset of the PC clock from GPS time This offset was applied to the data in the processing path before merging with navigation The ADCP was fitted in the forward well previously occupied by the unsuccessful ACCP and before that the ADCP prior to the 1992 re fit During fitting a nominal offset of 45 was intended but the April 2001 trials cruise ascertained that the offset was in fact 60 and this offset was accounted for in the RDI software Bottom tracking was switched on early in the cruise and at the end of the leg 1 for calibration purposes The 2 minute averaged data were written to the PC hard disk in files with a LTA extension eg D258005 000000 LTA D258006 00000 LTA Sequentially numbered files were created whenever data logging was stopped and re started The software will close the file once is reaches 48MB in size a user specified size though on Discovery 258 files were closed after 24 hr so they never became that large The L TA and ENX files were transferred to a networked Mac fo
35. off Re facing of the O ring seal by the onboard UKORS engineers a positive 3000 dbar pressure test and electronics repair resulted in later successful use of the modified system for deep ARIES tows 18 ARIES tows have been very successful deploying to a maximum depth of 2787m On leg 1 only the first and last were able to get as close to the seabed as wished since the other tows had to be deployed blind without the depth sensor The only two net failures were attributed to a large fish and then an even larger jellyfish clogging the revolving cod end and sensor mechanism The only CTD failure on tow 202 was due to water in a connector causing complete battery pack collapse Some spikiness in the readings of the conductivity cell in the early ARIES tows was caused by the 47 collapse of tubing in the plumbing circuit This has since been adjusted yielding improved results The reliability of the Optical Plankton Counter OPC has been 100 Ocean Sampler tows have generally been successful operationally to 400m However the deployment and retrieval of this lighter sampler in all but calm waters has been a problem The high radial flow onto and through the fine mesh nets caused by heave and extensive stern movement in any swell results in mechanical destruction of the nets The first Ocean Sampler tow in rough weather destroyed 8 of its 9 nets methods for alleviating this problem are being investigated In calm conditions rarely encoun
36. on JD 315 to 16 30 on JD 316 11 12 Nov the non toxic water supply leaked affecting data from the Surfmet water sensors On the morning of JDs 326 327 333 and 337 22 23 and 29 Nov 3 Dec the Ashtec attitude sensing system needed resetting to force the resumption of logging 12 5 Hardware problems The HP2000CM plotter reported a problem with the black print head and a spare was unavailable The reliance on software maintenance and the inaccessibility of vulnerable parts for cleaning makes this device difficult to use at sea Once cleaned the HP1200 plotter provided an adequate substitute The printhead was replaced with one supplied during the Reykjavik port call and plotting resumed The AJP laptop display failed completely during the cruise The Toshiba laptop battery is useless The Ni MH batteries bought at some expense for the Olympus digital camera have proved to be a disappointment A power blackout interrupted all data logging on JD 340 6 Dec between 15 56 and 16 20 The HP750 Designjet plotter was structurally damaged during a particularly violent roll it hung inverted from its stand due to a failure of a restraining bolt It was temporarily bolted and lashed back into place and continued to work 51 12 6 DartCom satellite system The lack of daylight in this region necessitated some experimentation with data channel combinations before adequate weather images could be processed On the whole despite little solar illuminatio
37. prevent the problem reoccurring After an apparent deterioration in signal quality from the 38 kHz transducer and problems experienced with the heel and pitch monitor on the towed body the towing wire transducer cable package was replaced between CTD stations 14276 and 14282 Although this provided a brief improvement in the signal from the heel and pitch monitor it did not alter any other factors Throughout both legs of the cruise significant interference was detected in the data particularly those from the 120 kHz transducer The cause of this interference was not discovered but it appeared extremely regular approximately 18 20 min periodicity and very consistent It did not appear to be related to the ship s scientific echo sounder as this was slaved via Ext Trigger to the TEK echo sounder during data collection and the source was likely to be electrical rather than acoustic as it could be detected in the data whilst the towed body was on deck The source of this interference should definitely be explored further on any future cruise if it remains a consistent feature Deployment techniques During the Clyde trials it was found that the planned deployment strategy using the crane to lift the towed body directly from the end of the 25 m lifting wire was not suitable even under flat calm conditions A new best practice was therefore developed to minimise the risks of deploying and retrieving the towed body and to maximise t
38. rig something and freeze samples as backup 4 Nov Sunday 308 On passage 263 Hove to around 1100 for the service of committal of Dave Ellett s ashes in the Rockall Trough at 55 17 N 10 23 W 5 7 Nov Monday Wednesday 309 311 Continued on passage with speed reducing due to head winds and swell down to 4 5 kn at times 8 Nov Thursday 312 The scheme agreed for the first line D11 D19 across the western Iceland Basin is nets at every third sampling site D19 D16 and D13 and CTDs at the two intervening sites with a CTD at the initial site D19 also for intercomparison After much improved passage speed overnight arrived on site D19 at 09 12 Total passage time thus 4 days 21 hr thus over a day of contingency used on the passage Both PES fishes were deployed and CTD 14191 occupied Couple of glitches in data but otherwise very clean Three hours for 3200m depth CTD LEK out at 13 02 but not enough weight in water to sink at acceptable rate so recovered TEK deployed at 13 57 then DM 14192 at 14 27 This was extremely slow to reach 800 m not inboard until 17 38 so over 3 hours One hour 20 mins turnaround needed before Ocean Sampler 14193 4 5 deployed at 18 57 Inboard at 20 38 so 1 hr 40 min for tow to 400m Disaster All nets shredded probably when it first went into the water and took a while to sink out of wave zone Finally after 50 min turnaround ARIES 14196 7 8 was deployed from 21 29 55 9
39. run restarted When it occurred mid way through a run a decision was made on a case by case basis what to do Generally this amounted to running second sets of standards after the baseline jump following flow cell shaking On all but one occasion a set of sample analyses was completed with a large number of duplicates This was the final run of ARIES cast 14296 For this station no P data has been reported Further to this problem odd individual phosphate peaks that appeared to be erroneous were manually edited from results files 7 2 2 Performance of the analyser Fig 19 shows time series of baseline values and calibration coefficients recorded for the analyser on each run The nitrate baseline was relatively invariant over the course of the cruise The silicate baseline increased over the course of the cruise and the phosphate baseline declined over the course of the cruise The phosphate calibration constant was approximately constant over the course of the cruise the silicate calibration constant steadily increased and the nitrate constant rose and then fell Fig 20 upper plots shows time series of calibration curve correlation coefficients Silicate correlation coefficients were uniformly high nitrate and phosphate correlation coefficients suffered occasional lapses P around 10 and 30 Nov but were generally of a comparable magnitude to the silicate correlation coefficients 7 2 3 Bulk concentration and nitrite column efficiency Fig 20 l
40. selected This means that the instrument s memory needs to be cleared regularly or there is the danger that the download time becomes greater than the time between stations The main interest in the 600 kHz ADCP for this cruise was the backscatter calculation Indeed velocity calculations produced no sensible results for the configuration we selected This needs to be further investigated However after a range correction see next sections the calibrated backscatter data seem to correlate with biology in the water column 2 6 1 Backscatter Backscatter may be calculated from echo intensity using the following equation 18 Sv C 10log T 273 16 20log R 10log L 10log P 2aR k e e where Sv is the backscatter coefficient dB C is a constant dependent on the instrument T is the transducer temperature C P is the transmit power watts R is the range m to each bin L is the binlength m a is the absorption coefficient dB m k a conversion factor from counts to dB e the echo intensity and e a reference or noise value of intensity see Deines K et al 1995 Sea Technol 36 61 for details The above equation was applied to data from the current cruise Fig 14 shows results from a single cast CTD 14200 Backscatter is plotted as a function of depth averaged to 10 m the four profiles correspond to each of the four beams There is clearly a range error in the data since bins at different ranges should se
41. some intriguing near bottom peaks which the net sample analysis and comparative analyses with the LADCP data should help to elucidate A good example of this occurred in sampling of the overflow of deep cold water from the Greenland and Norwegian Sea spilling down into the Irminger Sea through the Denmark Strait Overall it appears that there are not very high densities of Calanus in any of the Irminger Sea areas surveyed contrary to expectations based on upper ocean summer abundances primarily from CPR data This also appears to be true in the Iceland Basin populations with lower densities over the shallower shelf and ridge areas This lack of high overwintering densities has important consequences in that the relationship between hydrographic features and overwintering populations 46 in these regions may be different from that previously observed in the north eastern Atlantic and Norwegian Sea It implies too that the dynamics of production processes in the spring and summer may be a factor of greater importance than overwinter survival in maintaining the persistence of and generating variability in North Atlantic Calanus populations Cursory examination of the net caught material also indicated that Calanus were distributed into the deeper water but not at the high concentrations of overwintering populations that were anticipated There was speculation based on visual assessments by experienced researchers that there were differences i
42. sss cc asc Rename MLIST ASCII to ctd sss cc asc note dots rather than underscores doctd When prompted give the three figure station number Converts the LADCP times into Julian days cd proc cd Pctd matlab di0111ts sss cc cd proc cd Fitd matlab plist sss cc fd This step examines the derivative of the pressure from the CTD and the vertical velocity from the LADCP in order to match the timebases The automated matching is usually sufficient but examine the plot carefully to make sure that bottle firing positions match If there are problems then choose the interactive option and match them manually Alternatively matching problems usually occur because of problems with the CTD data eg pressure spikes so look at this data carefully If necessary copy the CTD data to the Pctd directory and remove problem data cd proc perl S add_ctd prl sss_cc perl S domerge prl c1 sss cc Note the one here These steps add the CTD data to the database and merge it with the LADCP data Before the final step a navigation file is required The same files are required by the 600khz and 150khz For this reason one file is created and then copied to the other tree From the 600 tree cd proc cd Rnav donav The donav script is neither efficient nor tidy and should probably be changed One option is to use the bestnavfile instead but so far this has not been tried up to you The product required for the last step is called sm mat Thi
43. stored managed and accessed must be agreed and suitably documented e The technological implications must be established digital data stewardship implies the need for an underlying infrastructure of IT equipment and support e The resources need to carry out these intentions over the planned life of the data in terms of staff whether in project teams or the Data Centre and IT equipment infrastructure must be estimated and sources identified e Areview mechanism must exist to reconsider periodically the costs and benefits of continuing to maintain the data The intention to destroy or put at risk data should be publicised in advance allowing time for response by interested parties The above NERC wide requirements will be looked after automatically for the MarProd datasets managed by BODC Nevertheless PIs need to be aware of this framework particularly if alternative means of longterm data stewardship are envisaged A6 5 Data and sample acquisition A well structured and user friendly identification system is essential for cruise based data collection and sample labelling Such arrangements are traditionally the responsibility of the cruise Principal Scientist For Marine Productivity an overall consistency in approach is necessary with cruise identifiers linked to unique combinations of site and station gear cast numbers MarProd protocols are being developed in the context of the first North Atlantic cruise Discovery 258 Nov De
44. straight line fit was found Chla 0 028 2 812 fluor with R 0 963 albeit over the limited range of low chlorophyll a values found Since nearly all sampled values fell within 0 05 mg m of this line it was accepted as a good fit for the cruise and applied to all lowered Sea Bird CTD data A later calibration using all CTD casts gave a revised fit Chla 0 0186 2 752 fluor However over the range of fluor values found 0 0 25 the differences in chlorophyll are insignificant For ARIES calibration was much more problematic The small water bottles do not give sufficient water for a good calibration and with bottles only tripped every 50m in depth there is at most one bottle in the mixed layer Therefore calibration was done by comparison with the lowered CTD by using mixed layer values from a nearby cast for the upper end values and by forcing a straight line fit through the fluorometer zero i e the deep values which decreased gradually from 0 01 at the start to 0 008 at the end Fig 9 shows the data used and the chosen fit Chla 0 022 2 73 fluor 16 2 4 Sea Bird oxygen calibration In each deployment of the CTD rosette oxygen was first measured with an oxygen sensor on the Sea Bird CTD and second by analysis of samples taken from the bottles The results from the oxygen titrations of the samples were used to calibrate the Sea Bird sensor Before calibration the results from the oxygen titrations which measure
45. the bulkhead connector caused by the sea cable extension leaking Data spiking continued on the first few casts of the second leg with no identifiable hardware problems being evident The replacement BOB was removed from the frame and tested It is possible however that these spikes are software induced as the data acquisition software has displayed some locking up and restarting Further investigations showed leakage had occurred at the altimeter connection This was cleaned and dried and the spiking ceased The problems with connectors did not seem to occur once the weather became warmer This was maybe a coincidence but there is no doubt that impulse connectors are much less malleable when very cold Data collection and software Seasave for Windows V5 22 was used to collect data Occasionally the software would lock up for a few seconds and then continue No other problems were apparent although it was suspected that an occasional spike in the data was software created and not real During leg 2 the DAPS data collection system was discarded in favour of running a second PC with Seasave as backup This worked well the only problem being that the backup PC cannot log bottle details For this reason bottle firing times were also recorded Chelsea Instruments Fluorometer Performance satisfactory calibrations were carried out Results are given in Sections 2 3 and 6 2 below Chelsea Instruments Transmissometer Performance satisfactor
46. the very loose lay of the wire on the drum from the first cast During the morning the leak in the CT lab had been fixed by cutting away the bulkhead to gain access to the joint in the non toxic pipework which had worked loose The supply was restored at about 10 00 Passage southwest back towards E1 was then set after deploying the TEK at 14 55 About 7 nm short of E4 the Ocean Sampler 14216 7 8 was deployed from 17 04 to 18 21 with a reduced number of nets given calm conditions and reached around 400 m with 850 m of wire paid out Next ARIES 14219 20 21 was deployed 3 6 nm short of E4 and towed past the station position from 19 16 to 22 32 13 Nov Tuesday 317 Finally the DM 14222 was streamed from 00 11 to 02 22 Passage 224 T was then resumed back towards E1 D11 which was reached at 09 43 The intention was to work 11 sites along line D to Cape Farewell with CTDs at even numbered sites and nets at odd numbered sites but with a CTD at D11 for intercomparison purposes Thus after recovering the TEK CTD 14223 was occupied at D11 from 10 04 to 12 42 immediately followed by LEK 14223 from 12 53 to 14 11 Beginning passage along line D the TEK was streamed followed by the DM net 14224 as soon as it could be prepared from 15 09 to 16 38 ARIES 14225 6 7 followed from 17 25 to 20 28 Finally Ocean Sampler 14228 9 30 was deployed from 21 30 to 22 48 Thereafter passage was set for D10 14 Nov Wednesday 318 On arriv
47. thin thread holding a calibrated steel sphere This was deployed on the starboard side using the crane Winds marginal but eased later Calibration of the TEK 2 frequencies and Lowered EK500 2 frequencies continued overnight 2 Nov Friday 206 and was completed at 06 20 TEK The TEK was redeployed briefly 09 17 09 33 using the capstan instead of the tugger winch This was an improvement allowing both the crane and capstan operators line of sight of the bosun controlling the operation Towing angle is improving but still further adjustment to be made 54 ARIES Two further deployments of the new ARIES were made during the morning with additional weights These will be used to calculate the optimum ballast for correct towing This vehicle was then stowed above the hangar for emergency use only After lunch the main ARIES vehicle was deployed 13 44 14 15 and worked satisfactorily Lowered EK500 LEK After a final trial of the TEK the LEK was tested over the stern This has 38 and 120 kHz echo sounders mounted in a metal frame about 1m It has to be stowed in the hangar for charging and to allow setup with a portable pc It records internally and is downloaded on recovery The original plan was to deploy it over the starboard side using a crane but this would have necessitated re leading the trawl winch wire from stern to the starboard side whenever it was deployed The solution is to deploy it using the trawl winch
48. to be fully rectified for MarProd cruises in 2002 The FRS ARIES sampler with integral CTD and OPC was then tested with 100 functionality along with its associated supporting components navigation logging merging programs depth telemetry units etc No initial testing could be performed on either the Ocean or the Dual Methot samplers due to extended testing of the EK500 towed system and failure of Discovery s winch After the first three stations early cable problems manifested with the acoustic hydrophone towed array mounted in the modified aft PES fish Inspection revealed the PES fish was smashed beyond repair and its towing wire had suffered water ingress and conductor breakage The shallow water lt 1000m depth telemetry receiver was then installed into a light towed paravane and tested over the ship s port quarter This proved to be incapable of staying submerged at ship speeds 71 5 knots The Scanmar receiver was then bolted onto the tail fin of the high speed u w towed EK500 tow frame This proved to be successful despite two further cable conductor breakages repaired The deep water IOS type 3500m depth telemetry unit was rigged to utilise the ship s forard PES fish 10 kHz hydrophone array with reasonable success and with the ship s echo sounder using the 12 kHhz hull mounted transducer A further unfortunate failure of the ARIES deep water depth telemetry unit was traced to water ingress caused by anodising on the O ring face seal flaking
49. up to date calibration sheets and the coefficients used were Temp m true 2 3x10 1 0011 Tm 1 00x10 T4 Temp h true 7 5x10 1 0006 Ty 6 0x10 Tp Bestnav positions from abnv258 were then merged into the output file smt258 and averaged into a 2 minute file smt258 av Note that for smt25801 positions were taken from the gps4000 file gp42581 as the RVS bestnav system was not started until after the beginning of surfmet logging The light sensor data have only 4 decimal place resolution on the level B measured in mV this restricts the resolution to a coarse 10 Wm The conversion factors below were applied to the light Sensors Ppar W m 1 0020x 10 Ppar raw Spar W m 1 0010x10 Spar aw 35 Ptir W m 0 9709x10 Ptitgaw Stir W m 0 8697x10 Stir Some median de spiking was added to this script because of noisy data temp_h cond fluor and trans and pintrp added to fill gaps in the data 3 smtexec1b The 2 minute average smt258 av files were merged with the master Ashtech file to add gyroHdg and a ghdg variables and calculate true heading In smt28514 raw a large backward time jump occurred at 04 48 on Julian day 319 15 Nov This was a single point with a time stamp of 00 48 20 and originated from the Surfmet PC it was subsequently edited out using pcopya 4 smtexec2 This script computed vessel speed and subtracted it from relative winds to obtain true wind speed and direc
50. water more or less parallel to the shelf edge Dual Methot 14268 13 44 15 14 was followed by ARIES 14269 70 71 16 06 18 57 and finally Ocean Sampler 14272 3 4 20 03 21 03 Between each deployment the vessel ran south so that the same berg free track could be followed each time This also avoided running into shallower water to the north as the bathymetric contours run east for a short way along about 62 N Sea surface temperature maps showed a cold water tongue extending east just north of that line After completion of our westernmost site on line G the TEK was recovered in order to look for a broken connection to the Scanmar receiver and the vessel remained hove to for an hour while light on deck were required to locate the problem At 22 35 course was set to the east 103 T towards GS 4 Dec Tuesday 338 On arrival at G5 CTD 14275 was worked from 04 47 to 07 08 followed by deployment of a float at 07 14 The TEK was deployed at 07 31 before passage towards G6 On arrival at site G6 ARIES 14276 7 8 was occupied from 13 28 to 18 20 This at last completed the site that had been aborted on leg 1 on 22 November Having completed the western end of line G course was set towards E5 with the intention of occupying a couple of sites across the Irminger Current towards E5 then working up the Reykjanes Ridge 5 Dec Wednesday 339 However on reaching the vicinity of the first intended site at H3 conditions had deteriorated and the v
51. widely available eg via a link from the main programme website Processed and project specific cruise data must be provided to BODC by the Principal Scientist and project teams as they becomes available not in the concluding few months or weeks of projects However great importance is given both by the programme and by BODC to protecting the interests of data originators and restrictions on the wider availability of BODC held datasets will therefore apply see A6 8 and A6 10 below A6 6 Data formats and data media Digital data should be collected and stored using standard widely available software products and their related data formats Whilst BODC has experience in handling a very wide range of software formats and media Investigators should discuss with them the proposed use of any data handling or storage protocols that might be regarded as non standard CD ROMs are currently the preferred means for making integrated data products from marine thematic available to the wider research community The MarProd Steering Committee will advise on the number of CDs and set target times for their release A6 7 Data backup policy Daily backup programmes apply at BODC and other NERC Designated Data Centres to safeguard major digital databases Project PIs and Co Is are responsible for providing appropriate back up strategies for unique digital data stored locally and or via other organisations As far as possible analogue data such as
52. work up line E with CTD casts deploying nets on the way back to E1 D11 the start of the prime D line across the Irminger Basin The TEK was therefore not deployed during the work from E2 to E5 because a there could be a straight run back along line E later and b the only remaining option for mounting the Scanmar receiver was to mount it on the TEK metal fish which would be attempted during the passage north 56 On passage towards E2 water was found to be flooding into the chemistry and constant temperature CT laboratories The leak was traced to pipework in the bulkhead between the ship s hull and the panelling on the port side of the aft end of the CT lab Turning off the non toxic supply at 17 30 stopped the flooding so the non toxic supply would have to be left off until the leak could be fixed the next day CTD 14212 was occupied at E2 from 20 25 22 23 With prevailing winds from the southwest the northeast course along line E was a much easier run than the previous line D This could be a problem with any line across the Irminger Basin 12 Nov Monday 316 Continuing up line E we occupied E3 CTD 14213 from 01 23 to 03 25 E4 CTD 14214 from 06 19 to 08 02 and ES CTD 14215 from 10 55 to 12 35 The LEK had by now been satisfactorily secured within its frame by strapping and by welding on extra metal bars After a delay therefore LEK cast 414215 was worked over the stern from 13 06 to 14 34 Deployment was slow because of
53. 00 1000 1500 2000 2500 3000 depth m Fig 14 Backscatter in dB plotted for four separate bins position relative to the instrument sorted on depth and then averaged over 10 metre depth ranges Example from CTD station 14200 Text section 2 6 1 Fig 14 w200 1 35 T T T 30r 25r n e T oi T Sv difference from bin 1 70 range m Fig 15 Backscatter difference in dB between beam 1 and each of the other bins averaged over the whole cast In this case the horizontal axis represents the depths of each bin beneath bin 1 The blue curve represents the original data error the red curve the correction calculated from the full model the green curve the correction from the partial model see text for more details Text section 2 6 2 Fig 15 w200 1 90 T T 95 iy Q eo T NAA Ma ANA I in corrected Sv ES E e a 110 H i i 0 500 1000 1500 2000 2500 3000 3500 depth m Fig 16 Profile of backscatter in dB from station 14200 after correction by the partial model central line Data is averaged into 10 metre depth ranges The upper and lower lines represent one standard deviation difference from the profile Text section 2 6 2 Fig 16 average of the four beams and 30 data ensembles for w239 1 ctd temperature w239 1 ctd salinity w239 1
54. 00492 1 0004386 1 000155 Std deviation of error post cal 0 0014 0 0011 0 0035 Mean absolute error post cal 0 0009 0 0009 0 0030 2 2 2 ARIES Sea Bird CTD sampling and implications for calibration The calibration was less good for ARIES than for the lowered CTD though the errors remaining are only of order 0 003 in salinity which is quite close to the state of the art This is due to two factors Firstly the ARIES CTD records 1 second mean data rather than the raw 24 Hz data recorded by the lowered CTD There is no filtering for spikes or other rogue values which may therefore contribute to the values used in the calibration Secondly and probably more importantly there are limitations in the sampling of water from the bottles on ARIES A description of ARIES sampling procedures is relevant here After the biologists have removed the nets and the three large yellow floats have been removed from the back of the vehicle the bottles can be sampled First the two screws on either side of the axle on which the rosette pivots are loosened Then the rosette is swivelled towards the back of the vehicle and clipped into position To sample from a particular bottle first locate the numbered outlet from the bottle on what is now the underside of the rosette and the lid to the same bottle on the upper side this is a two person job Next clip the blue sampling tube provided onto the outlet Then when the lid is raised water will flow out of the bott
55. 1 61 61 62 62 62 61 61 61 61 61 61 61 61 60 60 60 59 59 59 59 59 59 59 59 58 58 58 58 58 58 58 57 57 57 56 56 56 35 346 38 478 41 238 37 178 38 095 38 758 25 861 25 758 25 696 25 62 15 426 13 695 11 835 42 369 39 255 36 43 21 088 21 268 21 148 21 267 21 57 23 824 21 921 20 131 10 008 10 116 10 271 32 062 32 048 31 925 19 975 19 87 19 254 8 315 3 378 58 367 57 028 55 932 54 828 23 981 23 848 23 844 39 486 39 488 39 416 55 157 52 304 47 979 202 242 2022 22 Ze Ae Ze 2 ee eZ oe ee eZee LLZ LZ 40 40 40 40 40 40 39 39 39 39 38 38 38 26 26 26 28 28 28 28 28 28 28 28 29 29 29 30 30 30 29 29 29 28 28 28 28 28 28 28 28 28 28 28 28 28 28 28 40 899 40 063 38 643 42 067 41 485 40 623 37 011 36 923 36 885 36 927 22 47 31 866 43 317 27 446 27 542 27 764 21 5 21 08 21 684 21 294 20 008 19 362 21 201 22 487 59 749 59 819 59 448 57 698 57 276 56 183 45 063 45 184 45 051 31 106 29 567 29 652 30 252 31 183 32 341 30 189 30 359 30 651 27 204 27 142 27 325 23 86 18 035 11 35 2222222222222222222222222222222222222222222222225 65 A2 Processing paths A2 1 Sea Bird CTD processing Using an SBE911 CTD on Discovery 258 mounted on the lowered rosette CTD frame the processing path is as follows 1 During CTD data collection ensure that the latitude and longitude are written in the log at th
56. 13 36 14 07 14 34 17 03 17 35 18 21 19 16 20 57 22 29 00 11 01 16 02 21 10 05 11 08 12 42 12 53 13 16 13 48 14 11 15 09 15 55 16 37 17 24 18 57 20 26 21 29 22 02 22 49 01 06 01 32 02 17 03 43 07 31 08 03 08 36 09 39 11 20 13 02 10 10 12 05 13 56 17 42 18 08 19 02 20 24 23 40 00 34 01 27 02 56 56 56 56 56 57 57 57 57 57 57 57 57 57 57 57 57 57 57 57 57 57 57 57 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 56 60 60 60 60 60 60 60 60 60 60 60 63 32 39 52 41 52 22 51 45 11 95 11 84 11 41 31 02 30 93 30 71 30 62 30 56 30 34 30 28 17 80 16 50 14 64 14 29 10 36 7 21 7 28 4 81 2 24 14 39 14 58 15 25 15 31 15 56 15 53 15 61 14 49 14 62 14 83 15 24 17 02 18 75 19 64 20 53 21 72 33 67 33 51 33 72 33 76 48 04 48 91 49 63 50 66 52 96 55 59 26 63 27 00 28 50 38 87 39 04 38 96 38 76 47 79 48 49 49 31 51 31 22 22 Ze ZZ A E A A OZ ee ee eZ eee ee eee eee 35 34 34 34 34 34 34 33 33 33 33 33 33 33 34 34 34 34 34 34 34 34 34 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 37 37 37 37 37 37 32 32 33 34 34 34 34 35 35 35 35 27 57 55 36 55 22 54 81 21 91 22 57 22 75 47 55 47 02 46 17 45 72 45 23 44 93 44 49 11 24 13 47 16 91 18 87 24 97 30 55 33 23 35 47 38 07 4 28 3 96 3 40 3 22 2 99
57. 14205 was worked at D15 from 13 52 16 20 No LEK until brackets can be fixed and advice received from Aberdeen The TEK was deployed at 16 43 and passage resumed This sequence was repeated at D14 CTD 14206 being worked from 20 48 23 22 11 Nov Sunday 315 Five nm short of D13 the vessel slowed at 02 42 for deployment of ARIES The intention was to use the normal PES fish switched from echo sounding to interrogate the net monitor modified IOS transducer on ARIES This was found to be leaking however the problem being traced to breaks in the anodising on the end of the case just where the O ring seal is critical An alternative way of deploying the scanmar receiver was attempted it being mounted on a small metal fin fish This failed as the fish was topheavy and overturned in the water Thus ARIES 14207 8 9 had again to be flown blind This station was right over the southern extension of the Reykjanes Ridge with a water depth of only order 1500 m so only 1760 m of trawl wire was paid out The deployment therefore lasted only 2 hours from 04 37 to 06 35 After 1 5 hr of preparation the DM net 14210 was deployed to 800 m from 08 13 to 10 36 This dual net is designed to sample two depth ranges but the change over between the nets has not worked fully on deployments so far D12 was reached at 13 02 and the TEK recovered CTD 14211 was worked from 14 06 16 05 To give time for resolution of the various net problems it was decided to
58. 16 38 auto Leg 2 d258010 332 09 09 30 334 09 17 10 auto d258011 334 10 18 20 336 11 27 45 auto d258012 336 12 17 30 338 12 07 42 auto d258flt 338 12 51 00 338 12 57 00 auto 4258013 338 13 05 10 340 12 34 48 auto d258014 340 13 17 14 342 13 38 20 auto Non toxic turned off at 22 00 Jday 340 Back on 07 00 341 Two temporary files were written during this period which appear to represent data collected on auto acquire File names were 340161050 and 342133928 d258015 342 14 29 33 344 13 33 10 auto 4258016 344 14 20 48 346 12 50 50 auto d258017 346 13 38 01 349 14 44 04 auto John Allen Alexander Mustard Mark Moore 9 4 Precision Echosounder PES data A combination of two precision echosounders was used to record bottom depth throughout Discovery 258 The main instrument was the 10 12 kHz Simrad EA500 Hydrographic Echosounder mounted on a fish on the port side and the secondary instrument was the hull mounted 12 kHz transducer The data from both instruments were recorded as separate Level A B data streams ea500d1 for the hull and ea500d2 for the fish but were merged edited and corrected for the speed of sound in the Level C prodep data stream Preference was given to the PES fish data in prodep except during ARIES tows when the fish mounted transducer was switched to 10 kHz for tracking the movement of ARIES and after the PES fish malfunctioned For most of the cruise the data were of reasonable quality The Pstar proces
59. 19301 through 19324 if there are 24 data cycles in the file If fewer than 24 bottles were fired then there will be fewer than 24 data cycles in the file Sampnum is the key variable used to paste in data from other files 12 passam This exec replaces pasfir pasnut passal etc Passam takes as input a text file usually tab delimited and pastes it into the sam file The first step is to get the text files from various people Their format is now fairly flexible More than one cast may be included in one text file The column headings must at least include sampnum and the variables to be pasted in The names of these variables must match those in the sam names file which 1s created in the bottle directory at the start of the cruise However the cases may differ e g Sampnum and sampnum or even SampNum are all equivalent Names and units must NOT have any spaces in them If variables are found in the text file which are not in the sam names files then passam asks if they are to be omitted The input files do not need to contain lines for bottles not sampled The number of data cycles need not therefore be 24 nor need it match the number of data cycles in the sam file The text files should be placed in the relevant subdirectory to the bottle directory e g nut sal This is not essential but is strongly advised for neatness and to avoid any name clashes Passam requires the full pathname for the text input file for example data61 bottle s
60. 2 to 14 were removed from the rosette frame to test the theory that water trapped by the whole rig was being dragged down and biassing readings whenever the veering rate slowed The CTD was redeployed at 08 30 until 10 23 and given a new station number 14283 to allow comparison between the two casts to be made Although ARIES was not scheduled to be deployed it seemed prudent to make use of the weather window so ARIES 14284 5 6 was deployed from 11 28 to 13 46 A careful site survey was carried out first as depths were variable between 1200 m and 1500 m and two 100 m high cliffs were found just north of the CTD site Passage was then set 235 T towards G11 but by 18 00 the course could not be maintained and from 18 00 the vessel was hove due on heading 180 10 Dec Monday 344 In the morning an attempt was made to head towards G12 but excessive rolling again forced the vessel to heave to Later however a compromise course 300 T was set to take the vessel to the west of the Reykjanes Ridge to a new position G12 The swell precluded deployment of ARIES as had been planned but CTD 14287 was possible from 15 15 to 16 42 after recovery of the TEK That recovery was not easy as at present it requires the ship to reach over 6 kn in order to take the strain off the rear deployment cable to the 60 TEK so that it can be unshackled and taken through the fairlead This needs to be revised for future cruises However the TEK was re
61. 42_000000 LTA sur25835 341 115417 341 210424 D258Leg2045 000000 LTA BT sur25836 341 210503 342 123308 D258Leg2046 000000 LTA BT Sur25837 342 123542 343 161150 D258Leg2047 000000 LTA sur25838 343 161311 343 210714 D258Leg2048 000000 LTA sur25839 343 211320 344 141727 D258Leg2053_000000 LTA sur25840 344 152759 344 160359 D258Leg2054_000000 LTA sur25841 344 160443 346 172857 D258Leg2055_000000 LTA BT indicates bottom track files too indicates data not processed beyond raw owing to short time range 9 2 6 Processed data handling For leg 1 on station data sections for the ADCP data 150 and 75 kHz were identified using plxyed on the ship s velocities through speed pdf To create underway data files 150 kHz only all data left after removing the station profiles were plotted again through plxyed using pos pdf and areas of manoeuvring were identified In each case relevant profiles were then extracted with pcopya Once each underway 150 kHz file had been extracted for particular legs the top row was extracted using pcopyg retaining only two copies of the time variable The second time variable was then overwritten with the time difference between profiles using fdiff The time difference value was then 41 merged into the 75 kHz data on time datpik was then used to select only those 75 kHz profiles where the gaps between 150 kHz profiles was between 110 and 130 seconds This was a neat trick to avoid the plxyed pcopya routine a second time
62. 5 1466 W E02 14212 CTD BE 11 11 01 20 29 56 33 36 N 35 29 66 W BO 11 11 01 21 12 56 33 00 N 35 28 97 W 62 E03 E04 E05 E05 E04 E04 E04 D11 D11 D11 D11 D11 D10 D10 D09 D09 G10 G09 G09 G08 G08 14213 14214 14215 14215 14216 14219 14222 14223 14223 14224 14225 14228 14231 14232 14233 14236 14239 14240 14241 CTD CTD CTD LEK OS ARIES DM CTD LEK DM ARIES OS Float CTD DM ARIES ARIES Float CTD DM ARIES EN BE BO EN BE BO EN BE BO EN BE BO BU EN BE BO EN BE BO EN BE BO EN BE BO EN BE BO BU EN BE BO EN BE BO EN BE BO EN BO BE BO EN BE BO EN BE BO EN BE BO EN BO BE BO EN BE BO EN BE 11 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 12 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 13 11 01 14 11 01 14 11 01 14 11 01 14 11 01 14 11 01 14 11 01 14 11 01 14 11 01 14 11 01 14 11 01 21 11 01 21 11 01 21 11 01 21 11 01 21 11 01 21 11 01 21 11 01 21 11 01 22 11 01 22 11 01 22 11 01 22 23 01 27 02 05 03 25 06 22 07 00 08 02 10 55 11 30 12 35 13 06
63. 54 11 87 N 29 17 74 W D18 14199 LEK BE 09 11 01 08 28 54 11 84 N 29 17 75 W BO 09 11 01 08 56 54 11 55 N 29 17 94 W BU 09 11 01 09 25 54 11 27 N 29 17 96 W EN 09 11 01 09 58 54 11 08 N 29 17 98 W D17 14200 CTD BE 09 11 01 14 41 54 29 88 N 30 18 04 W BO 09 11 01 15 39 54 29 68 N 30 17 76 W EN 09 11 01 17 08 54 29 60 N 30 17 69 W D17 14200 LEK BE 09 11 01 17 22 54 29 62 N 30 17 81 W BO 09 11 01 17 34 54 29 56 N 30 17 91 W BU 09 11 01 18 07 54 29 29 N 30 18 34 W EN 09 11 01 18 21 54 29 21 N 30 18 56 W D16 14201 DM BE 09 11 01 23 11 54 35 50 N 31 16 30 W 14201 trap problem BO 09 11 01 23 53 54 35 56 N 31 17 72 W EN 10 11 01 01 22 54 35 89 N 31 24 904 W D16 14202 ARIES BE 10 11 01 05 20 54 34 60 N 31 29 885 W BO 10 11 01 07 02 54 33 40 N 31 37 30 W EN 10 11 01 08 37 54 33 11 N 31 44 29 W D15 14205 CTD BE 10 11 01 13 55 55 2 92 N 32 22 11 W BO 10 11 01 14 54 55 2 82 N 32 21 64 W EN 10 11 01 16 20 55 2 70 N 32 21 39 W D14 14206 CTD BE 10 11 01 21 14 55 19 74 N 33 26 58 W BO 10 11 01 22 04 55 19 77 N 33 2723 W EN 10 11 01 23 22 55 19 46 N 33 27 71 W D13 14207 ARIES BE 11 11 01 04 36 55 3520 N 34 2342 W BO 11 11 01 05 37 55 36 58 N 34 27 47 W EN 11 11 01 06 33 55 37 79 N 34 31 38 W D13 14210 DM BE 11 11 01 08 12 55 39 54 N 34 3291 W 14210 trap problem BO 11 11 01 09 23 55 42 78 N 34 36 83 W EN 11 11 01 10 36 55 46 26 N 34 39 96 W D12 14211 CTD BE 11 11 01 14 08 55 54 80 N 35 1463 W BO 11 11 01 14 54 55 54 91 N 35 14 85 W EN 11 11 01 16 05 55 54 98 N 3
64. 77 9 48 82 and A 1 0005 s d 0 0050 These compared well with the values obtained during Discovery 253 3 814 and A 0 9966 particularly as I suspect the cos term in the derivation of A normally negligibly different from 1 was missed out and in 39 fact A should have been 0 9988 As a compromise we used 4 48 82 and 4A 1 0000 in adpexec3 A power cut on Julian day 340 6 Dec at around 1600 corrupted some software files on the 150 kHhz PC and logging was eventually restarted at 1940 after the software was reloaded In fact the run into Reykjavik meant the ADCPs were switched off from midnight on JD 340 to 1154 on JD 341 On JD 344 the PC gave up the ghost and was replaced by another PC The hard disk on the replacement PC was small and so data were logged only to the Level B not the PC The date on the new PC was set incorrectly and so the time stamp of the Level B data was 24 hours ahead of true time The Pstar files were thus corrected to true time using pcalib after the datapup process in adpexecO and before merging with navigation and header data 9 2 5 75 kHz ADCP Discovery 253 was the first scientific cruise on which the new RDI Ocean Surveyor 75 kHz Phased Array ADCP was used and thus a new processing path was written No significant changes were made to this on Discovery 258 The instrument was configured to sample over 120 sec intervals with 60 bins of 16m depth pulse length 16m and a blank beyond transmit
65. ARIES Fig 24 shows the observed depth profiles of Calanus sized particles copepodite stages C4 and c5 Note that these are preliminary plots requiring further calibration and refinement The distribution of estimated Calanus standing stock at ARIES tow positions on this cruise is plotted in Fig 25 together with comparative data from previous winter studies mentioned on the figure At the sampling sites in the southwest Iceland Basin Calanus sized particles are mainly distributed between 300 1500m centred generally around 1000m These depths are consistent with those expected of overwintering Calanus At the shallower stations along the Reykjanes Ridge the depth distribution becomes more even throughout the water column and abundance is less Once the ship moved across towards Cape Farewell into the southern Irminger Sea Calanus sized particles are again found mainly between 500 1500m with some evidence of shallower concentrations on the more offshore station Later and further north on the ARIES deployments across the center of the Irminger Basin Calanus sized particles could be seen between 500 2000m and again with an apparent tendency for peak numbers to occur in the shallower depths of this distribution at the deeper stations At the stations around the northern rim of the Irminger basin the Calanus sized particles are also concentrated in the depths below 400m or so with greatest numbers generally between 500 1500m There are
66. BT sur25808 315 032128 316 013532 D258Leg1012 000000 LTA sur25809 316 013556 317 020601 D258Leg1013 000000 LTA Sur25810 317 020756 318 023602 D258Leg1014 000000 LTA Sur25811 318 023721 319 184930 D258Leg1015 000000 LTA sur25812 319 185102 320 183108 D258Leg1016_000000 LTA sur25813 320 183130 321 172138 D258Leg1017_000000 LTA sur25814 321 172347 322 172351 D258Leg1018_000000 LTA sur25815 322 172557 323 171805 D258Leg1019 000000 LTA Sur25816 323 171855 324 172501 D258Leg1020 000000 LTA Sur25817 324 172602 325 171607 D258Leg1021 000000 LTA sur25818 325 171706 326 171710 D258Leg1022_000000 LTA sur25819 326 171752 327 172602 D258Leg1023 000000 LTA Sur25827 327 172645 328 172452 D258Leg1024 000000 LTA sur25828 328 172647 328 180047 D258Leg1025 000000 LTA sur25829 328 185037 328 185037 D258Leg1032_000000 LTA BT sur25830 328 185401 328 185401 D258Leg1033_000000 LTA BT sur25831 328 185507 329 120712 D258Leg1034 000000 LTA BT Leg 2 sur25820 331 165250 332 212256 D258Leg2035_000000 LTA sur25821 332 212511 332 223913 D258Leg2036_000000 LTA sur25822 332 224035 332 224238 D258Leg2037_000000 LTA sur25823 332 224441 338 203709 D258Leg2038 000000 LTA sur25824 338 203825 339 202630 D258Leg2039_000000 LTA sur25825 339 202732 339 204933 D258Leg2040_000000 LTA sur25826 339 205135 340 155340 D258Leg2041_000000 LTA sur25832 340 163826 340 192228 D258Leg1038 000000 LTA sur25833 340 192422 340 194023 D258Leg1041_000000 LTA sur25834 340 200552 341 001553 D258Leg20
67. DM BE 29 11 01 09 18 64 20 184 N 32 6 307 W BO 29 11 01 10 15 64 20 397 N 32 11 09 W EN 29 11 01 11 08 64 20 165 N 32 15 267 W F05 14251 ARIES BE 29 11 01 11 50 64 20 295 N 32 16 068 W BO 29 11 01 14 37 64 21 23 N 32 32 671 W EN 29 11 01 16 54 64 21 796 N 32 46 45 W F03 14254 CTD BE 29 11 01 21 54 64 27 045 N 33 59 912 W BO 29 11 01 22 37 64 26 9 N 34 0 332 W EN 29 11 01 23 44 64 26 912 N 34 0 88 W F01 14255 DM BE 30 11 01 04 27 64 33 478 N 35 48 505 W BO 30 11 01 05 01 64 33 966 N 35 51 739 W EN 30 11 01 05 36 64 34 42 N 35 54 899 W F01 14256 ARIES BE 30 11 01 06 20 64 30 912 N 35 52 948 W BO 30 11 01 06 45 64 31 616 N 35 54 643 W EN 30 11 01 07 12 64 32 278 N 35 56 238 W F01 14259 CTD BE 30 11 01 08 02 64 33 947 N 35 59 78 W BO 30 11 01 08 23 64 34 011 N 35 59 921 W EN 30 11 01 09 03 64 34 078 N 36 0 131 W F01 14260 OS BE 30 11 01 10 04 64 34 176 N 36 2 218 W BO 30 11 01 10 38 64 32 527 N 36 3 991 W EN 30 11 01 11 38 64 31 912 N 36 6 932 W H01 14263 CTD BE 02 12 01 08 43 62 44 517 N 36 34 217 W BO 02 12 01 09 35 62 44 626 N 36 34 734 W EN 02 12 01 11 20 62 44 64 N 36 35 101 W H01 14264 ARIES BE 02 12 01 12 09 62 45 959 N 36 36 823 W BO 02 12 01 14 19 62 50 803 N 36 42 648 W EN 02 12 01 16 25 62 55 659 N 36 49 127 W H02 14267 CTD BE 03 12 01 05 20 61 59 612 N 39 24 525 W BO 03 12 01 05 59 61 59 534 N 39 24 245 W EN 03 12 01 07 12 61 59 537 N 39 23 81 W G04 14268 DM BE 03 12 01 13 44 61 35 472 N 40 37 821 W BO 03 12 01 14 28 61 36 924 N 40 38 69
68. LG 14233 D9 ARIES 63 1563 2709 2 W 60 0 C F T L G I 14236 G10 ARIES 70 1732 2456 2 W 60 0 C F T L G I 14240 G8 DM 2 801 3009 LG 14241 G8 ARIES 76 2667 2946 2 W 60 0 C F T L G I Leg 2 14246 F7 ARIES 62 1508 1600 2 W 60 0 C F T L G I 14250 F5 DM 2 830 2520 LG 14251 F5 ARIES 91 2220 2382 2 W 60 0 C F T L G I 14255 F1 DM 2 492 521 LG 14256 F1 ARIES 21 458 498 2 W 21 0 C F T L G I 14260 F1 OS 7 508 470 2 W 7 G 14264 H1 ARIES 93 2269 2427 2 W 60 0 C F T L G I 14268 G4 DM 1 807 1990 LG 14269 G4 ARIES 62 1508 1962 2 W 60 0 C F T L G I 14272 G4 OS 7 481 1948 2 W 7 G 14276 G6 ARIES 64 2485 2623 2 W 60 0 C F T L G I 14279 E16 ARIES 50 1184 1340 2 W 50 0 C F T L G I 14284 E13 ARIES 53 1269 1420 2 W 53 0 C F T L G I 14290 G14 ARIES 75 1824 2038 2 W 48 0 C F T L G I 14293 G14 DM 1 807 2136 LG 14296 G17 ARIES 73 2787 3127 2 W 60 0 C F T L G I 10 2 Deployment Whilst the DM gear was stored on deck it was essential to store both ARIES and OS inside the hangar to protect the nets from damage by wind and water and to allow sample removal under shelter The two vehicles sat side by side enabling either to be pulled from the hangar without moving the other To this end the hangar was cleared of features that narrowed it primarily the paint locker and compressed gas bottle rack A tugger winch was installed at the forward end of the hangar and this was used to pull the vehicles into the hangar To extract them they were pul
69. Nov Friday 313 ARIES recovered at 02 10 thus 4 hr 40 min for tow to 2720 m depth The tows had been on passage so by 04 45 we had reached the next sampling site From start of recovery of the TEK to being hove to ready for the CTD took 20 min beginning CTD 14199 at D18 at 05 15 Thereafter the LEK 14199 was lowered to 500 m and held there for 30 min With extra weight lowering rate of 20 m min was achieved just acceptable This deployment took 70 min but a further 20 min was needed to stow the LEK and prepare for TEK launch By 10 27 the TEK was deployed and passage set for D17 a total on station time of 5 75 hr Later the LEK was found to have switched itself off on reaching the surface but no data lost Site D17 was reached at 14 30 and the sequence repeated CTD followed by LEK both 14200 A new deploy ment method for the LEK was tested Instead of using the main trawl winch a deck mounted winch on board in case of emergency dragging was used This winch is on the after deck and can be used with a snatchblock diverter both for the LEK and TEK deployments replacing the capstan for the latter This was a great improvement lowering the LEK to 500 m in 11 min a saving of 20 min each way on the previous deployment On station time 2 5 hr for the CTD 1 hr for LEK 4 3 hr in total from start of TEK recovery to end of TEK redeployment after the station On recovery the LEK electronics cylinder was found to be loose with one out of
70. ON COUNTER PHYTO PLANKTON REYKJANES RIDGE RRS DISCOVERY SALINITY SCIENTIFIC ECHOSOUNDER SEA SURFACE TEMPERATURE ZOOPLANKTON ISSUING ORGANISATION Natural Environment Research Council Swindon SN2 1EU UK COPIES OF THIS REPORT ARE AVAILABLE HARD COPY AND ONLINE FROM British Oceanographic Data Centre Bidston Observatory Prenton Merseyside CH43 7RA UK Tel 44 0 151 653 1510 fax 44 0 151 652 3950 website www bodc ac uk CONTENTS Scientific personnel aaa 7 Ship s personnel 0 0000 sem 8 Acknowledgements O y j aan 8 1 The cruise aa 9 is r R 1 1 Introduction 1 2 Scientific objectives 1 3 Cruise overview Table 1 CTD operations ee 11 2 1 CTD operations rosette and frame Table 2 2 2 CTD salinity calibration including ARIES 22 1 Lowered Sea Bird CTD Table 3 2 2 2 ARIES Sea Bird CTD sampling and implications for calibration 2 2 3 Deleterious effects of ship roll and package dynamics 2 3 Chlorophyll calibration 2 4 Sea Bird oxygen calibration Table 4 2 5 150 kHz lowered ADCP 2 6 600 kHz lowered ADCP 2 6 1 Backscatter 2 6 2 Backscatter range correction 2 6 3 Temperature 2 6 4 Software 2 6 5 Averaging the bins 2 6 6 Backscatter spikes 2 6 7 Comparison with OPC data Lowered EK500 scientific echo sounder LEK 21 Towed EK500 scientific echo sounder TEK see 23 Salinometry a 25 Phytoplankton and pigment studies cee 26 6 1 Pigment studies 6 2 Chloroph
71. RF low water pressure meant no sample could be collected from the TSG sample tap The conductivity of the samples was recalculated using the housing temperature and zero pressure and compared to the TSG conductivities Fig 22 A linear fit was obtained the coefficients applied to the TSG conductivity and salinity recalculated The residuals between the bottle salinity and the calibrated TSG salinity were 0 00302 0 0037 for leg 1 and 0 0049 0 0058 for leg 2 9 1 4 Fluorescence calibration of underway data Samples for chlorophyll analysis were also collected every 4 hr analysed by Russell Davidson and compared to the underway fluorescence On leg 1 there was a good range of fluorescence and chlorophyll values though clustered in two groups thought to reflect two regions the Iceland Basin Reykjanes Ridge versus the Irminger Sea and a linear regression r 0 89 n 67 provided the following coefficients to calibrate the fluor Fluor cal 0 1193 2 8728 x Fluor raw ug l The residuals after the calibration chla fluorcal had a mean of 0 000 0 046 On leg 2 the chlorophyll and fluorescence values were consistently low at around 0 10 ug l and there was no statistically significant linear fit Instead a constant offset applied to the fluorescence 0 0272 gave the residuals a mean of 0 0000 0 0325 The results Fig 23 show the daily peaks of fluorescence observed during leg 1 are absent during leg 2 when with the exception of the
72. RRS Discovery cruise 258 Biophysical studies of zooplankton dynamics in the northern North Atlantic winter 1 Nov 18 Dec 2001 MARINE PRODUCTIVITY CRUISE REPORT No 1 Principal Scientists Raymond Pollard Southampton Oceanography Centre Stephen Hay FRS Marine Laboratory Aberdeen Document Data Sheet AUTHORS PUBLICATION DATE R T POLLARD S J HAY and Marine Productivity researchers with editorial assistance by P WILLIAMSON and G MONCOIFFE Mech 2002 TITLE RRS Discovery cruise 258 Biophysical studies of zooplankton dynamics in the northern North Atlantic winter 1 Nov 18 Dec 2001 REFERENCE Marine Productivity Cruise Report No 1 112pp ABSTRACT Discovery 258 was the first of four multi institute and multidisciplinary research cruises supported by the NERC Marine Productivity thematic programme within the wider context of the international Global Ocean Ecosystem Dynamics project GLOBEC It provided information on biological and physical conditions during early winter in the Irminger Sea along the Reykjanes Ridge and in parts of the Iceland Basin The main scientific effort was directed at mapping physico chemical features and estimating future water mass fluxes and particle trajectories using CTD ADCP and TSG systems float deployments SST satellite imagery and analysis of nutrients oxygen and SF collection of water samples for analysis of microplankton and plant pigments assesments of ph
73. S EMO dd eel dor E F xe veli EE POP PME 3b Conductivity correction factor 1 00043860307184 gt a i i i i i i 230 240 250 260 270 280 290 300 Discovery station number minus 14000 Fig 5 Salinity errors for second lowered Sea Bird CTD Text section 2 2 1 Fig 5 a Uncorrected error in S T T 50r Dese E f 1000r EA Te a o amp a p a D 1500 Eo PP rto enun GaN Sica 2 OOD nC gb LLL LLL rc E a 2000 A n EE eso 7 desde uctus Mao inte ERE 4 2500 0 015 0 01 0 005 0 AS x10 b Corrected error as fn of pressure 8 T T T T 6r eg E osuere o in epus 4 2 aANT Nerei porri a Qe Res ree rte eee nd MA TERM esses iege eee eee Fee eng NONIS 4 2L ys i 4 2A ee eRe eee ere ee eU a ee MT mos ds LIES MM LLL E 6 H 8 i i i i 0 500 1000 1500 2000 2500 P x 10 c Mean std dev of corrected error at each station 8 T T T T T T T T 6 bes E zd 4 J T 4 2 AE E ae ale P B a E 9 O certe tete et LU LI a c Lp etse tens s ea seb tts 4 2 4 rp eee eee emer CE ere TP PEE 4 6 s 4 a i i i i i i i i 210 220 230 240 250 260 270 280 290 300 Fig Discovery station number minus 14000 6 Salinity errors for ARIES Sea Bird CTD Text section 2 2 1 Fig 6 a Package downward velocity dbar s 2
74. These fluctuations meant that the bath temperature had to be adjusted on several occasions Since the instrument takes some 12 24 hr to re equilibrate after each such adjustment this represented a significant amount of down time for the salinometers That no serious backlog developed was due to the fact that a relatively small number of samples from the CTD were taken for salinity analysis for calibration purposes only Attempts to cool the chemlab by drawing in air from outside using a fan were unsuccessful 25 Despite these problems good quality salinity measurements were obtained The four duplicate samples measured blind differed by 0 0 1 and 3 in the last digit of double conductivity ratio where a difference of 6 corresponds roughly to a change of 0 001 in salinity the precision claimed for the instrument This result confirms that our sampling techniques were adequate Measurements on standard sea water SSW before and after each crate likewise showed drifts of less than 0 001 in salinity over the 2 hours or so taken to process each crate Occasional sample measurements during which no stable reading could be obtained were discarded This happened for between 0 and 2 bottles per crate We are confident that the remaining measurements are accurate to within 0 001 in salinity Salinity values were obtained from the double conductivity ratio measurements in the usual way using an Excel spreadsheet then transferred to the Unix syst
75. Turner Designs Fluorometer Chlorophyll standard solutions Sigma covering the expected chlorophyll range were used for calibration of the fluorometer before each set of samples were analysed The chlorophyll concentration of these were calculated from the absorbance measured at 750 664 647 and 630 nm in a Cecil spectrophotometer using the equations of Jeffrey amp Humphrey 1975 Biochem Physiol Pflanzen 167 191 4 6 3 Phytoplankton studies During leg 1 phytoplankton samples for microscope speciation studies at SOC were taken at the surface and at the chlorophyll maximum In leg 2 a further sample was taken at around 150 m Two amber glass bottles were filled for each depth and preserving agents Lugol s iodine and buffered formalin added to each Picoplankton samples were taken from the top six Niskin bottles leg 1 and top eight leg 2 and preserved with glutaraldehyde for subsequent analysis by flow cytometry at PML Samples were also collected and preserved for ciliate and heterotrophic dinoflagellate analysis by Dr David Montagnes Univ of Liverpool A total of 148 phytoplankton samples and 188 picoplankton samples were taken from 27 CTD stations Russell Davidson 7 Oxygen nutrients and SF 7 1 Dissolved oxygen Dissolved oxygen was measured on approximately half the bottles from all the CTD casts using a semi automated whole bottle Winkler titration unit with spectrophotometric end point detection manufactured by SIS Sa
76. WNO30 WM 1 WP00001 WB 1 WS0200 WV 400 WV170 WE 0150 CK WC 056 CS CP 255 PSO CLO EC 1500 BP 001 CP 0 BD 50 amp BX 2500 BL 0 200 600 BM 4 TP 000100 TE 00000200 amp R20 CF11101 amp PDO RDO CF11101 CK CS A2 3 3 Processing cd ladcp goes to data61 ladcp Here there are two directory trees 600khz and 150khz Each started the same with a copy of the Firing tree and the Visbeck directories Additionally there is a directory called data in which raw binary data files may be placed At present neither of the LADCP PCs is networked Data files must be transferred using zip disk Mischa and ftp Once in the data directory there are two symbolic links 150khz and 600khz which point to the raw data directories in the relevant tree just use mv Log files should be stored in 150khz logs and 600khz logs Depending on which data are to be processed source 150khz LADall or source 600khz LADall 71 This sets up various environment variables and adds the required directories to the MATLABPATH variable If the computer responds with too long it is because this variable has already been modified and now cannot hold any more directories Simply logout and start again One of the important settings is the cruise identifier This is a six character ID di0111 for the 150 kHz and wi0111 for 600 kHz They have been made different so that the data files have different names and can therefore be distinguished 150
77. a cycles and a maximum difference between median and data of 1 degree The data were then averaged to 2 minutes and further edited for 2 lt pitch lt 2 0 mrms 0 004 10 a ghdg 10 The 2 minute averages were merged with the gyro data files to obtain spot gyro values The ships velocity was calculated from position and time and converted to speed and direction The resulting a ghdg should be a smoothly varying trace that can be merged with ADCP data to correct the gyro heading do plotash was the script used to produce diagnostic plots to check this and this script resided in the P ASH directory with the data files During ship manoeuvres bad weather or around data gaps there were spikes which were edited out manually plxyed ashexec3 appended daily Ashtech files to a master file ash258smt ave after removing any overlapping time steps The master file was subsequently used in ADCP and Surfmet data processing 69 adpexec0 adpexec2 adpexec3 adpexec4 surexecO surexec1 surexec2 surexec3 surexec4 transferred data from the RVS level C adcp data stream to Pstar The data were split into two gridded depth dependent data were placed into adp files while non gridded depth independent data were placed into bot files Velocities were scaled to cm s and amplitude by 0 42 to db Nominal edits were made on all the velocity data to remove both bad data and to change the DAS defined absent data value to t
78. al GPS system and continued to provide differential corrections to the GPS 4000 system Thus an examination of positional accuracy whilst tied up alongside in Govan and Reykjavik showed that the corrected GPS 4000 system provided higher positional accuracy than the new Ashtech G12 system calculated with Pstar program gpsrms However results from all three of these systems Table 11 below indicate sufficient precision to enable a calculation of ship s velocities to better than 1 cms and therefore below the instrumental limits of the RDI ADCP systems Table 11 Comparison of port based positional accuracy determinations Mean latitude SD Mean longitude SD rms pos error o N o W Govan Ashtech G12 55 86633 0 00002 4 35270 0 00003 2 85m 2 16m 1 86 m Trimble GPS 4000 55 86634 0 00001 4 35266 0 00001 1 25m 1 08 m 0 62 m GPS GLOS 55 86629 0 00004 4 35274 0 00005 5 32 m 4 32 m 3 10 m Reykjavik Ashtech G12 64 15010 0 00004 21 93873 0 00003 3 05 m 2 39 m 1 89 m Trimble GPS 4000 64 15014 0 00002 21 93879 0 00003 2 79m 2 33 m 1 53 m GPS GLOS 64 15005 0 00003 21 93870 0 00006 m m m If there were gaps in the G12 data the bestnav process used other inputs as necessary These were turned to in the strict preference order GPS Trimble 4000 data GPS Ashtech 3D GPS Glonass which uses a combination of Russian and American satellite networks Or as a last resort if no GPS was availa
79. al at D10 the TEK was recovered and the first ARGO float deployed This was done at 01 06 over the stern in calm conditions by lowering it held horizontally on two ropes until close to the water There were no attachment points on the float to allow it to be lowered in a more controlled way on a single slip rope After moving a mile off CTD 14231 to 2460 m was worked from 01 27 to 03 43 A planned LEK deployment was abandoned instrument not pinging The TEK was deployed and passage set for D9 At 06 35 9 5 nm short of D9 the ship was slowed for the net deployments but the DM was not ready to deploy until 07 32 DM 14232 was worked from 07 32 to 08 38 followed by ARIES 14233 4 5 from 09 40 to 13 04 With wire out of 2000 m the weather conditions had deteriorated sufficiently that the vehicle was held until the ship could turn head to wind and ARIES was then recovered For safety the TEK was also recovered and all gear lashed down Further work was not possible 15 18 Nov Thursday Sunday 319 322 Remained hove to occasionally steaming during daylight hours to regain position near to line D 19 Nov Monday 323 The weather is not abating but has now switched from southerly to westerly winds Swells come in from several areas so that confused swell is probably more of a problem than the winds themselves Decision therefore taken to abandon line D for this leg and proceed further north into the Irminger Basin in the hope that the
80. al salts123 to 450 txt It also asks for the 3 char station number and the 3 char character descriptor i e sal nut oxy chl This is because passam now has no knowledge of which columns it 1s pasting It uses the 3 char descriptor to name the Pstar interim file and place it in the relevant subdirectory e g sal sal14235 Sea Bird CTD on ARIES Briefly processing path is very similar but stick an a on the front of all execs e g actdO actdplots asam0 Directories used are actd and abottle First step is to read in MRG and CNV files usually provided by Steve 68 on zip disk On a PC transfer these into the D258ariessb directory thus creating a backup Then ftp the cnv file into data61 actd and the mrg file into data61 abottle Try the following order of processing vi the MRG file in order to delete the first data cycle which appears to be always rubbish asamoO creates the ari file Mlist this to find the lat and lon for maximum pressure Use fmt lat DEG and fmt lon DEG to get lat and lon in suitable format Write these on top of the new CTD processing sheet actdO creates the ctd 1 hz file and you can now enter the correct lat and lon right away actd1 actd2 actdplots should now work asam1 merges the ctd and fir data to create the sam file apassam not yet fully tested A2 2 ADCP and navigation processing navexecO transferred data from the RVS bestnav stream to Pstar calculated the ships velocit
81. al thanks to Robert Pickart WHOI and staff of the Icelandic Marine Research Institute Reykjavik for access to their unpublished data Funding was primarily provided through research grants awarded through the NERC Marine Productivity thematic programme The assistance of the programme Steering Committee and Science Coordinator in the strategic planning and implementation of Discovery cruise 258 is gratefully acknowledged 1 The cruise 1 1 Introduction RRS Discovery cruise 258 was the first of four supported by the NERC Marine Productivity MarProd thematic programme The vessel sailed from King George V Dock Glasgow on the morning of 1 November 2001 Thursday and returned to Empress Dock Southampton in the evening of 18 December 2001 Tuesday a total time at sea of 47 days There was a mid cruise port call at Reykjavik Iceland from 25 27 November that included scientific discussions at the Marine Research Institute and a visit to Discovery by the British Ambassador Mr John Culver 1 2 Scientific objectives The MarProd cruise series provides the main opportunity for data and sample gathering to address the overall programme goal viz to develop coupled modelling and observation systems for the pelagic ecosystem with emphasis on physical factors affecting zooplankton dynamics The principal cruise specific research objectives for Discovery 258 were as follows e Map the physical features of the survey region Irminger Sea and p
82. al units bits mM Fig 19 Correlation coefficient Time series of calibration curve correlation coefficients 14 y L S EU ELLE E oO 0 998 4 H B oO 0 996 a H 0 994 4 0 992 Nitrate o Phosphate Silicate 0 99 T T T T T T T 1 5 Nov 10 Nov 15 Nov 20 Nov 25 Nov 30 Nov 5 Dec 10 Dec 15 Dec Date Time series of bulk nutrient concentrations 31 t 1 36 cz 297 ti 44 _ 14 34 ez t 8 PRO ODMPLSS rade 1 32 n 5 27 o 825 ae 54 o obg n 1 28 v n o o n 1 26 amp S 214 o V 124 Q g e LH o c S 19 eeeteg se e ogee Dy Aaa e o peu e Z 1 4 oO i 1 2 15 T T T T T T T 1 18 5 Nov 10 Nov 15 Nov 20 Nov 25 Nov 30 Nov 5 Dec 10 Dec 15 Dec Date Nitrate Silicate o Phosphate Fig 20 Time series of the calibration curve correlation coefficients of the auto analyser upper plot and of bulk nutrient concentrations lower plot Text sections 7 2 2 and 7 2 3 Fig 20 lat lat lat Fig 21 Spatial plots of a underway sea surface salinity and b temperature from the ship s thermosalinograph and c underway absolute wind speed measurements from the ship s anemometer Text section 9 1 2 53 0 52 0 51 0 50 0 53 0 52 0 51 0 50 0 on 20 salin psu 50 on Z var 20 trspeed m s 35 55 35 50 35 45 35 40 35 35 35 30 35 25 35 20 35 15 35 10 35 05 35 00 34 95 34 90 34 85 34 80
83. an be a depth dependence The Sea Bird CTD was changed after cast 14231 Therefore we show first the corrections botoxy oxygen that would need to be added to the SB computed oxygen values for downcasts 14191 to 14231 oxygen sensor SBE 43 0086 new and factory calibrated on 12 Sept 01 Below 1500 dbar there is no obvious drift with depth and the mean st dev fit is 13 7 1 5 umol kg In the top 180 dbar the fit over 45 points excluding 4 obvious outliers is 7 8 1 6 umol kg With rather scattered points between 200 and 1500 dbar our final choice is a correction of 7 8 13 7 13 7 umol kg at 0 1500 and 5000 dbar respectively linear between as shown in Fig 11 upper For the second Sea Bird oxygen sensor SBE 43 0076 new and factory calibrated on 17 Sept 01 used for the remaining casts the oxygen bottle CTD differences are plotted against pressure in Fig 11 lower graph for casts up to 14275 Strange behaviour is shown for the first two casts 14239 and 14244 with wild variation in the first cast and a fairly constant low value 5 6 2 1 for the second of these Remembering that the bottles are fired on the upcast but the CTD values have been taken from the downcast at the same pressure shortly after the sensor went in the water for the very first time it appears that the sensor has taken a while to settle From cast 14245 on there is a reasonable fit over 82 points after excluding 3 outliers with a constant value inde
84. ants Between these points the thiosulphate breakdown was regularly every few days monitored using an in house standard prepared on board by dissolving 0 3567 g reagent grade KIO in 1 1 Milli Q water Changes in the volume of thiosulphate required to titrate 5ml aliquots of the in house standard were used to calculate the volume of thiosulphate that would be required to titrate similar aliquots of certified standard This volume was then used in the calculation of oxygen concentration which was performed on an Excel spreadsheet following the equations supplied by Dickson 1994 27 At the end of the cruise the calculated volume of thiosulphate required to titrate the certified standard determined from the volume required to titrate the in house standard was compared with the actual volume of thiosulphate required to titrate the certified standard The two volumes were within 0 196 of each other The reagent blank was evaluated at the start of the cruise and found to be 0 0006ml for the single batches of reagents used during the cruise This value was applied to all calculations undertaken The thiosulphate solution was found to be extremely stable with the percentage increase in thiosulphate volume required to titrate 5 ml of the in house prepared standard being 1 15 over the seven weeks of the cruise Fig 18 A minimum of one bottle of each cast was sampled twice to gain an estimate of the analytical precision The mean difference in calculated
85. articipants while the programme is running and also to provide wider access and exploitation of datasets of longterm importance Properly managed environmental data provides a key NERC resource which will be used long after the formal end of individual projects and programmes The scale of effort dedicated to data stewardship should reflect the anticipated longterm value of the data In the context of NERC Data Policy data may be held in either analogue or digital form and be stored either on paper or a variety of computer compatible media physical specimens in curated collections are outside the usual sense of the word Nevertheless it is appropriate for sample management issues to be also considered here making clear which aspects apply in different sections A6 2 Role of BODC The British Oceanographic Data Centre BODC is the NERC Designated Data Centre for digital information arising from the Marine Productivity programme BODC has provided data management services for many other multi laboratory and multidisciplinary marine programmes NERC and non NERC eg BOFS LOIS PRIME and OMEX and has delivered high quality accessible data sets primarily via CDs for further scientific use Costs have been allocated in the MarProd budget for BODC services and Dr Gwen Moncoiff gmon bodc ac uk has been appointed contact person for liaison with the Steering Committee and individual projects BODC effort will focus on the quality contro
86. arts of the Iceland Basin in terms of water mass distribution velocity field and mixed layer properties e Obtain additional information to estimate future water mass fluxes and particle trajectories via float deployments and tracer analyses e Collect water samples for plant pigment and microscopic analyses to estimate the biomass of different taxonomic functional groups of microplankton e Measure high resolution profiles of inorganic and organic nutrient concentrations e Determine the 3D abundance of mesozooplankton of interest primarily the copepod Calanus finmarchicus and their planktivorous predators primarily euphausiid spp obtaining material for further taxonomic physiological and biochemical studies There was strong emphasis on obtaining an integrated interdisciplinary data set not only to bring together researchers involved in survey related MarProd projects but also to set the scene for subsequent cruises during 2002 involving additional groups and to facilitate comparisons with historical datasets eg NORWESTLANT 1963 and Continuous Plankton Recorder surveys EU supported zooplankton programmes TASC and ICOS and other national and international studies The MarProd programme provides the main UK contribution to the Global Ocean Ecosystem Dynamics project GLOBEC co sponsored by IGBP SCOR and IOC 1 3 Cruise overview It was clear to the MarProd Steering Committee from the start that a winter cruise carried high
87. be occupied en route However encountering icebergs well off the coast changed things First reaction was to head further offshore but persistent westerlies had driven icebergs over 300 km offshore so it was necessary to work in the area of possible bergs After another ARIES deployment had to be abandoned at the last minute on 1 December when the weather blew up it decreased equally rapidly and a CTD was worked the next morning at H1 Over the next two days the western end of line G was completed except for the shelf site G1 in remarkably good conditions except for icebergs The good weather was the result of what appeared to be a common weather pattern with the mountains of Greenland driving northerlies very close to land which then turned offshore to become westerlies Working close in was therefore good because of the low fetch From line G it was planned to work sites across the Irminger Current back to pick up line E at E6 Shortly after heaving to at the first intended site in bad weather the second engineer was injured when a lever recoiled and hit him in the face It took two days to reach Reykjavik for the medical evacuation the engineer was able to fly home after treatment and a further day to return to deep water Clearly line E had now to be occupied from NE to SW Useful ARIES sites E16 and E13 were worked on two days to fill in the NE of the Irminger Sea but bad weather again stopped work on 9 December We could not get far en
88. ble the Chernikeef electo magnetic log velocity data and gyro heading were used to dead reckon the ship s position 37 Data were transferred daily from the Level C bestnav stream to the Pstar absolute navigation files abnv2581 leg 1 and abnv2582 leg 2 The G12 gps 4000 gps glos and gyro gyronmea data streams were also transferred daily Processing scripts nav gyro gps execO etc are summarized in Appendix A2 2 9 2 3 Heading The ship s attitude was determined every second with the ultra short baseline 3D GPS Ashtech ADU2 navigation system Configuration settings from previous calibrations Trials cruise in April 2001 were used throughout the cruise Four antenna two on the boat deck two on the bridge top measured the phase difference between incoming satellite signals from which the ship s heading pitch and roll were determined The data were used to calibrate the gyro heading information using the ashexecs listed in Appendix A2 2 Ashtech 3D GPS coverage was generally good Dropouts occurred several times but on only one occasion was it necessary to reset the Ashtech Unit in the Comms Room Gaps over 1 min in the data stream are listed in Table 12 below Table 12 Gaps in Ashtech 3D GPS coverage Time gap yr JD hr min sec Duration Leg 1 01 307 21 01 00 to 01 307 21 02 07 1 min 01 313 13 52 54 to 01 313 13 54 08 1 min 01 313 13 56 54 to 01 313 13 59 04 2 min 01 317 14 27 26 to 01 317 14 31 03 4 mi
89. bly nor the 30t cranes port and starboard aft and power packs 11 6 Non toxic water system Used for the duration of the cruise A leak was found in the Chemistry laboratory the non toxic system was shut down overnight to allow for a joint effort between the ship s engineers and OED technicians to gain access to the leaking pipe flange A defect report has been made requesting that new gaskets be fitted There are no instructions onboard for the flushing of the system 11 7 Workshop The workshop was used for various repairs and modifications to scientific equipment The workshop should be re stocked with materials and tools whilst the ship 1s laid up The workshop was flooded due to water from the hangar leaking in past the door seal The floor covering has lifted in places The chuck guard to the lathe still needs replacing this was noted during a safety inspection The gym store ended up awash with oil again better storage for the drums of oil would be a good idea 11 8 Winch control cab One of the aft window wipers is not working the others are a bit tired 11 9 Crane for TEK deployment The towed EK deployment and recovery was mentioned in the safety meeting The use of the crane in rough weather is not ideal It has been suggested that a Schatt davit and deck winch may be used to 49 deploy the towed EK A base plate may have to be made to give enough height to swing the EK over the side This should be looked at whilst the ship i
90. c 2001 with direct BODC involvement Further information is provided in the D258 Cruise Report this document Sorting procedures and sample preservation protocols are being developed for biological material collected on MarProd cruises Whilst formaledehyde solution 1s used for bulk zooplankton samples from ARIES and Dual Methot nets other preservation techniques apply to sub samples for specific purposes for example liquid nitrogen for lipid work ethanol for molecular biology and genetics and 20 C freezing for isotope ratio analyses Investigators with other needs should discuss their proposed preservation methods with the cruise Principal Scientist The longterm curation of biological material is discussed under A6 9 below Station identifiers navigational information and basic oceanographic data for which BODC will have quality control responsibilities must be provided to BODC by the Principal Scientist immediately after a MarProd cruise Normal practice will be for BODC to meet the ship when it docks and to take delivery of this material together with a copy of the logs calibration data and sensor information A copy of the Cruise Summary Report ROSCOP form should be provided to BODC by the Principal Scientist within one working week of the end of the cruise A copy of the full cruise report should also be sent to BODC preferably 82 electronically as soon as it is completed BODC will then assist the MarProd in making this more
91. cal to use the RMS deviation of the phosphate data points from the line of best fit as an indicator of data quality Table 7 Table 7 RMS deviations of phosphate data from best model II regression between nitrate and phosphate data from the entire cruise and for work periods within it Period RMS phosphate deviation from line of best fit uM Leg 1 pre storm to 15 Nov 0 02 2 33 Leg 1 post storm after 20 Nov 0 02 1 81 Leg 2 pre medevac to 5 Dec 0 03 2 58 Leg 2 post medevac after 8 Dec 0 03 2 72 All data 0 04 3 03 The mean deviation of phosphate data from the line of best fit was 0 04 uM or 3 This value ranged between 1 8 and 2 72 Clearly the modifications to the phosphate line undertaken between 32 the first and second work periods were useful However the problems suffered by the phosphate line in the second half of the cruise reversed these gains to some extent Richard Sanders 7 3 SF Samples for sulphur hexafluoride analysis were taken from the bottom bottles on nine stations These stations together with the date on which they were sampled their locations and the Niskins from which samples were drawn are listed in Table 8 below Samples were drawn directly from the Niskin bottles into 500ml glass bottles using tygon tubing before any other samples were taken They were then capped either using a plastic seal and screw cap or by a ground glass stopper secured using elastic bands and cable ties They we
92. cially in regions of sharp vertical gradient This happens even during the downcast when the CTD sensors are ahead of the main bulk of the package and theoretically unaffected by wakes and such It is believed that this error is a result of ship roll one possible mechanism being as follows It is likely that a bolus of water is carried along with the rosette package When the package decelerates during the downcast due to the ship rolling the bolus will not be decelerated but will flow down over the sensors At this point the properties of the water in the bolus entrained from some metres higher up the water column will be measured Hence broad spikes of typically higher than ambient temperature are observed Corroboratory evidence for this is provided in Fig 7 which shows the downward velocity and acceleration of the package and the time rate of change of the measured temperature dT dt from a minute long section of an arbitrarily chosen downcast when the package was passing through a thermocline region The 24 Hz data have been filtered with a running mean of length approximately 1 5 seconds The figure clearly shows the periodic acceleration and deceleration of the package associated with ship roll and that dT dt oscillates at a similar frequency Close examination of the figure shows furthermore that dT dt is at a maximum shortly after the deceleration is a maximum or equivalently shortly before the velocity is a minimum This observat
93. comparable to those of physical variability within the environment Kolber ZS amp Falkowski PG 1993 Limnol amp Oceanogr 38 1646 65 The instrument was kept permanently attached to the ship s non toxic supply in order to provide a continuous record of changes in near surface phytoplankton physiology and provide a comparison and means of data quality verification with the other instruments deployed in situ Power was provided to the instrument using a standard Chelsea Instruments deck box Data from this instrument 42 were recorded internally and downloaded every 48 hr to a Mac laptop A total of 9 files were collected during leg 1 and 11 files during leg 2 Table 14 On day 338 the dark chamber of the FRRF was filled with filtered seawater through GF F paper to determine the background optical properties of the seawater The optical chamber was cleaned every 4 days using a small finger and white gentle tissues The data were not analysed on board Table 14 _ FRRF files File Start Gain Jday hr min sec Stop hr min sec J day Leg 1 d258001 310 14 20 53 312 17 25 30 auto d258002 312 18 34 03 314 18 29 53 auto 4258003 314 19 22 49 315 18 35 00 auto non toxic turned off at 17 25 Jday 315 Back on am 316 d258004 316 17 30 34 318 18 53 00 auto d258005 318 19 39 57 320 18 12 00 auto d258006 320 18 54 31 322 16 29 20 auto 4258007 322 17 11 15 324 21 14 02 auto d258008 324 22 04 14 326 21 41 35 auto d258009 326 22 22 51 328 16
94. d as it is brought onto the side of the ship Currently between deployments the towed body is stowed against the mooring bollards just forward of its deployment position This provides easy attachment points and some security against the towed body sliding up and down the deck and is well placed to provide sufficient slack in the towing cable package for the boom to be brought inboard However it is not ideal as it means the steel frame of the towed body is resting directly on the steel deck plates which provide little resistance to movement During passage out to the study area the towed body was swung forward using the crane onto the wooden decking ahead of the winch cabin and fixed against the outboard side The towing cable package was secured against the outer bulwark with the slack placed in a figure of eight and secured at all points Although this provided a secure attachment point it is not ideal as the rear fins in particular are vulnerable to damage whilst in the scuppers This is also true of the normal storage position and significant changes in the behaviour of the towed body in the water were noticed after each extended period of storage on deck This was attributed to the distortion of the rear fins by waves coming up through the scuppers or incorrect lashing of the towed body In future a proper cradle for securing the towed body would greatly improve matters This would provide a protected and secure fixing position on the metal
95. d the lifting wire is paid out at least 15 m out of 25 m total The towed body should fly out from the side of the ship at all speeds over 1 knot although significant vibration in the towing cable and boom arrangement is expected at slow speeds TEK retrieval procedures are as follows e Whilst the ship is steaming at between 7 and 10 knots sufficient slack should be taken in on the lifting wire that it can be removed from the snatch block on the deck and reset using a wire stopper so that instead of leading out through the fairlead it leads directly over the side of the ship from the deck winch e A snatch block is then set on the lifting wire and attached to the crane hook The crane arm is swung out and forward over the side of the ship until it is above and just forward of the towed body The snatch block on the deck used during deployment and use is removed so that it does not impede the retrieval of the towed body e Once the crane is in position over the towed body the ship s speed is dropped to between 1 5 and 2 knots and the towed body is lifted using the lifting wire on the deck winch and is manoeuvred inboard using the deck winch in conjunction with the crane arm e As soon as the towed body is over the side of the ship the rapid retrieval inboard of the towing wire transducer cable package helps stabilise its swing e The boom is then brought inboard with particular care paid that the transducer cable does not get pinche
96. d to bring them all together in one location This can be executed via Start Run A previously executed command should be easy to find you should only have to change the station number but beware that the edit keys behave slightly idiosyncratically make absolutely sure that you ve got the correct number Another version of the program ctdstuNoBottles bat is available for the case when no bottles were fired This happened once on Discovery 258 when a cast was aborted fairly soon after the beginning of the downcast but 67 useful data were still recorded This version uses a different DatCnv psu file DatCnv258NoBottles psu and doesn t have a RosSum step so that the program doesn t attempt to generate a btl file Sam file for lowered SeaBird CTD Now we have to create the sam file to hold the bottle samples up to 24 usually The old code makeblanks pasfir etc has been entirely revised First the btl file is created on the Sea Bird PC This can contain a lot of useful variables including the time of bottle firing and the standard deviation of each mean Since this file is the greater part of the sam file the new processing path turns this into the sam file by adding only the extra variables needed for bottle values of salts nutrients chla etc 9 On the PC run rossum to average the ros file into one value per bottle Input file is ros output is btl both in the Processed directory under the cruise directory D258CTD
97. deck It would also reduce the problem of the towed body sliding across the deck as it 1s retrieved assuming that the front of the frame could be caught in the cradle as it is lowered to the deck The use of a davit specifications of those available to be confirmed in place of the crane would also help to control the deployment and recovery operations The TEK would be deployed from the same place on the deck and the 5 t Lebus winch currently used could be replaced with an equivalent 2 t winch Overall this would expand the 24 range of sea conditions in which the towed body could be safely retrieved and 1s likely to reduce the number of people required for the deployment and retrieval operations Data collected During the cruise TEK data were collected between the following stations CTD except where stated 14191 and 14199 14199 and 14200 14200 and 14205 14205 and 14206 14206 and 14211 14215 and 14223 14223 and 14231 14231 and 14233 end of ARIES tow 14236 ARIES not CTD deployment and 14239 14239 and 14244 14244 and 14244 deployment curtailed due to bad weather 14245 and 14249 14249 and 14254 14254 and 14259 14259 and 14262 OS no as CTD station aborted due to weather conditions 14263 and 14267 14267 and 14272 OS no as TEK recovered due to Scanmar hydrophone problems 14275 and 14276 ARIES no as deployment aborted due to weather conditions 14282 and 14287 14287 and 14288 14288 and 14289 Cairist
98. deployed after the CTD on passage With the swell easing one site along line E was possible to the southwest and CTD 14288 was completed at E9 from 22 07 to 23 58 From there it was decided to head eastwards partly to make passage towards the Irish Sea at the time the preferred route for the passage home because of forecast of strong southerly winds and swell and partly because an important scientific objective was to complete an ARIES tow east of the Reykjanes Ridge 11 Dec Tuesday 345 Sites at 40 nm intervals were planned and the first G13 was reached at 03 52 After recovering the TEK CTD 14289 was worked from 04 19 to 05 53 The TEK was redeployed and 40 nm further on at G14 ARIES 14290 1 2 was towed from 11 12 to 15 11 followed by Dual Methot 14293 from 16 12 to 17 30 During this period a report of water in the forepeak chain locker and bowthruster space was investigated A slight leak possibly a popped rivet was found and subsequently pumped out the following day While on site G14 the decision was taken not to proceed through the Irish Sea which would allow significantly more science time at the risk of adverse conditions on the long passage The optimal science strategy therefore was to work south towards the very first site occupied D19 with the expectation that it would be possible to complete several stations before breaking off for passage home This line of sites to be labelled G15 G16 etc would now run al
99. e approximately the same scatterers with depth 2 6 2 Backscatter range correction To correct for this error consider Fig 15 in which the backscatter blue line is plotted as a function of bin number Deeper bins exhibit a linear trend with range while the decay towards the origin may be represented by a log term in line with the form of range dependence in the original calibration equation above So we choose to fit ASv alog R bR c where R is range from the transducer and y is the estimate of backscatter Form a least squares fit of the model to the data S 2 9 ASv ASv Y alog R bR c ASv Solve by finding a local minimum os on 2a log Ry 29 x logy R 2c log R 29 ASv log R 2 0 a r 2a gt _R log R 2b R 2c9 R 22 ASv R 0 aS ab 2a log R 2b R 2031 29 ASv 0 Solving this system of linear equations in three unknowns for station w200 01 results in the equation ASv 11 4763log R 0 2608 R 5 4650 Fig 15 shows the fit of the model to the range error curve The blue curve is the backscatter in each bin relative to the second bin The red curve represents the model fit to this data including a Pragmatically we would like simple powers of R in the equation Since the a coefficient is near to 10 we instead apply ASv 10l0g R bR c where R is range from the transducer and y is the estimate of backscatter range correction Form a least square
100. e rather than between profiles This was for qualitative comparison with the OPC data As a result of carrying out this step the spikes in the data discussed below were observed 2 6 6 Backscatter spikes The backscatter plots appear to have spikes as well as steps in the profiles Fig 17 upper plots These need to be treated with caution Smoothing over these steps results in realistic looking yet erroneous data 20 2 6 7 Comparison with OPC data There appears to be a good initial comparison between the LADCP backscatter profiles and the OPC data for example CTD station 14245 Fig 17 lower plots and ARIES station 14246 Leg 2 Mark Sidall Richenda Houseago Stokes Stuart Brentnall 3 Lowered EK500 scientific echosounder LEK The lowered EK500 scientific echosounder package LEK comprises a drop frame housing the Behemoth an EK500 echosounder with a logging control notebook PC a battery pack two transducers operating at 38 kHz and 120 kHz and a Scanmar transmitter It is deployed on station to collect good resolution higher frequency echo sounder data from depths greater than 500m and this cruise provided the first opportunity to deploy the equipment in the current configuration Before any data were collected and as part of the trials in the Clyde the equipment was calibrated to allow the correct integrator and target strength gain values to be applied during post processing see Appendix A3 At the beg
101. e end of the down cast Enter lat as dd mm mmN S and lon similarly While these can in theory be entered later with an exec using the bestnav file GPS data are so good nowadays that it is recommended that they are entered immediately Bear in mind that the PC is logging using its own internal clock which may be a little out anyway This is not important for a CTD but does mean that the time variable cannot be used to cross reference the bestnav file accurately 2 At the end of the cast UKORS technician will back up the dat file and copy it to another PC for processing with SeaSoft 3 On the pc using SeaSoft run the following routines all on the 24 Hz full rate data These steps can be done in the script c d258ctd ctdstu bat see below 3 1 datcnv Original dat file should be named ctd14nnn dat using Discovery station number For output use time elapsed time in seconds press temp temp2 cond cond2 oxygen fluor V7fluor trans V3trans OBLS6000 V6OBLS and altim Do not include derived variables salin potemp sigma etc in the output Output directory should be processed under the directory with the dat files 3 2 wildedit Spikes in the 24 Hz data should be edited right away before averaging Edit all the parameters in the file with first standard deviation set to 2 second to 10 500 data points at a time Overwrite the cnv file 3 3 repeat wildedit with same parameters Overwrite the cnv file 3 4 align This is pr
102. elow that It appears that the calibration is stable as long as the sensor is in regular use After a gap of a few days it may jump for unknown reasons Raymond Pollard Ulrike Riemenschneider 2 5 150 kHz LADCP The 150 kHz LADCP is configured as for previous cruises and processed in exactly the same way using Eric Firing s software See for example Allen JT et al 2001 SOC Cruise Report 37 Discovery 253 FISHES A copy of the command file used is provided in Appendix A2 3 2 and the log sheet is given in Appendix A2 3 5 together with the deployment steps required On leg 2 there appears to be a problem with the 150 kHz data from station 14283 The raw velocity data is about 600 m short of the full depth range 2 6 600kHhz LADCP Leg 1 report The 600 kHz Workhorse LADCP is new to SOC on this cruise The instrument proved accessible only via the RDI Workhorse application Separate applications used to talk to the 150 kHz such as BBTALK did not appear to work A command file was created using the PLAN application see Appendix A2 3 2 This was then loaded by the Workhorse application see log sheet in Appendix A2 3 6 for the sequence of steps required Two points should be noted e Be careful to choose the cast name correctly The log files associated with cast 14214 were lost because those for 14215 overwrote the contents of this directory e The application only downloads all data from the instrument so individual files cannot be
103. em in the form of a tab delimited ASCII file containing the four columns statnum sampnum botsal and botsalf a simplification compared to the practice on earlier cruises Data from the ASCII files were incorporated into the sam files using the new Pstar script passam If the CT lab is unavailable in future a preferable location for the salinometers might be the stable laboratory gravimeter room next door to the gym on the lower deck While not temperature controlled this laboratory is undisturbed and less prone to temperature fluctuations The stable lab has been used for this purpose before notably on the ACSOE cruise Its only real drawbacks are the lack of a nearby source of deionised water and the need to carry the sample crates down two flights of stairs which could be a problem in bad weather Towards the end of the cruise it became difficult to get water to flow through the 8400A despite replacing the peristaltic pump with a newer one Either a blockage or some problem with the air pump system is suspected this problem will need to be addressed before the salinometer is taken to sea again The backup salinometer 8400 was used for the last couple of crates on the cruise Prior to the next cruise we strongly recommend that proper packing cases for the salinometers are purchased since the present plywood crates provide no protection for the salinometers during transport It would also be a good idea to overhaul the spares box serv
104. ephen Groom Plymouth Marine Laboratory 14 Photography including video An extensive photographic and video record was made during the cruise particularly during leg 2 eg Fig 27 Still photography used a 35mm SLR camera with 50 and 100 ASA slide film stock Video was taken using a digital video camera At times this was linked to a microscope mounted analogue video camera for recording live zooplankton specimens collected in the nets The subjects recorded in both the photographs and on video were similar and included Work on deck deployment and recovery of ARIES Ocean sampler and Dual Methot CTD bottle rosette sampling towed EK500 acoustics On board laboratory work Zooplankton sample sorting ARIES set up and instrument work algal and plant pigment analyses nutrient and oxygen analyses Wildlife dolphins seabirds zooplankton and nekton from nets Environment and miscellaneous waves icebergs ice on the ship RRS Discovery in port Reykjavik This material will be available for scientific usage also for PR and training purposes Alexander Mustard James Creswell and Steve Hay 53 APPENDICES Al Diary and station information Al 1 Discovery 258 diary Leg 1 1 November 2001 Thursday Julian day 305 09 38 All clear from KGV Dock Govan Dropped pilot at 11 52 Passed Dunoon at 13 00 Trials were run in Bute Sound where there was over 100 m water depth on a straight 16 nm run from southeast to northw
105. er than 0 002 were excluded Fig 4a Such anomalies occurred only in the surface layers where the vertical gradients of salinity tend to be large Because some motion of the CTD package is inevitable due to motion of the ship the properties of the water sampled instantaneously by the firing of the bottle may well not be the same as those measured in the time average by the CTD 3 Calculate corrected CTD conductivities as K times the uncorrected conductivities 4 Calculate corrected CTD salinities from the corrected conductivities and the temperature and pressure data using peos83 or cond2sal m Steps 1 3 may be carried out and step 4 applied to the CTD data corresponding to bottle fires as follows when logged in to discovery2 as user pstar 1 Ensure that all appropriate sam files are listed in the for in statement of script sjbsals exe in directory data6 1 bottle 2 Run sjbsals exe 3 Runsjbsals in a Matlab session This prints the calculated value of K on the screen Results of this procedure are plotted in Fig 4b With a K value of 1 00004637 errors in salinity have been reduced to order 0 001 which is better than the accuracy claimed for the CTD salinity sensor The horizontal axis in this figure is the standard deviation of pressure during the 7 sec averaging period of the CTD data This value is large where the CTD package was moving vertically due to ship motion It is clear that there is no strong dependence of the error
106. es of Calanus sized particles as a function of depth from Discovery 258 ARIES data calibration subject to confirmation Text section 10 3 Discovery 258 OPC ARIES 225 13 11 01 56 17 00N 36 10 91w 500g det se eg i 1000 EE e 150042 855 7 Depth metres seabed 2456m Depth metres T T T T T 0 8 10 15 20 25 CALABUS C5 m 3 Discovery 258 21 11 01 oP ARIES 236 60 26 94N 32 58 32W Depth metres seabed 2456m T T T T 10 15 20 26 CALABUS C5 m 3 C ARIES 246 Discovery 258 28 11 01 OP 65 12 71N 29 37 25W Re ae seabed 1595m Depth metres T T T T 0 5 10 15 20 26 CALABUS C5 m 3 ARIES 256 64 31 59N 35 54 62W m WE asam 10005 Discovery 258 30 11 01 J OP 15004 2000 Depth metres 25004 38000 1 3 rL 1T ol 0 5 10 18 20 25 CALABUS C5 m 3 Depth metres Depth metres Discovery 258 11 12 01 OPC ARIES 290 59 03 398N 28 29 56W seabed 2039m Depth metres T T T T T 10 15 20 26 CALAB US C5 m 3 Depth metres Depth metres OPC ARIES 233 Discovery 258 14 11 01 56 52 91N 37 42 65W SG 5004 K seabed 2709m 0 1 st 0 5 10 15 20 25 CALABUS C5 m 3 DERE Anion 2AE CT TES ME 4 500 Ep Teese 28460 1 T 0 5 10 15 20 25 CALAMUS C5 m 3 ARIES 251 Discovery 258
107. essel hove to at 10 53 Shortly afterwards the second engineer received a serious injury to his upper jaw when the handle of the emergency generator recoiled Both PES and TEK were recovered safely despite the poor conditions and course was set for Reykjavik for a medical evacuation Luckily with strong swell and wind from WSW the ship was running before the wind and the course was reasonably comfortable 6 Dec Thursday 340 On passage all day A helicopter rendezvous was scheduled for daylight but the condition of the engineer was stable and the weather conditions bad so it was decided that the risk of a helicopter evacuation was not warranted 7 Dec Friday 341 Second engineer put ashore at Reykjavik between 03 00 and 04 00 then reciprocal course back towards the Reykjanes Ridge Tried tacking 265 T then 180 T to make the course but hove to from 14 00 8 Dec Saturday 342 By 11 00 conditions had eased sufficiently to consider working and an ARIES deployment was possible and particularly useful in the northeast corner of the Irminger Basin close to a TASC site After deploying the PES fish at 11 26 ARIES 14279 80 81 was deployed from 11 28 to 14 25 at site E16 Passage continued southwest along the Reykjanes Ridge 9 Dec Sunday 343 CTD 14282 was deployed at E13 at 08 30 but had to be recovered after a short time because of loss of signal While the cause of the problem was sought three bottles in positions 1
108. est The PES fish was deployed at 14 20 all times are GMT Towed EK500 To detect larger zooplankton the towed EK500 TEK carries echo sounders at 38 120 and 200 kHz to detect objects of order 7 8 2 and less than 1 5 cm respectively A pole extending 3 m outboard had been welded onto the starboard side just aft of the pilot gate from which to tow the TEK on a 25 m long lead The 10 cm diameter lead contains the strain cable a backup strain cable power and signal cables The rig is deployed on another 25 m cable attached to the stern fins on the TEK fish When speed is picked up the TEK rises and any slack on the deployment cable can be taken up 14 35 On the first deployment the 25 m deployment cable was lifted on the crane This was unworkable as crane does not have the reach and pendulum effect on the cranehook would be unacceptable For the trial the strop was doubled up However fish towed nose down Recover for adjustment Excessive heel was adjusted by hammering the wings 16 50 On the second deployment the 25 m deployment cable was led via two snatchblocks to the tugger winch in the hangar The cable could not be fully paid out because snatch block too small More serious was that there was no line of sight for the tugger winch operator Towed better but still needed adjustment to pitch angle Scanmar The PES fish has been modified by FRS Fisheries Research Laboratory Aberdeen to carry Scanmar and modified IOS recei
109. for ARIES stations I I I I 0 22 diuo Chl mg m3 0 022 2 73 x fluorctd 0 17 0 15 2 0 12 _ 0 10 0 08 T A 0 05 _ TG 0 03 NOM E 0 001 l 0 00 0 15 0 30 0 45 0 60 chla mg m3 Fig 9 Best fit of chlorophyll concentration to nominal fluorescence for the lowered CTD fluorometer upper plot and from the ARIES CTD fluorometer lower plot Text section 2 3 Fig 9 Oxygen up 300 Stations 14191 to 14223 275L 250 botoxyk umol kg 225 200 200 225 250 275 300 oxygen umol kg Fig 10 Oxygen calibration for CTD casts 14191 to 14223 scatterplot of the oxygen concentration in wumol kg measured on water samples botoxyk versus oxygen measured by the Sea Bird oxygen sensor Text section 2 3 Fig 10 Bottle SeaBird oxygen differences 30 CTDs 14191 to 14213 20 x N x x 9 x 5 X x DREA ge alus Videt d dosi odio ird E Sey cpt LaL P uq n gt gs 6 10 x X 13 7 1 5 x g x X B x x B KAY X X x x x 7 9 1 5 0 zl X x x 10 1 0 500 1000 1500 2000 2500 3000 3500 pressure dbar 40 x D CTDs 14245 to 14275 x x 26 8 2 8 x X x x x x s gO E ECT TD a Oe a E 4 NE x x x X x xx e x A x x 9 pes x x x x s n X yea een E ee De ep Se uet q dps S SURE EE EMR a mimm dom amp k x g 20r 4 x S o x Te x CTDs 14239 and 14244 10r 5 6 t 2 1 x J LERNEN SF Srey cups tet teeta Gre eles Oy ae
110. gp42581 file and applied to the ADCP velocities The end product is the absolute velocity of the water The time base of the ADCP profiles was then shifted to the centre of the 2 minute ensemble by subtracting 60 seconds and new positions were taken from abnv2581 this last stage was not done in the processing scripts on Discovery 253 Output files sur258 abs sbt258 abs A2 3 LADCP processing A2 3 1 Acquisition Data should be collected as described on the ADCP logsheets A2 3 5 and A2 3 6 below Copies of the logsheets are stored on BMac in Word format under the logsheets folder When the data have been successfully recovered rename as specified on the logsheets Data should then be transfered via Zip disk Currently a backup is held on the 150 kHz logging computer c ladcp d258 Data are then transferred to Misha ladcp and then ftp d to required location as specified below 70 All the log files should be transferred as well as the binary data files For the 600 kHz these are named with extensions scl whp A third file written by the software is binary For the 150 kHz two text files are created with extensions log and txt A2 3 2 Command files 150kHz command file 600 kHz command file RS CR1 CR1 CF11101 PSO EA00000 CY EB00000 CTO ED00000 EZ 0011101 ES35 EC 1500 EX11101 EX 11101 EZ0011101 WD 111100000 TE00 00 01 00 WL 0 4 TP00 02 00 WP 00001 WB1 WN 010 WD111100000 WS 1600 WFO0088 WF 1600
111. he Pstar value The depth of each bin was determined from the user supplied information Output fles adp258 bot258 this merged the ADCP data both files with the Ashtech a ghdg created by ashexec2 The ADCP velocities were converted to speed and direction so that the heading correction could be applied and then returned to east and north Note the renaming and ordering of variables Output files adp258 true bot258 true applied the misalignment angle and scaling factor A to both ADCP files The ADCP data were edited to delete all velocities where the percent good variable was 25 or less Again variables were renamed and re ordered to preserve the original raw data Output files adp258 cal bot258 cal merged the ADCP data both files with the Trimble GPS 4000 navigation file gp42581 created by gp4exec0 and the bestnav navigation file abnv2581 created by navexecO Ship s velocity was calculated from 2 minute spot positions taken from the gp42581 file and applied to the ADCP velocities The end product is the absolute velocity of the water The time base of the ADCP profiles was then shifted to the centre of the 2 minute ensemble by subtracting 60 seconds and new positions were taken from abnv2581 this last stage was not done in the processing scripts on Discovery 253 Output files adp258 abs bot258 abs data read into Pstar format from RDI binary file psurvey new program written on Discovery 253 by S Alderson
112. he net systems was the considerable time required to swap from one to the next It took typically an hour to bring in one vehicle download electronic data then fire up and deploy the other vehicle These deployment preparations could not be done ahead of time because of limited battery life Initially the ship remained hove to during this transfer but later it was decided to steam on between deployments in the direction of the following station In fact on this winter cruise the OS was deployed only a few times On the spring and summer cruises Discovery 262 and 264 when it expected that all three systems will be routinely deployed it will be important for there to be two experienced personnel on each watch to help speed up the changeover 10 3 Results Considerable sub sampling of plankton specimens from the ARIES and DM nets has already been done for biochemical analyses This material will be used for studies of lipids isotopic ratios and genetics Steve Hay Adrian Bunker Anna Ingvarsdottir Ryan Saunders Alex Mustard Jen Mower and James Cresswell established the sampling methodology and spreadsheet databases for documentation as documented below All samples from the Ocean Sampler were preserved for later microscope examination and counting of species Full results for the zooplankton sampling await detailed onshore sorting and identification However some provisional data are available from the Optical Plankton Counter deployed on
113. he range of sea states in which it can be used The revised TEK deployment procedures are as follows e The initial phase of the deployment takes place with the ship steaming at 1 5 2 knots e The boom forward of the CTD is deployed with particular attention paid to the placement of the towing wires in relation to the stabilising line run aft to the side of the ship from the end of the boom e The lifting wire from the back of the towed body is run in through the fairlead in the side of the ship via a snatch block fitted to the deck to the deck winch placed athwart ships 23 e A spring release hook is used to attach the lifting bridle at the back of the towed body directly to the crane hook with the lifting wire running over the side of the ship and in through the fairlead e Aline is looped through the front of the towed body to control its swing whilst it is lifted over the side by the crane The lifting wire and the rapid deployment of the towing wires transducer cable package over the side of the ship are also used to provide stability Great care must be taken that the towed body does not twist or enter the water over or ahead of the end of the towing cable The crane hook should not be released or the lifting wire paid out until it is clear that the towed body is hanging correctly in the water e Once the towed body is settled in the water the ship s speed is raised to the working rate ideally 10 kn no more than 11 5 kn max an
114. ice the peristaltic pumps and buy a good thermometer Stuart Brentnall Penny Holliday 6 Phytoplankton and pigment studies 6 1 Pigment studies Chlorophyll and HPLC sampling in leg 1 focused on the surface layer with the top 6 Niskin bottles from the CTD usually fired at around 100 75 50 25 10 and 5 m being sampled at 14 stations However in leg 2 the number of samples drawn was extended to 8 with 150 and 200 m samples also being taken due to the increased mixed layer depth Thirteen stations were sampled on leg 2 Samples were collected in 5 litre carboys which were rinsed in the sample prior to being filled For HPLC analysis water samples 2 litre and duplicates were filtered through 25 mm Whatman GF F filters using a specially developed positive pressure filtration unit The filter papers were then immediately stored in cryovials and stored in a 80 C freezer for subsequent HPLC analysis at SOC For chlorophyll analysis two 300 ml aliquots were filtered through Whatman GF F filters at low pressure The filters were then placed in amber glass vials containing 10 ml 90 acetone and immediately stored in the dark at 5 C for 24 hr to extract the chlorophyll In total 27 CTD 15 ARIES 2 Ocean Sampler stations and 144 underway samples to calibrate the FRRF and underway fluorometer were analysed during the cruise 26 6 2 Chlorophyll analysis Samples were warmed to room temperature before the fluorescence was measured using a
115. ill be arranged by the programme for as many samples as possible to maximise the exploitation of the taxonomic information that they contain Before MarProd researchers dispose of biological material in their possession an assessment should therefore be made as to whether it might be of value to other groups not necessarily part of the MarProd programme A6 10 Data and sample availability It is NERC policy to ensure that individual scientists principal investigator teams and participants in programmes will be permitted a reasonable period to work exclusively on and publish the results of the data collected by such individuals and teams Nevertheless as the MarProd programme develops there is necessarily a sequential widening of access to data and samples This process has already been outlined with respect to data under A6 8 above It can be generalised with reference to three access levels Level 1 Project Availability limited to the investigators responsible for data sample collection for MarProd cruises data sample collection is expected to be a shared responsibility thus group ownership applies under overall control of the Principal Scientist any wider sharing at the discretion of the investigators Level 2 Programme When data is transferred to BODC their availability is automatically extended to other investigators within the MarProd programme Nevertheless their further use is still under the control of the data origina
116. imarily to advance the oxygen variable The manual suggest that 2 5 seconds are enough I found that 10 sec gave reasonable match over top half of deep profiles 3 5 Unless you swopped to ASCII in datcnv run translate to convert cnv file from binary to ASCII 4 On the PC open a DOS window programs DOS prompt cd D258ctd Processed to get to the processed directory ftp 192 171 133 202 to link to Discovery2 login as pstar with the usual password ascii cd data61 ctd put ctd14nnn cnv quit exit which closes the DOS window Now swap to Pstar 5 ctdO The first CTD exec translates the cnv file into a Pstar ctd14nnn 24hz file It checks that the output file ctd14nnn 24hz does not exist and exits if it does Use rm to remove it if you wish to recreate it ctdO requires the number of the CTD nnn and its lat and lon Take these from the logsheet If not on the logsheet extract them from bestnav Either way please write the lat and lon on the top of the Pstar logsheet On the listing of the output file check that lat and lon are correct and enter the version code etc in the Pstar log 6 ctd1 This exec does further editing on a copy of the 24hz file averages over one second to a 1hz file interpolates the pressure variable and calculates sal and potemp for both primary and secondary also sigma0 and sigma2 for the primary 66 PMDIAN Although most spikes should have been removed in the wildedit PC processing a
117. in a single day it is clear that additional cleaning of the phosphate line needs to be undertaken see later a regime of cleaning after each run where time allowed was introduced 10 mM Standards were prepared fresh from weighed dried salts on 2 and 3 November Working standards 40 30 20 10 uM Si 20 15 10 5 N 2 1 5 1 0 5 uM P were prepared on a daily basis by dilution into nutrient free artificial seawater It was noted that on occasions residual phosphate peaks were present in the diluting seawater c 0 05 uM This factor has not been corrected for Secondary standards prepared on 4 November and 14 December were intercalibrated against Ocean Scientific International marine nutrients kit standards on the same days The intercomparison conducted early in the cruise immediately after the replacement of the power supply was unsatisfactory as the concentrated solutions supplied by OSI contain nutrients in addition to the one they are the standard for No further intercomparison was possible at this point as station work began almost immediately The comparison undertaken on 14 December yielded the following values for the SOC standards value in parentheses represents the nominal concentration P 1 46 1 48 1 49 1 52 1 5 uM 1 5 uM N 14 91 14 95 14 97 14 93 14 94 uM 15 uM Si 15 68 15 67 15 68 15 79 15 6 uM 15 uM 29 It is planned to use the same primary standards for the entire series of MarProd cruises and they we
118. inning of the cruise a successful trial deployment of the frame was achieved in the Clyde in calm sea conditions using the ship s main winch and trawl wire run over the A frame at the aft end of the ship The Scanmar tow fish deployed over the port side to communicate with the various nets proved suitable for receiving the Scanmar transmitter s signal from the frame and a deployment depth of 100m was achieved However the first full deployment of the frame at CTD station 14191 had to be aborted due to the relative lightness of the frame in water which meant that it would not sink sufficiently fast under the swell conditions A lead weight approximately 60 kg was bolted to the calibration plate stand which allowed a full second deployment to 500m at CTD station 14199 although problems were still experienced with the lightness of frame effecting the main winch s efficiency Also it was noted that the transducers stopping transmitting at the water s surface on recovery The frame was again successfully deployed at CTD station 14200 but as before the transducers stopped transmitting at the surface and signs of vibration damage were found The bolt securing the Behemoth s platform and the Behemoth s metal banding were both lost and the banding around the battery pack was loose Retaining bars were fitted to secure the platform more firmly and two sets of metal strap banding were fitted to the Behemoth for security The frame was successfully depl
119. inograph TSG measurements were made by the RSU UKORS Surfmet system throughout Discovery 258 The instruments used together with their serial numbers and manufacturer are listed in Table 10 below and were the same as those used on Discovery 253 FISHES Table 10 Sensors for Surfmet and thermosalinograph Instrument Manufacturer Serial number OTM temperature Housing FSI 1374 OTM temperature Remote FSI 1360 Fluorometer WetLabs 117 Transmissometer SeaTech T1005 Barometric Pressure Vaisala 361008 Temperature Humidity Vaisala 1850014 PAR DRP 5 Didcot ELE 30471 PAR DRP 5 Didcot ELE 30470 TIR Pyranometer Kipp amp Zonen 994132 TIR Pyranometer Kipp amp Zonen 994133 OCM Conductivity FSI 1376 Sensor collector QLI50 Vaisala R381005 Anemometer Vaisala P50421 Wind Vane Vaisala R07101 9 1 2 Processing Processing of the underway data was undertaken daily after 18 00 hrs GMT using a number of Pstar scripts described below l smtexec0 This script was used to read the data stream Surfmet on the RVS level C into Pstar format using datapup The resultant file was smt258 raw At first the dataname was just set to smt CRUISE but on Leg 2 the script was modified to give the dataname smt258 2 smtexec1a Ensured absent Surfmet data values were set to 999 The script also calculated TSG salinity using housing temperature conductivity and a zero pressure value Calibration of temperature variables followed the most
120. ion is made more quantitative in Figs 8a and 8b where lagged correlations between changes in dT dt and speed and with acceleration respectively are shown The correlation of largest magnitude is that between dT dt and the acceleration with the latter leading the former by about 0 83 seconds The velocity lags dT dt by about 1 1 seconds This is only a first step towards solving this problem which has the potential to be quite serious in regions of sharp vertical gradient at least half the data seem to be contaminated by this effect Other mechanisms need to be considered perhaps involving the effect of the large number of sensors at the base of the package which may provide an effective barrier to flow through the package There is also a hysteresis between up and downcasts which is particularly apparent in benthic boundary layers in which there are sharp gradients Is this hysteresis also due to a bolus effect does it perhaps take a relatively long time for ambient water to be entrained far enough into the package to be felt by the sensors More work is required Stuart Brentnall 2 3 Chlorophyll calibration Samples were regularly drawn for chlorophyll a analysis from the top 6 rosette bottles on each CTD cast The Sea Bird calibration was used to convert the fluorometer reading in volts to nominal fluor in mg m For casts 14191 to 14263 these fluor values were plotted against the filtered chlorophyll values chla Fig 9 A good
121. iona Anderson Ryan Saunders 3 Salinometry Two Guildline Autosal salinometers were installed in the chemistry laboratory chemlab a model 8400A serial no 57738 and as backup the older model 8400 serial no 43382 Both had been serviced by OSI Ltd immediately before the cruise The chemlab rather than the constant temperature CT laboratory was used because the latter was required for biological experiments Not having access to controlled environmental conditions is a problem for salinometry According to the manual the 8400A can operate satisfactorily at lab temperatures between 4 C below and 2 C above the bath temperature the preferred temperature being in the middle of this range Operating at the extreme ends of the range can lead to a situation where for instance sample water introduced into the salinometer cell can cool the bath water sufficiently that the heaters stay on permanently rendering the data worthless This happened in a preliminary trial run Efforts to maintain the chem lab at an appropriate temperature were hampered by several factors the lack of an adequate thermometer temperature fluctuations associated with variations in the state of the air conditioning or the number of doors to the outside which were open and leakage of heat to and from the neighbouring CT lab when the door to the latter was left open The last problem was most severe when the CT lab was being dried out with heaters following the burst pipe
122. isation to the following day Raymond Pollard A1 3 Site and station lists Reference information on sites sampling locations and stations gear casts hauls is given in Tables 18 and 19 below Code BE begin BO bottom EN end 61 Table 18 RRS Discovery 258 station list leg 1 MarProd Station no Instru Code Date Time GMT Latitude Longitude Comments position cast haul ment DD MM YY HH MM site 14190 CTD BE 01 11 01 20 48 55 35 56 N 5 672 W Test BO 01 11 01 20 55 55 35 59 N 5 673 W EN 01 11 01 21 11 55 35 56 N 5 671 W D19 14191 CTD BE 08 11 01 09 35 53 57 28 N 28 14 35 W BO 08 11 01 11 03 53 57 84 N 28 14 20 W EN 08 11 01 12 43 53 58 19 N 28 14 84 W D19 14191 LEK BE 08 11 01 13 02 53 5827 N 28 15 00 W 14191 aborted frame not heavy EN 08 11 01 13 18 53 58 48 N 28 14 9 W enough in water D19 14192 DM BE 08 11 01 14 27 53 56 91 N 28 1828 W 14192 trap didn t close on ascent BO 08 11 01 15 58 53 58 38 N 28 25 47 W gt treated as 1 integrated sample EN 08 11 01 17 34 53 59 78 N 28 31 552 W 0 800 m D19 14193 OS BE 08 11 01 18 56 54 0 11 N 28 31 72 W 14193 most nets ripped from start BO 08 11 01 19 39 54 0 77 N 28 35 48 W 1 pup net ok only EN 08 11 01 20 36 54 1 36 N 28 38 99 W D19 14196 ARIES BE 08 11 01 21 28 54 1 68 N 28 38 78 W BO 08 11 01 23 46 54 3 99 N 28 45 88 W EN 09 11 01 02 08 54 6 12 N 28 53 98 W D18 14199 CTD BE 09 11 01 05 25 54 12 84 N 29 17 34 W BO 09 11 01 06 31 54 1230 N 29 17 46 W EN 09 11 01 08 15
123. issometer 11 e RDI 150 kHz LADCP e RDI 600 kHz WHLADCP e Benthos altimeter e Seatech LSS e 10kHz pinger A total of 28 CTD casts were carried out including the initial test cast Each cast generated dat hdr bl and con files related to the station number Data backup is on zip disk Sea Bird SBE32 bottle firing rosette Generally performed satisfactorily although on several casts there was a single bottle that did not fire The misfire appears to be random and no error messages were returned This will be investigated at SOC The problem continued through leg 2 when bottle position 7 did not fire at all and the occasional other misfire occurred Sea Bird 9 CTD with 2 TC pairs and SBE43 oxygen sensor Instrument performance in terms of accuracy appears good with derived salinities being checked against Autosal The data on several casts however had large spikes on all channels including the auxiliary instruments Up to 300 modulo error counts were recorded The cause of this was not found despite the cable being re terminated and electrical connections checked Further attention will be given to this matter While preparing for cast 14236 the sea cable fuse in the deck unit blew Fuse changes proved unsuccessful and the cast was aborted hence 14236 became an ARIES cast It appears that a leaking connection caused the problem and that the sea cable interface board within the CTD has been damaged CTD serial no 0635 was rem
124. ith associated analysis of frontal features Fig 27 Examples of the photographic record of the cruise ARIES recovery and zooplankton sorting Scientific personnel Pollard Raymond SOC Co Principal Scientist Hay Stephen FRS Aberdeen Co Principal Scientist Alderson Steven SOC LADCP leg 1 Allen John SOC underway data FRRF leg 1 Anderson Cairistiona St Andrews EK500 systems Brentnall Stuart SOC salts physical data Bunker Adrian Heriot Watt biosorting leg 1 Cresswell James SOC biosorting photographic assistant leg 2 Davidson Russell SOC phytoplankton and pigment studies Holliday Penny SOC underway data leg 2 Houseago Stokes Richenda SOC physical data processing leg 2 Hunter James FRS Aberdeen all FRS gear Ingvarsd ttir Anna Aberdeen Univ biosorting leg 2 McLeod Paula SOC physical data processing leg 1 Mower Jennifer SOC biosorting leg 1 Moncoiff Gwenaelle BODC data protocols oxygen analyses leg 1 Mustard Alex SOC biosorting FRRF and photography leg 2 Riemenschneider Ulrike SOC physical data processing leg 1 Sanders Richard SOC oxygen analyses nutrients and SF Saunders Ryan St Andrews biosorting euphausiids Sidall Mark SOC physical data processing leg 2 Keogh Robert SOC UKORS Technical Liaison Officer Benson Jeffrey SOC UKORS electronics leg 2 Edwards Terry SOC UKORS electronics Lloyd Robert SOC UKORS shipboard computing Wallace Robert SOC UKORS mechanical Whittle Ste
125. kHz files should be named dccc ss 000 and 600 kHz files should be wccc ss 000 where sss is the station number eg 191 and cc is the cast number which is usually 01 In the text below D is also used to denote either the d or w identifier Firing must be used first This is because the Visbeck software has been modified to find parameter values in the Firing tree see below cd proc Firing processing is a mixture of programs written in C with a front end in perl and matlab routines Typically the perl routines write summary files into files in subdirectory casts sss cc scanload relative to proc perl S scan prl sss cc Check that the information extracted from the data file is correct for the cast it is supposed to correspond to This 1s particularly important for the 150 kHz data since the software used to download from the instrument provides an arbitrary name which must be changed manually to a station name putpos sss cc latdeg latmin londeg lonmin This stores the latitude and longitude in an ASCII file for later reference For the southern or western hemispheres the degrees though not the minutes should be negative matlab magvarsm sss cc This puts up a small window with a yes and no button Click yes and then quit Don t look at me I didn t write this The magnetic variation for this station is calculated and stored in file mag var tab perl S load prl sss cc This converts the data into CODAS data format The data
126. l integration and longterm stewardship of datasets obtained from MarProd supported cruises under Phase 2 of the programme For Phase data and laboratory derived data and models BODC will not necessarily have such close involvement Thus for non cruise data BODC is not expected to undertake quality control and other data stewardship arrangements may apply For Phase 1 awards that involve joint work with non NERC bodies project specific data storage and access procedures may need to be negotiated Nevertheless BODC needs to be aware of the totality of data arising from the MarProd programme and the programme Steering Committee needs to be assured that similar quality standards for data stewardship see A6 4 below apply to all data collected through MarProd support The programme recognises the importance of direct involvement of BODC staff in planning MarProd fieldwork including the opportunity to attend cruise planning meetings and relevant agenda items of Steering Committee meetings BODC cruise participation is also welcomed subject to berth availability particularly when novel and or relatively complex sampling arrangements are involved A6 3 Links with GLOBEC Some additional data management considerations result from the Marine Productivity programme being the main UK contribution to the international GLOBEC project Global Ocean Ecosystem Dynamics Whilst it is not a condition of award all MarProd PIs are encouraged to provide the fol
127. last three days there were lower light levels and deeper mixed layers The final calibrated Surfmet files are smt2581 cal and smt2582 cal Penny Holliday John Allen Paula McLeod 36 9 2 Navigation and vessel mounted ADCP 9 2 1 Introduction Two RDI vessel mounted Acoustic Doppler Current Profilers VM ADCPs were operated on Discovery 258 the 150 kHz VM ADCP and a new 75 kHz Phased Array instrument Ocean Surveyor that had been fitted immediately prior to Discovery 253 FISHES May June 2001 The majority of this report duplicates that of Penny Holliday and Helen Johnson for Discovery 253 The 150 kHz ADCP was mounted in the hull 1 75 m to port of the keel 33 m aft of the bow at the waterline and at an approximate depth of 5 m The 75 kHz ADCP was also mounted in a second well in the hull but 4 15 m forward and 2 5 m to starboard of the 150 kHz well The following section describes the operation and data processing paths for both ADCPs and describes a brief comparison exercise between them The navigation data processing is described first since it is key to the accuracy of the ADCP current data 9 2 2 Navigation Discovery s best determined position was calculated by the process bestnav The main data source was a newly purchased Ashtech G12 positioning system Thus the GPS Trimble 4000 system used for most recent cruises was recorded separately In fact the Ashtech G12 electronics board replaced the Sea Star Mark III Differenti
128. le through the tube and can be decanted into glass or other sample bottles The flow can be arrested by raising the free end of the blue tube One also has to be careful to sample only from bottles fired during the upcast ARIES fires about half its bottles during the downcast The ARIES operators provide a printed list of which bottles fired at which depths shortly after recovery of the vehicle One problem with this sampling procedure is the use of the blue tube that makes it difficult to be sure that the sample is not contaminated by water remaining in the tube from previous samples The other main problem is that the ARIES bottles are only 300 ml so that there is not much water for rinsing the 200 ml salinity bottles especially when the tube also needs to be rinsed On this cruise the bottles were rinsed two or three times with a small amount of water approx 25 ml each time Given these shortcomings calibration to within about 0 003 in salinity is probably about as good as could be achieved One possibility for future cruises might be to use a shorter sampling tube though this would make some of the bottles difficult to sample from 2 2 3 Deleterious effects of ship roll and package dynamics Despite the CTD temperature and salinity sensors being calibrated to high precision many of the casts on this cruise show fairly large and physically unrealistic excursions of order 0 1 C for 15 example at a period of several seconds espe
129. led out already attached to the main warp ready for deployment Unfortunately alternative stowage could not be found for the LEK which was on a pallet on the starboard side next to the steps up to the winch cab This meant that ARIES had to be manhandled sideways every time it was extracted from the hangar it For future cruises it is hoped the LEK will be moved to the starboard deck Apart from this obstruction the hangar space proved well fitted for the ARIES OS operation Two blue heavy duty pipes were bolted to the deck as guides for the vehicles to prevent them sliding sideways uncontrollably in rough conditions This simple system worked well Deployment and recovery were done in the usual way for vehicles of this size They were lifted from the deck and paid out using the main warp and rear gantry both controlled by the winch operator Two trailing 45 lines were attached to the rear of each vehicle On deployment these were slid round cleats on the bulkhead on either side of the gantry operated by two deckhands both wearing safety harnesses On recovery boathooks were used to catch the trailing lines which were then quickly taken up on the cleats Lines were run from the gantry bulkhead to the rear of the hangar so that the safety harnesses could be clipped onto them giving the seamen freedom to move the length of the deck and to clip on the harnesses well clear of the stern rail The only problem with sequential deployment of t
130. les 1 Samples must be kept chilled and covered to avoid desiccation and or decomposition All specimens for biochemical analysis should be picked out within one hour on a frozen surface to maximise freshness of sample 2 All samples should be gently washed through meshes 200 um for ARIES 95 um for Ocean Sampler 3 All ethanol samples should be stored in push stopper 26 ml glass tubes and formaldehyde fixed samples in 28 ml screw cap tubes Ensure that the ratio ethanol sample is at least 10 1 and 3 ml of concentrated form aldehyde is added to each vial being preserved with formaldehyde A5 6 2 Processing of pup and reel net samples AP and AR 1 Remove and secure the two pup samples live tube and dead codend net fully wash and retain each pup net sample onto 200 um mesh squares preserving the dead sample in ethanol and temporarily storing the live sample in a petri dish on ice or in a bucket of chilled water in the fridge Note the live sample is retained in case additional specimens are required to be picked out for the future analysis priorities after which the sample is stored in formaldehyde solution 2 Record the position number of the last net as you remove the ARIES net reel and place it onto stand 3 Transfer reel codend nets into lidded individually numbered jars noting which nets contain abundant Calanus Use the chill room 5 C to store the jar trays 4 If possible wash 2 nets containing abu
131. ll measure to the efforts of the UKORS technical staff working with the science team These were aided in the resolution of deployment strategies and safe working practices for these unfamiliar gears by the ship s officers and deck crew The problems solved will go a long way towards ensuring the smooth operation of these complex gears on future MarProd cruises The main technical problems with the plankton gears and some of the resolutions achieved are described below Table 15 Net haul summary also see Tables 18 and 19 for further station information Key to associated sampling W water bottles O Optical Plankton Counts C Sea Bird CTD F fluorometer T transmissometer Plus specimens extracted for L lipids hormones G genetics isotope ratio studies Haul no Site Plankton No of Max Pup Associated sampling Discovery gear samples sampler Seabe net see Key above SUED depth m d hauls depth m Leg 1 14192 D19 DM 1 802 3142 L G l 14193 D19 OS 0 402 3066 14196 D19 ARIES 70 2720 3026 2 W 60 0 C F T L G I 14201 D16 DM 1 534 2852 L G l 14202 D16 ARIES 64 1536 2600 2 W 60 0 C F T L G I 14207 D13 ARIES 41 983 1500 2 W 41 0 C F T L G I 14210 D13 DM 1 739 1468 LG 44 14216 E4 OS 2 401 1924 2 G 14219 E4 ARIES 58 1416 1800 2 W 58 0 C F T L G I 14222 E4 DM 1 739 1559 LG 14224 D11 DM 1 805 2483 LG 14225 D11 ARIES 78 1944 2456 2 W 60 0 C F T L G I 14228 D11 OS 7 405 2611 2 G 14232 D9 DM 1 400 2980
132. lowing information to GLOBEC for international access 1 a basic project description ii metadata coverage scope and derivation of a dataset and iii information on how actual data can currently or in future be obtained 81 A DIF Directory Interchange Format entry should be used to provide this summary information to the GLOBEC International Project Office Several projects have already done so and their DIFs can be accessed via www globec org click on Data in the Menu Bar then Metadata Portal etc with UK selected as Location Hester Willson hew pml ac uk will be pleased to give further guidance on this matter A6 4 Minimum standards of stewardship for NERC corporate data The following minimum standards are expected to apply when digital datasets form part of NERC s enduring data resource e The ownership and Intellectual Property Rights to the dataset must be established and NERC s policy towards exploiting and making it available to third parties agreed e The dataset must be catalogued to the level of detail required by a NERC Designated Data Centre so that it can be mentioned in web based NERC data catalogues e Formal responsibility for the custody of the dataset must be agreed e The data must be fully worked up ie calibrated quality controlled etc with sufficient associated documentation to be of use to third parties without reference to the original collector e The technical details of how the data are to be
133. lways be hand labelled with the Date Haul number station no Sampling gear Net type Species and Number contained Double labelling on cryovial and tape is used Sampling details are available from the written deck file or the computer files for each tow Please ensure that all specimens removed from samples are detailed in the log book which should then transferred to the Excel spreadsheet set up for each sampling method 79 AS 5 Dual Methot DM 1 Remove both sampling codends placing upper net codend red tape mark in the bucket also marked with red tape and the lower net codend in plain bucket 2 Gently wash each net sample separately into a sorting tray 3 Carefully remove target species into partitioned petri dish kept on a cold tray measure using microscope measuring stage recording values and preserve in order of priority Keep specimens chilled 4 Iftime permits repeat for other dominant species in sample 5 Remove identify and measure the diameter and volume of any large jellyfish and if necessary store in formaldehyde solution 6 Store the remainder of each sample in formaldehyde solution using either a 500 or 1000ml plastic container Clearly label each sample internally and externally with Date Sampling gear DM Net upper lower Site and Haul numbers NB If the upper and lower Dual Methot nets do not close properly then treat as the haul as a combined sample A5 6 ARIES A5 6 1 General storage of samp
134. ment and battery pack N B Refer to Charging Safety Sheet run BBTALK and END Battery Volts gt PT2 Now charge the batteries Te gm 0 SHOL eed Quit BBTALK using lt ALT gt X and then close the window Run BB ADCP ht and return Set deployment no to recover RY check it s the latest use RA Transfer Receive file receive note the filename return and enter CZ to put the instrument to sleep Quit program file exit Using explorer rename file in c ladcp d258 data to d 01 000 where is station number RunBBLIST fl0 to main menu And start and stop times of recovered file from BBLIST START Comments STOP A2 3 6 Log sheet for 600 kHz LADCP Lat LADCP Cast No Long CTD Cast No Date Nominal Depth Pre Deployment Connect with ADCP comms lead amp run RDI Instruments SC ADCP e Configure ADCP for new deployment SAY NO TO DEPLOYMENT WIZARD File gt ADCP terminal File gt Break Check ADCP Time with GMT GMT TS reset if necessary ADCP TS yy mm dd hh mm ss to reset countdown to lt RETURN gt Recorder Free Space RS number after comma free space wm e Quit Terminal Deployment run RDI Software SC ADCP e Functions gt Import planning file c RDI Workhorse mprod cmd e Functions gt Deploy e Name deployment file Location c RDI Workhorse Deployment directory name w station number N B mu
135. most due south along 28 5 W After recovering the TEK CTD 14294 was occupied at G15 from 21 21 to 23 14 As we were now well into the Iceland Basin the primary objective was to determine the circulation and it was decided not to deploy the TEK between the last two CTD and ARIES stations 12 Dec Wednesday 346 The next site G16 was reached at 04 14 and CTD 14295 was worked The final site G17 was reached at 11 00 where ARIES 14296 7 8 was deployed until 15 43 During recovery hauling had to be halted briefly when ARIES was close to the surface in order to clear the after deck of wire being rewound The swell had increased by now and on recovery the ARIES bridle was found to be seriously bent upwards by 10 20 From G17 the distance to run to the Needles Isle of Wight was 1104 nm which required passage at an average speed of 8 25 kn to make the scheduled ETA on 18 December Given the likelihood of a rough passage towards Lands End it was decided to cease station work and begin the passage After recovering the PES and firmly lashing gear passage commenced at 16 18 13 18 Dec Thursday Tuesday 347 352 The passage to Southampton was difficult with continuous headwinds and heavy swells Speeds of barely 5 6 kn were all that could be maintained for the first few days In the event we did well to dock on the Tuesday as planned but arrival was in the evening at 19 00 rather than the morning as hoped for This delayed demobil
136. mples were drawn directly from the Niskin bottles into 100ml calibrated oxygen bottles their temperature measured and fixed immediately using alkaline iodide and manganous chloride solutions prepared following Dickson AG 1994 Determination of dissolved oxygen in seawater by Winkler titration WOCE operations manual WOCE Report 68 91 Revision 1 Nov 1994 The dispensers used to fix the samples were thoroughly cleaned in hot water at the start of the cruise and whenever they became sticky Samples were shaken twice once on deck and a second time shortly afterwards in the lab and then titrated in the Decklab within 12 hr Acidification was performed using a 5ml Finn pipette The user variable parameters in the SIS supplied software are in the parameters screen arrived at through the options menu The following values were determined by trial and error at the start of the cruise and applied throughout Stepsize 5 Wait time 10 Fast delay 5 Slow delay 5 Fast factor 0 5 This parameter set resulted in titration times of less than 4 min A single one litre batch of sodium thiosulphate 25g l was prepared at the start of the cruise This strength solution results in titration volumes of about 0 25 ml thus all oxygens determined on the cruise were titrated using a single solution This solution was standardised at the start and end of the cruise using a commercially available 0 01N potassium iodate standard Ocean Scientific International Petersfield H
137. n 01 317 14 33 34 to 01 317 14 36 53 3 min 01 324 23 52 23 to 01 324 23 56 24 4 min 01 325 08 48 00 to 01 325 08 49 05 1 min 01 325 09 22 33 to 01 325 09 23 36 1 min 01 326 09 39 29 to 01 326 10 15 54 36 min 01 326 21 42 40 to 01 326 21 44 14 2 min Leg 2 01 329 18 59 10 to 01 329 19 00 11 61s 01 330 19 02 54 to 01 330 19 04 00 66s 01 331 20 42 00 to 01 331 20 43 04 64s 01 333 09 20 17 to 01 333 09 33 25 13 1 min 01 337 09 04 44 to 01 337 09 54 55 50 2 min 01 340 00 44 54 to 01 340 00 46 28 94s 01 340 17 26 49 to 01 340 17 33 52 7 0 min 01 341 08 30 45 to 01 341 08 31 50 65s 01 342 08 25 41 to 01 342 08 26 44 63s 01 345 20 22 13 to 01 345 20 23 47 94 s 9 2 4 150 kHz ADCP The 150 kHz RDI ADCP was logged using IBM Data Acquisition Software DAS version 2 48 with profiler software 17 20 The instrument was configured to sample over 120 second intervals but unlike its use on Discovery 253 FISHES we chose to use 100 bins of 4 m thickness pulse length 4 m and a blank beyond transmit of 4m the higher vertical resolution would better support the remote detection of zooplankton patchiness Early in leg 1 and during the steam into and out of Reykjavik the ADCP was switched to bottom and water track mode over shallow ground to enable calibration The two vessel mounted ADCPs were configured to synchronise their pings over the ensemble period with the 150 as the master and the 75 as the slave as recommended by RDI and discussed by Pen
138. n one or two weather images were created each day 12 7 Training Leg 1 provided an opportunity for Jeff Bicknell to receive training particularly on the Level C software A number of ad hoc seminars were held covering all the programs in rvs bin that Jeff has not used on previous cruises the UNIX family of text processing utilities grep awk sed vi pr etc the Level C software use of environment variables device independent plotting DIPF Jeff s extensive electronics and PC experience provided a valuable adjunct to the cruise support Robert Lloyd Jeff Bicknell 13 Satellite imagery sea surface temperature SST It was not possible to obtain any ocean colour eg SeaWiFs images for the Irminger Sea and Iceland Basin during Discovery 258 Such sensors not only require clear skies but also a relatively high angle of incident light lacking in near polar regions during winter However some remotely sensed sea surface temperature SST data were available in cloud free areas providing relatively good coverage for the northern North Atlantic over the period mid November to mid December This SST information was derived from the Advanced Very High Resolution Radiometer AVHRR 3 sensor on board the US NOAA 16 satellite processed at Plymouth Marine Laboratory Cloud free data were composited together to calculate 7 day median SST images together with composite front maps that enhanced thermal structures detected d
139. n size lipid density and in the degree of lethargy activity compared to hibernating Calanus from other regions We encountered a wide range of other zooplankton species in the ARIES and Dual Methot nets with visual assessments indicating lower diversity of species in the Irminger Sea compared with the Iceland Basin As well as all of the MarProd target species Calanus spp and the euphausiids Thysanoessa longicaudata and Meganyctiphanes novegica there were a number of other dominants Notably these included the predatory copepod Euchaeta glacialis and a range of other predator species including a variety of euphausiids mainly Euphausia krohnii in the southern samples and Thysanoessa inermis on the Greenland shelf Also the chaetognath Sagitta maxima several exotic medusae the amphipod Parathemisto sp and a range of other species including some beautiful deep water fishes We collected additional specimens of some of these abundant non target species for later biochemical analyses Steve Hay 10 4 Technical problems and solutions The cruise started with testing of the new NERC funded ARIES system in the Clyde This proved fully operational However although the towing hydrodynamics of the sampler revealed an even heel a positive pitch of approximately 11 was found Two further tows with additional ballast installed in the tail fin area resulted in pitch being reduced to approximately 1 5 positive These adjustments allow the frame balance
140. nalytical Drift error Analytical error error error Leg 1 post storm after 20 Nov 91 9 42 58 70 30 Leg 2 pre medevac to 5 Dec 75 25 59 41 78 22 Leg 2 post medevac after 8 Dec 66 34 75 25 51 49 All data from above 75 25 61 39 67 33 Table 6 indicates that uncorrected instrument drift dominates the error involved in the determination of nutrient concentration contributing around three quarters of the error in nitrate determination 60 of the error in phosphate determination and two thirds of the error in silicate determinations A possible solution to this problem is to use more drift corrections within the analytical run On this cruise a drift standard was run every 20 40 samples mainly because of the large volumes of samples that ARIES produces This is clearly not adequate and one should be run every 10 20 samples 7 2 5 N P ratio The N P ratio of the entire dataset and of the four sub datasets has been evaluated A model II regression analysis has been undertaken to find the linear fit which best describes the data This regression technique works by minimising the deviations of both parameters from the line of best fit and thus makes no a priori assumptions about the correctness or otherwise of either of the parameters This contrasts with a model I analysis which assumes implicitly that the x parameter normally P is correct Given the problems experienced with phosphate analyses on this cruise it seems logi
141. nd transferred using floppy discs as the USB zip drive would not work with the Windows 95 software on the oxygen laptop This computer failure had the knock on effect of delaying the analysis of all subsequent samples taken on the cruise by at least 24 hr and in some cases by 36 hr Version 1 4 of the Scalar supplied processing software was used with both the baseline and drift corrections applied Following the completion of a run the peak assignment was manually checked and any electrical spikes bubbles poorly formed peaks or mis assigned peaks corrected Excel files were then created of the results and these combined with the dissolved oxygen results to create a single results file for each station Prior to 15 November the single analysis of each sample was reported after 20 November the mean of the two determinations was reported unless there were reasons for rejecting one of them This was particularly the case for some of the phosphate peaks see later discussion Finally a further QC check was undertaken by eliminating datapoints on a case by case basis that deviated from the bulk Redfield ratio calculated for the cruise split into four sections pre and post storm on leg 1 and pre and post medevac on leg 2 Each line was cleaned daily using a solution of 10 decon and exceptionally 10 NaOH phosphate by pumping it through the lines for 15 min at the beginning and end of each day On occasions when 3 runs of 70 100 samples each were analysed
142. ndant Calanus onto separate meshes and place in Petri dishes over ice Ideally nets should be chosen from the upward sampling leg and include a deep and shallow sampling depth 5 First carefully remove CV Calanus specimens and preserve in order of priority Lipids Isotope Ratios and Genetics and only then pick out additional specimens of dominant species for future analysis 6 Once specimens are picked then wash out and formaldehyde fix preserve the remainder of these and all the other samples then label and store them 7 Refill the cod end reel with the clean washed out nets and return to ARIES Ensure sound net attachment of codends and no holes A5 7 Ocean Sampler processing and storage of samples OP and OS e Remove both Pup nets OP from sampling frame wash out onto 95 um meshes and store one in ethanol and the other in formaldehyde solution 80 e Remove the 7 depth numbered net samples OS 1 7 from sampling gear and place in labelled holders individually wash onto 95 um meshes and store in 4 formaldehyde solution in 28 ml glass tubes A6 Data and sample management policy for the Marine Productivity programme The policy document that follows provides the framework for short term and longterm management of data and samples arising from the Marine Productivity thematic programme A6 1 Introduction NERC requires all thematic programmes to carefully look after the data they collect for the mutual benefit of programme p
143. ning up the instrument when conditions permit The TEK was deployed at 08 34 followed by Dual Methot 14250 and ARIES 14251 2 3 Work was completed at 17 07 Conditions on deck were slippery a consequence of snow cover ever since Reykjavik F3 was reached at 20 00 the TEK recovered and CTD 14254 worked from 21 54 to 23 44 The TEK was deployed at 23 55 and course set for the final site on the shelf 30 Nov Friday 334 The optimum order of work at a site with all nets and CTD is Dual Methot ARIES recover TEK CTD LEK deploy TEK Ocean Sampler This allows time for the changeover from ARIES to Ocean Sampler This order was adopted on arrival at F1 with the exclusion of the LEK as the water depth 500 m was too shallow to make this worthwhile The Dual Methot 14255 from 04 27 to 05 36 was followed by ARIES 14256 7 8 from 06 20 to 07 12 After recovering the TEK CTD 14259 was worked from 08 02 to 09 03 Finally after deploying the TEK at 09 21 the Ocean Sampler 14260 1 2 was deployed from 10 04 to 11 38 Passage south 197 T towards G8 commenced At 15 25 icebergs were sighted which severely changed the cruise programme Several bergs were seen in the vicinity of 64 N 36 4 W much further offshore than usual driven out the continuing westerlies To allow passage at full speed our first inclination was to alter course to the east to seek the outer limit of bergs from the Greenland coast A site was planned for 63 N 34 W Howeve
144. ns under which it can be deployed To achieve this the 5 ton Lebus winch currently used for aft deployment of the LEK and deploying the TEK could be sited in the water bottle annex on a bedplate attached to the deck matrix The wire could then be led directly out over gantry using the coring block If it is not possible to use the water bottle annex due to the pressure on lab space the winch could be sited on the aft starboard side with two diverter sheaves one on the deck and one welded to the side of the hanger used to lead the wire to the back of the gantry However the water bottle annex option is heavily favoured due the simplicity of the installation and maintenance As part of same change in deployment strategy the CTD railway would be extended aft with a new trolley built to fit the LEK so that both the CTD and LEK could be moved easily in and out of the central deployment position This arrangement would provide both a secure position for the frame when not in use and a safe method for moving it along the deck Additionally the relocation of the winch would provide a method for deploying mid ships plankton nets to depths greater than 100m Under this arrangement the mains and battery charger cables could be fed out from the hanger to the frame through a goose neck so that they could be used with both the Behemoth and the battery pack remaining on the frame An external aerial could also be used so that the Behemoth could be controlled
145. nual extraction may not be necessary However visbeck and firing velocities have in the past found to differ often significantly Comparison of firing velocities with 150 kHz shipboard ADCP data showed close agreement while the visbeck values differed by up to 20cm s Brian King on the Drake Passage cruise at the same time as Discovery 258 1s trying to resolve these differences so it may not be worth using visbeck for velocities yet A2 3 5 Log sheet for 150 kHz LADCP Lat LADCP Cast No Long CTD Cast No Date Nominal Depth Pre Deployment Connect with ADCP comms lead amp run BBTALK Fog dele Hit F3 key and enter filename Check ADCP Time with GMT GMT TS reset if necessary ADCP TS yy mm dd hh mm ss to reset Battery Volts gt PT2 VMVDC Recorder Free Space RS You may need to erase the recorder ErASE ENNNNUUSUN C 00 Get factory defaults Quit BBTALK using lt ALT gt X and then close the window Deployment run BBSC e goto deployment menu use command file mprod cmd DEPLOY verify YES deploy OK amp record time of deployment from master clock e setup deployment sequence log file FILE d 01 log exit BBSC by escape x2 and then EXIT under FILE turn off battery charger N B Refer to Charging Safety Sheet Now fit blanking plugs on the ADCP amp battery case Tell CTD Winch operators to proceed with deployment Recovery Connect instru
146. ny Holliday on Discovery 253 The result is that each ADCP has only 40 water track pings in 38 the 2 minute period Spot gyro heading data were fed into the transducer deck unit where they were incorporated into the individual ping profiles to correct the velocities to earth co ordinates before being reduced to a 2 minute ensemble The main difference between the 150 ADCP on Discovery 253 258 and previous cruises was that it had been refitted in dry dock prior to Discovery 253 and given an offset of 45 on the advice of RDI This offset was accounted for in the DAS software on Discovery 253 however it was missed out of the setup file at the beginning of 258 This is not a problem in itself as the user s calibration process will correct for the orientation however it could be alarming to derive a tan O I if unaware of the offset The other major advance was that the ADCP PC clock has been synchronised with the ship s master clock so removing the tedious need for logging the drift of the PC clock and correcting for it in the processing old adpexecl As good practice however a check on the ADCP clock time was still made every 24 hr as was a record of the ADCP electronics temperature see the two sheets stapled to the inside cover of the 150 kHz log book The ADCP data were logged continually by the level C computer From there they were transferred once a day to the Pstar data structure and processed using standard processing scripts in Ps
147. om the 38 kHz split beam transducer single target detection data adjusted for the relative positions of the transducers The TS gain values were calculated using single target detection values exported directly from Echoview v 2 10 39 SonarData 1995 and the equation all values in dB New TS Gain Old TS Gain Mean measured TS Expected TS of sphere 2 T The SV gain values were calculated using the SA NASC in Echoview values derived from the integration in Echoview of the target sphere s echo for single on axis pings and the equation gain values in dB SA values in m nmile New SV Gain Old SV Gain 10 Log Mean measured SA Theoretical SA 2 Theoretical SA values are calculated from the expected TS of the sphere the transducer s 2 way beam angle and the distance to the sphere from the transducer face The final calibrated gain values are given in Table 20 below Table 20 Integrator SV and target strength TS gain values for TEK and SEK calibrations Echosounder Transducer Frequency SV Gain TS Gain TEK 38 26 62 26 95 120 20 55 20 70 200 23 24 23 38 LEK 38 25 02 25 17 120 20 44 20 29 NOTE During the cruise all data were collected using the standard SV and TS gain settings of 26 5 dB the calibrated gain values were only applied during post processing Andrew Brierley Eric Armstrong Cairistiona Anderson Ryan Saunders A4 Pstar backup Five rolling tapes Do Is Irt
148. on this standard deviation only when vertical motion is combined with a large vertical gradient are the errors relatively large Fig 4c displays the mean and standard deviation of the corrected errors at each CTD station No drift in the calibration is apparent over the admittedly quite short timespan of these observations We can be confident that the CTD measures accurately the salinity of water going past its sensors The extent to which the water going past the sensors is representative of the ambient water is a different question addressed elsewhere see section 2 2 2 below for a brief discussion Salinity calibrations for the second CTD used and for the CTD package on ARIES were carried out in a similar fashion with slight variations on the method of excluding rogue data points The 14 corresponding executables for the second CTD are sjbsals2 exe and sjbsals2 m and for ARIES they are sjbasals exe in data61 abottle and sjbasals m These last two calibrations are illustrated in Figs 5 and 6 and a table summarising all three calibrations is salcal xls Note that the error for ARIES appears to vary systematically with depth A least squares fit of a straight line to the remaining error yields the following correction to be added to the product of K and the uncorrected conductivities for ARIES 1 4545x10 P 0 0018615 where P is the pressure in decibars Table 3 CTD salinity calibrations First CTD Second CTD ARIES K 1 00
149. ot transfer them to parties outside the programme without the explicit agreement of the originator Steering Committee advice will also need to be sought if major data transfers are involved to avoid compromising the interests of other programme participants e The mechanism for entry into the public domain is expected to be the release of the MarProd CD ROM at the conclusion of the programme e A condition of CD ROM usage is that it is regarded as a data publication and all usage of the data contained therein should acknowledge the data originator through citation 83 A6 9 Longterm sample curation Biological material obtained on MarProd cruises is owned collectively by the programme However during the programme lifetime sample originators have responsibility for the stewardship of material recording any removals and 1f shared with other research groups keeping track of its movements and usage It is recognised that indefinite storage of all biological material is impractical and that some identification and analytic procedures require sample destruction Nevertheless it is expected that nearly all net collected zooplankton and representative sub samples of micro plankton will be stored for the duration of the programme by sample originators Exceptions may be made for larger size zooplankton eg jellyfish and organisms removed for biochemical analyses and experimental purposes Subsequently longterm archiving of at least 5 10 yr w
150. ough west to complete G11 but a CTD was possible at G12 and priorities were revised to ensure an ARIES deployment in the Iceland Basin in order to see if Calanus advect around the Reykjanes Ridge E9 G13 and G14 were occupied and a decision had to be made whether to continue east then returning home via the Irish Sea or try to work southwards Scientifically the latter was highly desirable and there appeared to be time so three further sites G15 G17 were worked south from G14 towards D19 Work ceased for the homeward passage when a mean speed of 8 25 kn needed to be maintained Unfortunately the persistent westerlies had by now change to persistent southeasterlies which were against us for the entire passage to Lands End Thus arrival at Southampton was at 1900 instead on 0900 on 18 December Note that time records for Discovery 258 relate to GMT throughout the cruise Whilst dates in the text of this cruise report are mostly given as calendar days Julian days are also used in the context of data logging where 1 Nov and 18 Dec the cruise start end dates are JD 305 and JD 352 respectively Raymond Pollard Stephen Hay 2 CTD operations 2 1 CTD operations rosette and frame The CTD package consisted of e 24 way stainless steel frame e 24x 101 sample collection bottles e Sea Bird SBE32 bottle firing rosette e Sea Bird 9 CTD with two TC pairs and SBE43 oxygen sensor e Chelsea Instruments fluorometer e Chelsea Instruments transm
151. oved and replaced with serial no 0637 which appeared to perform satisfactorily but once again spikes occurred in the data For an outline of calibrations and serial numbers for each cast open the con file as if to modify it and generate a report which gives the user a notepad document of the instrument set up including the auxiliary instruments The con files are called D258MAIN con prior to cast 14239 and 0637 con afterwards Additional reference data are given in Table 2 Table 2 Sea Bird CTD sensors and calibration dates SBE 0635 SBE 0637 Temperature primary 03 2919 21 21vi01 2728 2Tii01 Conductivity primary 04C 2637 29vi01 2164 9iii01 Pressure 83007 9i01 79501 6xi99 Temperature secondary 03 2758 4vi01 2729 8ii01 Conductivity secondary 04 2407 3vi01 2164 6iii01 SBE oxygen 43 0086 12ix01 43 0076 17ix01 Cl transmissometer 161047 20iv01 same Cl fluorometer 088241 28iv01 same Seatech LS6000 346 5vii97 same Data spiking continued to be a problem after the CTD was exchanged and the cable re terminated In port further attempts were made to find the causes The sea cable was cut back 100 m and re terminated The BOB was checked and was found to contain water This was cleaned and a spare unit fitted as well 12 Attempts were made to repair CTD serial no 0635 A replacement DC DC converter was obtained from the Marine Research Institute Reykjavik but this proved not to be the fault Problems were eventually traced to damage on
152. ower shows time series of bulk nutrient sample concentration The concentrations of nitrate and phosphate decreased by about 2 and 0 1 uM over the course of the cruise The silicate concentration remained relatively static compared to the nitrate and phosphate concentrations The maximum deviations of individual samples from the mean line which provide some estimate of day to day precision of the analyses are estimated to be Si 1 0 uM 3 P 0 04 uM 3 and N 0 3 uM 2 where the values in parentheses indicate the approximate percentage of bulk nutrient concentration that these deviations represent The reduction efficiency of the cadmium column used for nitrate reduction was 102 1 87 96 7 2 4 Duplicate samples The analysis of duplicate samples has been divided into two sections The first concerns the period before the large storm on leg 1 15 20 Nov and the second the rest of the cruise split into three sections post storm on legl before the medical evacuation on Leg 2 to 5 Dec and after the 30 medevac after 8 Dec During the first part of leg 1 one or two samples were run in duplicate on each run The average difference between these duplicate pairs expressed as a percentage of their average value was 0 4 1 7 and 1 06 for nitrate phosphate and silicate respectively For the remainder of the cruise every sample was analysed in duplicate The true and absolute differences between each pair of duplicate samples analysed ha
153. oxygen in umol l had to be converted into umol kg the WOCE standard The equation to convert the units is the following O umol kg O2 umol l 1 0 001 co where oo is the density of the oxygen sample at the time at which the sample is fixed It can be computed using Tx the temperature of the sample at time of fixation and the salinity of the sample the pressure is set to 0 since the samples are fixed on deck ie at sea level Our first attempt to calibrate the Sea Bird oxygen values used data from casts 14191 to 14223 Fig 10 shows a scatterplot of botoxyk the bottle oxygen in umol kg versus oxygen from the sensor A regression line produced by performing a least squares fit to the data for the upcast was as follows Botoxyk 11 9098 0 9962 Oz sensor As there is an observed hysteresis between the oxygen measurements of the upcast and the downcast of the CTD the same least squares fit was done for the bottle oxygen against the sensor oxygen of the downcast The oxygen data from the downcast were extracted from a 2 dbar averaged CTD file by matching the pressure values at the bottle firing points with the pressure values in the 2db file The regression line takes the following form Botoxyk 12 2775 0 9924 Oz sensor While it appears that the most significant adjustment is the addition of 11 9 or 12 3 umol kg on the up and down casts respectively plotting against pressure Fig 11 upper graph shows that there c
154. oyed at CTD stations 14215 and 14223 before the problem of transducer cut out was apparently resolved The connectors between the transducers and the Behemoth had worked loose and a small quantity of water had entered them This was rectified before the deployment at station 14231 However this deployment had to be abandoned as Ethernet communications could not be achieved between the EK500 and its logging and control PC On opening the waterproof housing it was found that a connection was loose probably due to the vibration experienced and this was easily rectified No further deployment opportunities arose on leg 1 of the cruise On leg 2 a successful deployment was made at station 14249 and a full set of data was recorded However communications could not be established with notebook PC on recovery and the transducers had again cut out on the surface At the next attempted deployment CTD station 14254 no communications could be established between the notebook PC and the EK 500 and the deployment had to be abandoned When the Behemoth s housing was opened evidence was found that suggested a failure in the EK500 itself On investigation it was discovered that the power board supplying the communications circuits had worked loose and that this might provide an alternate explanation for the problems experienced with transducer cut out Although this problem was solved no further opportunities for deploying the LEK arose during the cruise 21
155. passed the pressure test and been reinstalled Thus it was possible to fly to within a few hundred metres of the bottom Passage was continued to G07 where the TEK was recovered and a float launched at 12 00 noon over the stern CTD 14224 was worked to the bottom where a layer of DSOW less than 2 C was found At 15 00 the TEK was deployed and passage set for the third ARIES deployment This was scheduled for 18 30 as conditions had remained calm despite forecasts of gale to storm force winds However at 18 00 rapidly rising seas and winds forced cancellation of the TEK deployment The vessel hove to overnight in storm force winds 23 Nov Friday 327 At 11 45 it was decided that no further scientific work was possible and course was set for Reykjavik It had been agreed that personnel needed two nights in port rather than the planned single night in order to gain sufficient rest and respite from the continuous severe conditions If it is possible to berth on Sunday 25 November then the extra night in port could be achieved without loss of time on the second leg 24 Nov Saturday 328 The PES fish was recovered at 13 00 Damage to the fish and cable found 25 Nov Sunday 329 Nearing Reykjavik strong winds from NW made the final approach to the harbour likely to be difficult so vessel hove to at 07 00 Later the wind abated a bit and final passage was resumed docking at 14 42 thus still ahead of the scheduled end of leg on
156. peak shape from the pointed nitrate shaped peak which resulted in high phosphate carryovers a consequent requirement for long wash times and poor calibration curves observed on Discovery 253 FISHES to a square silicate type peak which it was hoped would circumvent these problems In the early part of leg 1 prior to 15 November both sample and wash times were 90 sec During the sequence of storms which prevented work from 15 20 November extensive tests were carried out to examine the impact of decreasing the wash time on the linearity of the calibration curves These tests produced satisfactory calibration curves and the wash time was therefore decreased to 45 sec From 20 November all samples were analysed in duplicate a substantial increase over the two per station analysed in duplicate before 15 November The following changes were also introduced during the 15 20 November storm e Air compressor controlled bubble injection was introduced to all bubble points including the bubble point on the phosphate line which had previously been removed due to its adverse impact on peak shape and quality e All sample and reagent tubes were renewed they had previously been renewed on 5 Nov e A new cadmium column was fitted attempts to repack the existing Cd column fitted on 5 Nov in response to degrading peak shape on 15 Nov had resulted in an accelerated deterioration of the nitrate peakshape and carryover in the calibration curve 28
157. pendent of pressure of 26 8 2 8 umol kg The correction 5 6 has been applied to the first two casts and 26 8 to the remained However it is not clear why there should have been a jump in the calibration It is probably that the jump is a consequence of the time history CTD14244 was the last cast of leg 1 on 22 November CTD14245 was the first cast of leg 2 on 28 November six days later In between the CTD and sensors sat exposed on deck and temperatures in Reykjavik and often were below freezing For that reason the usual practice of filling the sensors with milli Q water to avoid biofouling was abandoned for fear of freezing Could this have changed the calibration After applying these calibrations the scatter of bottle oxygens recalibrated SB oxygens is shown in Fig 12 Following a gap of several days for the medical evacuation to Reykjavik 6 more CTD 17 casts were done with the second oxygen sensor SBE 43 0076 The calibration for these casts is shown in Fig 13 and mean fits for individual casts are given in Table 4 below Table 4 Oxygen calibration data for CTD casts 14283 14295 Cast No points Mean St Dev 14283 7 18 0 2 1 14287 10 16 5 1 2 14288 8 17 1 1 2 14289 8 17 3 3 4 14294 7 16 1 3 4 14295 9 17 0 2 9 From these numbers the calibration appears stable and a constant offset of 17 0 2 4 was applied although there is a hint in Fig 13 of depth dependence with lower offsets in the top 600m and higher ones b
158. photographs should be disaster proofed by transferring them into digital form eg by scanning Such duplication is not a waste of effort even though the original analogue version may have a longer lifetime than the format media used for the digital transcription Such data may then be included on a programme CD Note that BODC has considerable experience in managing and publishing image data A6 8 Protection of data originators Intellectual Property Rights The following arrangements have been developed to ensure an appropriate balance between the protection of data originators intellectual property rights and the potential benefits that may arise via data use by the programme the wider research community and other interested parties e All data collected in the Marine Productivity programme through NERC funding and provided to BODC should be freely available to all programme participants PIs and Co Is for MarProd purposes on the condition that the originator is kept informed about how the data are being used and is duly acknowledged in any exploitation of that data e Due acknowledgement is considered to be co authorship specific reference to the data source or a share of any financial reward The form of this should be negotiated between the data originator and the data exploiter If a dispute should arise then the problem will be referred to the Steering Committee for resolution e Until MarProd data enter the public domain BODC will n
159. r another berg was sighted at 63 N 34 5 W c 300 km from shore so speed was reduced to 6 kn at night and the sampling site moved to 63 N 33 5 W a safe distance east of the berg 1 Dec Saturday 335 However by the time the site was reached and ARIES fully ready to deploy conditions had worsened with a strong wind and swell and the site had to be aborted We remained hove to from 02 36 until 08 00 The TEK was recovered at 08 55 to try to hold station for a CTD cast but it proved too difficult to hold the ship on station At 10 12 it was agreed to begin to work slowly west back towards the original line from F1 to G8 2 Dec Sunday 336 At 04 00 vessel was hove to in blizzard conditions but by 07 30 a CTD was possible so CTD 14263 was occupied at site H1 from 08 43 to 11 20 After deploying the TEK ARIES 14264 5 6 was worked at the same position from 12 09 to 16 25 in excellent weather sunny though cold light seas Course was then set towards G4 at 10 11 kn during daylight but 6 kn or less at night 3 Dec Monday 337 En route to G4 after recovering the TEK at 05 05 CTD 14267 was worked at site H02 from 05 20 to 07 12 The TEK was redeployed and passage resumed at 07 36 The afternoon was spent working site G4 within sight of the Greenland coast in excellent conditions apart from the need to plan courses between icebergs 59 Swell and wind were from the north so that net tows could be worked in deep
160. r ftp ing to the unix directory data62 surveyor ENX files contain the raw ping by ping profiles ready for averaging and were recorded in case they could be useful for looking at deep acoustic backscatter signals Broadly speaking the new processing path followed the steps outlined for the 150 kHz ADCP In the following script description indicates the daily file number No decent calibration was obtained at the beginning of the cruise and therefore the values derived during Discovery 253 were used instead That calibration was established from bottom tracking data collected on long straight SeaSoar runs of Fine Scale Survey 2 The values were 1 3578 sd 0 078 A 1 0050 sd 0 0031 The equivalent execs to the adpexec are the surveyor execs surexec0 4 summarized in Appendix A2 2 The ADCP files and their Pstar equivalents are listed below Table 13 for the convenience of future users of the ENX files 40 Table 13 ADCP files and their Pstar equivalents File Date range J day hr min sec ADCP file name Note Leg 1 sur25801 307 150818 309 185847 D258Leg1005 000000 LTA BT sur25802 309 190017 310 190121 D258Leg1006 000000 LTA BT sur25803 310 190237 311 190445 D258Leg1007 000000 LTA BT sur25804 311 190615 313 004026 D258Leg1008 000000 LTA BT sur25805 313 004110 314 004517 D258Leg1009 000000 LTA BT sur25806 314 004621 315 003231 D258Leg1010 000000 LTA BT sur25807 315 003453 315 030856 D258Leg1011_000000 LTA
161. rage System including 37kW Powerpack Inboard Compensator and Inboard Diverter Sheaves was used for CTD deployments No faults noted The 20t Storage System including 37kW Powerpack Inboard Compensator and Inboard Diverter Sheaves during the lack of back tension caused by the loss of boost pressure the trawl warp jumped off the diverter sheave on the scrolling gear A new keep plate was welded to the horizontal sheaves on the scrolling gear As the cruise progressed the winch became increasingly difficult to load up An increase in boost pressure and high amps on motor 1 was also noted This needs to be addressed during Discovery s recertification period The 10t and 20t cable haulers were used throughout the cruise and operated satisfactorily however several problems were noted On the final recovery of ARIES a peak load of 7t was noted This was caused by an exceptional roll of the ship at about 30m wire out The wire should be cut at about 100m and re terminated The cable haulers have caused some wear to the wire over this length The cooling water valve handles on the power pack need to be replaced with locking type handles one of the handles has rusted away The haulers tend to slip when in haul possibly due to a dirty or worn valve This should be investigated further whilst the ship is laid up No faults were noted on either the 10t outboard hangar deck diverter sheaves the 20t system hangar deck diverter sheaves and roller assem
162. rated so fast that the planned ARIES deployment had to be abandoned at the very moment that it was ready to go outboard conditions having been relatively benign half an hour earlier This was the first example of how rapidly conditions can worsen in the area After being hove to overnight it became clear that no further work was possible and our best course of action was to head for Reykjavik early After so much severe weather it was considered essential to have an extra night in port for all to get sufficient rest before leg 2 By heading in early we gained that extra night ahead of the intended arrival on 26 November thereby not reducing the duration of leg 2 10 Departure from Reykjavik was delayed by some hours because of poor weather but conditions quickly improved and leg 2 began well with sites F7 F5 F3 and F1 occupied over two days The site numbering allows for further sites to be interleaved on future cruises if desired Note that F7 was occupied in the central Denmark Strait to look at the biological features of the Denmark Strait Overflow Water DSOW While Calanus was fairly abundant above the DSOW it was sparse in the dense DSOW at the bottom Tentatively it does not seem that there is major transport of Calanus from the Greenland Sea Note too that F5 was a repeat of an Icelandic TASC site T13 see Fig 2 From the Greenland Shelf at F1 it was intended to head south to complete line G sites G1 G7 One or two sites might
163. re returned to SOC at the end of this cruise for further testing particularly the silicate standard A bulk sample was taken on the first station in the western Iceland basin 14191 station in the deep Antarctic bottom water layer This sample was run in duplicate on each analytical run A 20 uM nitrite solution was run on each run to evaluate the reduction efficiency of the cadmium column On a day to day basis the following instrument parameters were logged slope of the calibration curve bits uM baseline the correlation coefficient R value of the calibration curve and a parameter described in the Skalar software manual as the relative standard deviation of the calibration curve In practice this turns out to be closely related to the correlation coefficient of the calibration curve and it has therefore not been reported here The phosphate line gave problems throughout leg 2 This was manifested by sudden dramatic increases in baseline and deterioration in peak quality particularly in the second or third run of the day Overall somewhere around one half of the runs were affected to some extent If this were spotted early enough it could be rectified by removing the flow cell from its housing and shaking it vigorously to dislodge what I assume was accumulated reaction product If left to itself then the baseline normally returned to close to its original value When this occurred early in a run the run was terminated the lines cleaned and the
164. re then placed inverted in an outer jacket containing water from the same Niskin bottle and sealed inside a plastic bag They were stored in the cold room on Discovery packed in ice chests with freezer blocks and returned to the University of East Anglia for subsequent analysis by Marie Jos Messias and Andrew Watson Table 8 SF samples taken during cruise Samples marked with an asterisk were drawn in duplicate Station 14239 14244 14245 14249 14254 14259 14263 14267 14275 Date 21Nov 22Nov 28Nov 29Nov 29Nov 30Nov 2Dec 3Dec 4Dec Latitude N 60 65 61 04 65 25 6433 6445 6457 62 74 61 99 61 43 Longitude W 34 34 37 05 29 49 31 99 33 99 34 00 36 57 39 41 39 62 Sampled Niskin 1 1 1 1 1 1 1 2 2 2 2 2 2 2 3 3 3 3 3 3 3 4 4 4 4 4 5 5 4 4 5 5 5 5 5 6 6 5 5 6 6 6 6 6 8 8 6 6 8 7 8 8 8 11 9 8 9 8 10 9 10 10 9 10 12 12 11 Richard Sanders 8 Floats The original intention to deploy four floats on the southern transect line D of the Irminger Sea and two on the next transect line C was thwarted by the weather Instead four floats were deployed one on line D and two somewhat further north as documented in Table 9 The Martec floats drift at 1950 m the Apex floats at 2000 m They surface every 10 days to have their position ascertained by Service Argos and to broadcast the TS profile obtained during their ascent These floats will provide information about the deep currents which advect the zooplankton
165. re will less fetch and hence less westerly swell and it may be possible to occupy part of another line towards the Greenland shelf 57 20 Nov Tuesday 324 Best course that can be made 050 takes us east of B11 now defined as G11 After turning at 15 00 only 5 kn could be made 285 Into wind and swell which will pass south of G11 However as pressure rose and wind abated realistic chance of work in the next 24 hr along a line to the west approximating G 21 Nov Wednesday 325 CTD deployed at 06 03 after strapping on the ARIES transducer for pressure test However the CTD failed at 50 m and was recovered After tests the fault was shown to be in the CTD which will take significant time to swop over Therefore move on to net tows Initial intent was to deploy ARIES first in order to give time to rerig the Dual Methot Before either of these the TEK with Scanmar needed to be deployed so that in turn needed initial tests after being exposed on deck throughout Also the release hook being used to deploy it from the crane hook needed a load test after fixing the spring mechanism Despite these delays the TEK was deployed at 09 43 and ARIES 14236 7 8 at 10 11 Since ARIES lacked depth information it could not be flown close to the bottom Weather maps indicated a weather window lasting until late Thursday so it was decided to occupy a line of sites at 40 nm intervals on a course between the current ARIES position defined
166. remotely with the laptop kept in the main laboratory rather than brought to the frame itself before and after each deployment Even with the change in deployment strategy certain modifications need to be made to the frame before the next cruise A more permanent method of making the frame heavier in the water is required and the various elements need better protection from or securing against vibration damage Specifically the Behemoth s platform needs a permanent method of stabilisation and the brackets used to support the Behemoth and the battery housing need improving to remove the need for separate banding to secure the upper parts of each housing to the frame Also the arrangement of the internal components of the Behemoth needs to be modified so that they are more resistant to both general vibration damage and the shocks associated with deployment and retrieval of the frame Data collected During this cruise full data sets were collected from a deployment depth of 500m at CTD stations numbered 14199 14200 14215 14223 and 14249 Cairistiona Anderson Ryan Saunders 22 4 Towed EK500 scientific echosounder TEK The towed EK500 echosounder package TEK comprises a towed body containing three transducers operating at 38 kHz 120 kHz and 200 kHz directly connected to an EK500 echo sounder which in turn is connected to a desktop logging PC The system is deployed whenever the ship is off station to collect broad scale survey data
167. rts to drop NB Write the data cycles on the pstar log sheet start dc1 bottom dc2 end dc3 You will find this invaluable when you have to redo the processing for whatever reason Output files are ctd14nnn 2db and ctd14nnn ctu 8 ctdplots Finally create some standard hardcopy plots These are automated by typing ctdplots and pressing return when asked for the plotting device Specify which colour plotter when asked To look at the plots on screen reply mx11 for the plotting device and default the plotter Of course plotxy can be used to generate any plots but hardcopy of these standard plots is most useful Documentation of c d258ctd ctdstu bat PSTAR processing Located on seabirdpc Arguments 1 Input directory assumed on C drive and same for con and dat files Full path excluding the initial C and the trailing 2 Output directory on C drive Again full path excluding the initial C and the trailing First level of name eg ctd14190 Example c d258ctd sbebatch ctdstu bat D258ctd D258ctd Processed ctd14200 Two ASCII files are produced in the output directory a cnv file containing the entire data from the cast at 24 Hz and a btl file containing data averaged over the times surrounding each bottle fire Note that psu program setup files in C D258ctd Processed are used with names such as DatCnv258 psu rather than the default psu files This is an attempt to avoid accidental overwriting of the psu files an
168. s cd data61 ladcp 600khz backscatter visbeck d258 For reference the procedures are stored in data61 ladcp 600khz backscatter visbeck m For this the Firing procedure must be run up to the first load step in order to set up the ASCII files i e up to toascii These are then used by a script created on Discovery 253 to run the Visbeck method The original Visbeck code included an m file called demo m which has to be modified for each cast On Discovery 253 a script was written called visbeck which starts with a copy of demo and edits in the correct information for each cast creating a file called v14sss m One further modification made to visbeck on that cruise was to change its CTD loading from Sea Bird format to simple ASCII format using m file loadascctd m Now that we seem to be using Sea Bird permanently this step could be reversed but has not been yet Once v14ssscc m has been created it can be run from within matlab But note that the pathname of the m directory must be first added to MATLABPATH Further modifications have been made by Nick Crisp The backscatter calculation calibrated LADCP amplitude data has piggy backed the visbeck route since he reads the relevant data from the rdi format binary file For this reason the original visbeck m files have modified versions with number 2 at the end The backscatter routine svcalc2 m is a new m file inserted into laproc2 m to do the backscatter calculation If this is all that is required
169. s 369 in August 2001 only three months previously Following agreement to share our data Dr Pickart kindly made available his station positions and CTD files and our station positions were to some extent designed to fill in gaps in Oceanus coverage The combined map of station positions is shown in Fig 2 An example of what can be done by combining the two data sets is shown in Fig 3 the potential temperature at 1000 m After two days of vital trials in sheltered waters Discovery headed west This passage 3 8 Nov took a day longer than expected because of persistent westerlies Line D was worked from the middle of the Iceland Basin to the Reykjanes Ridge D19 D12 These sites showed problems with the net deployments so CTD stations E2 E5 were worked up the Ridge to give time for these to be resolved Unfortunately the weather broke on 14 November after only three sites on line D across the Irminger Basin D11 D9 had been worked For the next six days no further sampling was possible and line D subsequently had to be abandoned Off the SE tip of Greenland we were fully exposed to westerlies and southerlies giving unworkable swell conditions even when the wind reduced We began to head towards Iceland thus reducing the passage to port time and intending to occupy a line G somewhere between lines C and B The start of the line was determined by when conditions became workable and four sites G10 G7 were occupied At site G6 conditions deterio
170. s been computed as value 1 value 2 where values 1 and 2 are the first and second determinations respectively The mean true and mean absolute differences were then evaluated as shown in Table 5 below Table 5 Mean true and absolute differences for nitrate phosphate and silicate determinations Period Nitrate Phosphate Silicate True Absolute True Absolute True Absolute difference difference difference difference difference difference uM uM uM uM uM uM Leg 1 post storm 0 04 0 90 0 20 0 99 0 00 1 14 0 05 2 57 0 08 0 29 0 16 0 41 after 20 Nov Leg 2 pre medevac 0 08 1 07 0 15 1 30 0 01 0 81 0 03 1 21 0 04 0 50 0 21 0 54 to 5 Dec Leg 2 post medevac 0 30 2 10 0 40 2 66 0 00 2 68 0 03 3 24 0 01 0 98 0 14 1 52 after 8 Dec All data from above 0 14 1 40 0 24 1 72 0 01 1 46 0 03 2 10 0 03 0 63 0 18 0 86 The mean absolute differences for N P and Si across the whole data set were 1 7 2 1 and 0 86 respectively and their maximum values all of which occurred in the final period of the cruise were 2 66 3 24 and 1 52 respectively The true differences were always smaller than the absolute differences The mean true difference is lower because analytical precision which is assumed to be random is as likely to make value 1 greater than value 2 as it is to make value 2 higher than value 1 Thus in an ideal world we would expect this parameter to be zero When these parameters are not zero it indicates that uncorrected in
171. s fit of this model to the data S 9 ASv ASv Y 101og R bR c ASv Solve by finding a local minimum E 2 10R log R 2b R c 2c R 2 ASVR 0 2 2a log R 2D R 202 1 22 ASv 0 The green curve in Fig 15 represents the two parameter model fitted to station w200 01 It represents the equation ASv 10log R 0 2856R 4 1918 For the 600 kHhz typical figures for the terms in equation 1 are 19 Sv 139 34 10log 7 273 16 201og R 10log L 9 0 20R k e e O I0log A 20R rewriting the equation into a part dependent on the range and a part involving all the rest where Q 139 3 10log T 273 16 10log L 9 0 k e e T is the transducer temperature and L is the blank beyond transmit To correct the range error this term must be subtracted from the backscatter calculated from equation 1 This gives a corrected backscatter Sv Sy Sv ASv 0 10log R 26 101og R 0 2856R 4 1918 Q 10log R 2a 0 2856 R 4 1918 Q2 10log R 0 02R 4 1918 For reasons not yet understood the correction removes the quadratic dependence on range from the backscatter equation Apparently the beam spreads linearly and not quadratically Further the effective absorption has become almost negligible at the ranges used here Note that this correction is effective for 2 m bins only For longer bins there is an increasing range error per bin which again is charac
172. s laid up 11 10 Clam system The CTD display worked without fault The trawl display crashed several times on startup This should be investigated during recertification Bob Keogh Robert Wallace Steve Whittle 11 11 CAMM 2 engraver On this cruise the CAMM 2 engraver was investigated This instrument can be used to create signs in metal or plastic for display around the ship Unfortunately although it was purchased some years ago no one has found the time to get it working On inspection it was discovered that an interface lead was missing All that was required was a normal parallel port printer lead Operation turned out to be simple A sequence of one line ASCII commands need to be sent via the parallel cable to the instrument This can be achieved by printing from a text handler such as Notepad for Windows Once the basic method had been devised a front end was constructed in Visual Basic This has been loaded into the PC in the Technicians Office and is available for use Labels can be made in either brass or trafflite It would be a good idea to order some engraving media in the near future if use of the system is to be encouraged Steven Alderson Robert Wallace 12 Shipboard computing systems 12 4 Level ABC logging Data were logged using the ISG ABC System The Level A system collects data from individual pieces of scientific equipment The Level B collects each of the Level A SMP messages and writes them to a disk monitoring
173. s should be copied to the 150khz Rnav directory cp sm mat data61 ladcp 150khz raw diO1171 gps cd proc matlab plist sss cc have_sm 1 do_abs This creates the same set of plots as the first run of do_abs but this time the velocities are absolute Print off only dussscch ps Further steps involve conversion to Pstar and comparison with the shipboard 150 kHz ADCP and any Visbeck processed data For this end there is a cshell script in proc toascii sss cc converts the mat velocity data into an ASCII file ccc asc in subdirectory prof 73 In prof there are further scripts dopstar converts ASCII file to Pstar updating the header with correct position creates la14ccc and la14ccc asc in prof dogrid grid a set of Pstar profiles into a section doing stuff like calculating along and across track velocities dosection this uses dogrid and an ASCII file called section to create a section file It simply means you do not have to type in lots of profile numbers on the command line of dogrid dosections this uses the section file to create all gridded files docomp compare the LADCP profiles with on station shipboard averages which must already exist and Visbeck data dopict create a plot part 1 advanced read indecipherable dodisp create a plot part 2 advanced read indecipherable The Visbeck route has mainly used to look at backscatter data from the 600 kHz system The directory you need to be in to access this software i
174. s the nature of the packing cases in which they are supplied There is nothing to prevent the floats from moving back and forth inside the cases during transport or storage on board Two of the three floats examined had bent antennae as a result of this One of these serial no 34 passed the Argos transmission test prior to deployment the other no 35 has not been tested or deployed yet Two deployment methods were tried The more successful involves lowering the float horizontally off the stern using two ropes attached to the rail while the ship steams slowly forward at half a knot This is a skilful operation carrying the risk of the float being dropped from an undesirable height but has been carried out successfully on all three occasions when it has been tried by the Bosun and his mate Webb Research suggest lowering the float on a line passed through a small hole in the stabilising flange On the one occasion this was tried the line became tangled and the float had to be cut loose with a length of line still attached Fortunately this does not appear to have compromised the functioning of the float indeed all three floats deployed on leg 1 have reported back satisfactorily There was not the opportunity to query Service Argos concerning the fate of the fourth float during leg 2 of the cruise Stuart Brentnall 34 9 Underway data 9 1 Thermosalinograph and Surfmet data 9 1 1 Instruments Underway surface meteorology and thermosal
175. satellite system Training 12 1 12 2 12 3 12 4 12 5 12 6 12 7 Satellite imagery sea surface temperature Photography and video Table 11 Table 12 Table 13 Table 14 Table 15 Table 16 Table 17 APPENDICES A1 Diary and station information 54 Al 1 Diary leg 1 A1 2 Diary leg 2 A1 3 Site and station lists Tables 18 and 19 A2 Processing paths 1 11 1 1 000 00eee 66 A2 Sea Bird CTD processing A2 2 ADCP and navigation processing A2 3 LADCP processing 150 kHz and 600 kHz A2 3 Acquisition A2 3 2 Command files A2 3 3 Processing A2 3 4 Bottom track data A2 3 5 Log sheet for 150 kHz LADCP A2 3 6 Log sheet for 600 kHz LADCP A3 Calibration of scientific echosounders LEK and TEK 7able20 77 A4 Pstar backup y Ka 78 AS Zooplankton sorting procedures 79 A5 1 Sampling on deck A5 2 Preservation methods of samples for future analysis A5 3 Species list A5 4 Sample labelling and data logging DM ARIES and OS AS 5 Dual Methot DM A5 6 ARIES A5 6 1 General storage of samples A5 6 2 Processing of pup and reel net samples AP and AR A5 7 Ocean Sampler processing and storage of samples OP and OS A6 Data and sample management policy for the MarProd thematic auuu 81 LIST OF TABLES Table 1 Time distribution between scientific and non scientific activities Table2 Sea Bird CTD sensors and calibration dates Table 3 CTD salinity calibrations Table 4 Oxygen calibration data for CTD casts
176. sing steps are as follows 43 simexecO transferred data from the RVS ea500d2 and prodep streams to Pstar Output sim25877 and sim258 cal After this stage some manual editing of the sim258 cal file was carried out with plxyed followed by pintrp simexec1 merged sim258 cal with navigation and vessel speed data from the bestnav file and average to 5 minute intervals Output sim258 nav and sim258 5min simexec2 append daily files to master files dep2581 nav dep2582 nav dep2581 5min and dep2582 5min and remove on station data using a criteria of speeds less than 2 knots dep2581 track dep2582 track Penny Holliday 10 FRS towed zooplankton net systems 10 1 Sampling summary We collected zooplankton and associated specimen samples with the Autosampling and Recording Instrumented Environmental Sampler ARIES Dual Methot DM and Ocean Sampler OS gear as outlined in Table 15 in order to obtain data on zooplankton populations and environmental conditions and to integrate with standard CTD cast data Water samples were collected from ARIES and a few Ocean Sampler tows along with OPC CTD fluorometer and transmissometer data Technical problems with the plankton net systems were almost all resolved There remained some outstanding deployment and repair issues and there was some loss in data quality However the sampling programme has been successfully undertaken as far as the weather allowed This has been due in no sma
177. st be 5 characters e Disconnect ADCP N B Refer to Charging Safety Sheet e OK no response given but ADCP will now be pinging e Record time of deployment from master clock e Tell operators to proceed with deployment Recovery Connect instrument and battery pack N B Refer to Charging Safety Sheet run SC ADCP File gt ADCP terminal File gt Break We 0a 1 J 76 GU wes p p o 3 Quit terminal File gt Recover recorder data Recording directory c RDI Workhorse w _ dir as above Using explorer rename file in c ladcp d258 data to w 01 000 where is station number Run RDI Software BBLIST from Explorer f10 to main menu File Size when recovery complete bytes Ensembles Read And start and stop times of recovered file from BBLIST START Comments STOP A3 Calibration of scientific echosounders LEK and TEK The lowered EK500 LEK and the towed EK500 TEK scientific echosounders were calibrated at the beginning of the cruise using a standard method for a towed body calibration after MacLennan amp Simmonds 1992 Fisheries Acoustics Chapman and Hall London The calibration procedures were carried out between 2030 on 1 November and 0800 on 2 November whilst the ship was at anchor in Brodick Bay Isle of Arran approximately 55 35 N 05 06 W Once the equipment was assembled calibration data were collected from the TEK first
178. strument drift is occurring such that all determination 1 values are greater or less than all determination 2 values The absolute difference includes both this drift effect and the analytical imprecision effect since now a situation where determination 1 is larger than determination 2 for sample A is cancelled out by determination 2 being larger than determination 1 for sample B is not averaged away but included The absolute differences are therefore the most appropriate values to compare with the figures derived for the pre storm period of leg 1 shown above They are much larger than these values probably a consequence of the replicate samples from leg 1 being run close to their duplicate pair a close analogue to this situation in this second period can be derived by considering the difference between the duplicate bulk determinations since they were done consecutively these values were 0 47 1 74 and 0 42 for N P and Si which are very close to the values shown above for the first part of leg 1 We can use the difference between the mean absolute and mean true differences shown above to gain an insight into the proportion of the total absolute difference which is due to analytical imprecision versus that which is due to uncorrected instrument drift Table 6 31 Table 6 Nutrient analysis errors due to uncorrected instrument drift and to analytical imprecision Period Nitrate Phosphate Silicate Drift error Analytical Drift error A
179. tar which are presented below Until Julian day 313 9 Nov we experienced communication problems between the ADCP PC and the level C Three times a day the data stream would hang and the adcppro level C process would have to be restarted As there is no warning alarm this frequently went unnoticed at the very beginning of the cruise leading to quite large gaps up to a few hr duration in the data logging A strange artifact of this was that just the top 16 m bin of the ADCP data would be logged for a particular time step associated with each hanging of the adcppro level C process Thus some manual editing was required to obtain a gridded data file of 100 bin profiles In addition one in every three dropouts each day would log bottom track info associated with the single bin data and thus this also had to be edited out of the bottom track file these edits were made with mlist and pcopya The problem was solved during the evening of Julian day 313 The header file log on the level C was write protected and although we do not subsequently use this header each time the PC began a new ping data file the communications fell over when it tried to write a new header Within a few days of the beginning of the cruise it was clear that the quality of the 150 kHz data was deteriorating rapidly with the maximum value of 10096 good return echoes per 2 min ensemble in a 24 hr period dropping to less than 90 This was indicative of air in the transducer well
180. tered on Discovery 258 the system worked well Dual Methot net sampler deployments suffered various problems These included connector water ingress optical sensor obscurity and intermittent cable faults One frame proved inoperable but all problems on the other were remedied Despite early problems with obtaining two depth stratified samples each deployment has at least yielded a single integrated sample The later use showed the sampler working fully to the operation depths of 400m and 800m Jim Hunter 11 Mechanical systems Main equipment used CTD towed and lowered EK500 ARIES Ocean Sampler Dual Methot net 11 1 Gantries The starboard gantry was used for the deployment and recovery of the CTD Although still noisy this functioned without any problems The stern gantry was used for the deployment and recovery of ARIES Dual Methot net Ocean Sampler and lowered EK500 The gantry extension operates but creeps back probably due to a sticking valve 11 2 Powerpacks The midships scientific powerpack was used to power the starboard gantry This functioned without any problems The aft scientific powerpacks were used to power the aft gantry and two deck winches The fault warning light on the start panel situated in the hanger came on several times after using the aft gantry or 5t deck winch No obvious fault was found and the light can be reset suggesting perhaps a partially blocked filter The drawers containing hydraulic fi
181. terised by a logarithmic plus linear equation Fig 16 shows the profile for station 14200 after correction Leg 1 Steven Alderson Paula McLeod Ulrike Riemenschneider John Allen Terry Edwards John Wynar Leg 2 report 2 6 3 Temperature The temperature dependence of the backscatter was found to produce stepped results in the final backscatter plots The LADCP derived temperature is lagged therefore when bottle samples are taken on the upcast there is a resulting step in the temperature As a result it was decided to use independent temperatures taken from the CTD data for which a line was added to the loadascctd2 script As a result the final plots were much smoother 2 6 4 Software There appears to be a problem with the navigation file Occasionally the data is out of order giving a matlab error claiming that the file is not monotonic To overcome this a sort command has had to be added to the donav code It is not known why the software rewrites latlon asc as this appears to be a cause of the scripts falling over A similar problem also occurs with get adcp however this is believed to be a hardware problem 2 6 5 Averaging the bins As an alternative to the svavrge script we attempted to use means of the ensembles rather than means of the bins using svavrge2 script The standard deviation was calculated after removing the vertical mean from each ensemble in order to consider the standard deviation within one profil
182. the frequency of the messages and warns the operator when messages fail to appear The Level C system takes these messages and parses them into data streams Table 16 Table 16 Summary of data collected on Discovery 258 via level ABC logging Chernikeef Log LOG CHF MkII Level A Ships Gyro GYRONMEA MkII Level A Trimble GPS GPS 4000 MkII Level A Ashtec ADU GPS ASH MkII Level A Ashtec Glonass GPS GPS GLOS MkII Level A Echo Sounder EA500D1 MkII Level A EA500D2 MkII Level A G12 GPS G12 MkII Level A Winch WINCH SEG PC ADCP Level C direct log ADCP PC Surface Logger SURFMET SIG PC The new Ashtec G12 system is an integrated Seastar Differential GPS and normal GPS system that provides differential corrections for the other GPS systems Paradoxically observations by John Allen suggest the Trimble thus corrected is the most accurate system On two occasions JD 313 and 314 the Level B crashed co incident with the restarting of the Winch PC The system was reset quickly with little data loss 50 12 2 Email system The system worked well whilst the ship was at sea but within the confines of the Clyde links were difficult to achieve Three problems may well have contributed to this the installation of a new high frequency cellphone mast adjacent to King George V dock multi path errors due to mountainous terrain and a problem at SOC that was cleared by a reboot of the sea system and its associated hardware Many cruise participan
183. til samples removed and then clean nets with freshwater hose Use seawater deck hose to wash down all sampling nets Set up the sink and the wash down hoses using the non toxic seawater supplied not firehose seawater or freshwater A5 2 Preservation methods of samples for future analysis In order of priority specimens need to be picked out for future laboratory analyses as follows Lipids use the plain cryovials store in liquid nitrogen Genetics use red banded cryovials store specimens in pure ethanol Isotope ratio use acetone cleaned foil store envelopes in screw top vial within 20 C freezer A5 3 Species list To date the following plankton species have been picked out for further analysis A typical number of sets of individuals dependent on abundance is given in parenthesis denotes target species defined in Phase 2 of Marine Productivity Copepoda Picked from ARIES nets i Calanus 3 4 sets x 10 ii Euchaeta glacialis 3 sets x 10 Euphausiidae Mostly from Dual Methot nets i Meganctiphanes norvegica 3 sets x 5 ii Thysanoessa longicaudata 3 sets x 5 iii Euphausia krohni 3 sets x 5 Chaetognatha Sagitta maxima 3 sets x 5 Amphipoda Parathemisto 3 sets x 5 A5 4 Sample labelling and data logging DM ARIES and OS Printed labels for most samples can be obtained from the net launch recovery team However specimen samples removed for future analysis described above should a
184. tion To save version codes on the dataname smt258 the script was run on the leg 1 master hdg file and thus the resultant file was smt25800 met Rob Lloyd advised that wind speed and direction from the Surfmet system should be viewed with caution since the Surfmet PC had a tendency to do a straight average of directions of 0 and 360 At the end of leg 1 the master file smt25800 met contained very spiky data some periods of bad data and uncalibrated light sensors Thus the daily files were abandoned and this master file cleaned up ready for salinity and fluorescence calibration and renamed smt2581 met in keeping with file naming protocol for other data streams The clean daily files from leg 2 were appended to the master file smt2582 met TSG surface salinity and temperature and windspeed data are shown in Fig 21 The ship s non toxic water supply was turned off at 17 30 on Julian day 315 11 Nov following the discovery of a leak in the supply pipe behind the wall panels of the CT laboratory This leak had caused a significant volume of water to flood the floors of both the CT and chemistry laboratories Whilst the leak was fixed the following morning when a panel was cut out of the wall of the CT lab to provide access the non toxic supply was not turned back on until 16 30 that day 316 12 Nov 9 1 3 Salinity calibration of underway data Samples for salinity analysis were collected every 4 hr from the non toxic supply as it left the FR
185. to fluorescence for lowered CTD and ARIES CTD fluorometers Fig 10 Oxygen calibration for CTD casts 14191 14223 Fig 11 Oxygen corrections against pressure for SBE 43 0086 and SBE 43 0076 Fig 12 Oxygen residuals after calibration against pressure Fig 13 Difference in oxygen concentration between bottle samples and CTD sensor against pressure for casts 14283 14295 Fig 14 Backscatter for four bins as a function of depth for CTD 14200 Fig 15 Backscatter differences between bins averaged over the whole cast Fig 16 Backscatter profile after correction Fig 17 Backscatter temperature and salinity profiles for CTD 14239 and CTD 14245 Fig 18 Time series of thiosulphate required to titrate iodate standard and the difference between duplicate samples Fig 19 Time series of nutrient auto analyser baseline values and calibration coefficients Fig 20 Time series of nutrient auto analyser calibration curve correlation coefficients and bulk nutrient concentrations Fig 21 Spatial plots of underway sea surface salinity temperature and windspeed Fig 22 Calibration of TSG salinities Fig 23 Underway time series of solar irradiance surface fluorescence and chlorophyll Fig 24 OPC estimates of Calanus sized particles as a function of depth Fig 25 Winter abundances of C finmarchicus in the central and eastern North Atlantic combined data 1991 2001 including provisional MarProd data Fig 26 Sea surface temperature composite image for 19 25 November w
186. tor and any wider sharing is at the discretion of the MarProd Steering Committee Level 3 Public Data publication at or near the end of the programme Availability extended to external users either openly for academic use or at the discretion of BODC NERC for commercial exploitation in consultation with data originators Post programme availability of biological material to be controlled by the body responsible for its archiving on the basis that ground rules will then have been established by the Steering Committee and that sample originators will be consulted wherever practicable It is to the benefit of the programme as a whole that inter project collaborations are developed under Level 1 and that the transition between Levels 1 and 2 is made as rapidly as possible A6 11 Identifying data and samples for management purposes It is important that the MarProd programme maintains an awareness of all data and samples collected through its support including outputs from partnership arrangements eg from use of non NERC vessels or through collaborations involving other funding agencies Thus it is likely that a reporting system will be established to gain information on such data samples and their stewardship arrangements if not via BODC However the Steering Committee is keen to minimise any duplication of reporting effort and a version of the GLOBEC DIF system see A6 3 above may therefore be adopted for such purposes 84
187. ts used their own PCs for email It was some time before the disparate mailers in use were correctly configured leading to problems in the scratch area on comms 12 3 GroupWise and Arcserve The Novell system was rebooted once during the trip after a period of very slow response 12 4 Data Processing The GDD Pstar team did the majority of physics data processing The Level C plotting suite was used extensively to produce annotated plotting sheets showing the GEBCO depth contours True wind data was produced using windcalc see problems section Depths corrected for Carter s area were produced from an edited composite of EA500D1 and D2 data Raw depth data existed on two data streams interrupted by the use of the pinger on the CTD These data have been integrated into a single stream and corrected for Carter s Area into the prodep stream The wind data were observed to be incorrect with the apparent wind from ahead This is due to a naive averaging routine in the Surfmet PC that take no account of the 0 to 360 range of the sensor There was no expertise or software onboard to correct this The initial logging of ADCP data was intermittent This was corrected on Julian day 310 6 Nov when file permissions on the ADCP_ header file were found to have been set incorrectly on a previous cruise From JD 344 10 Dec 14 00 the ADCP PC clock was erroneously set 24 hours ahead this was corrected in the Pstar processing From 17 00
188. ttings need to be secured 11 3 PES winch davit and powerpack Two starboard tow PES winches were used during the cruise and operated with faults noted The valves used to change between the two winches need to be looked at with a view to reducing the chance of causing damage to the winch motor by not changing all four valves correctly 11 4 300kW Powerpack 20t and 10t Cobra Unit The 10t cobra unit was used for CTD deployments using the CTD wire The 20t cobra unit was used to deploy ARIES Ocean Sampler Dual Methot net and lowered EK500 using the trawl wire The lowered EK 500 was found to be too light to deploy successfully using the trawl warp due to a loss of traction on the cobra The 5t Lebus deck winch was used with the aft gantry to deploy the LEK 500 with much better results It has been suggested that modifications to the CTD railway be made to allow both the CTD and the LEK to be positioned under the starboard gantry without the use of a crane and a deck winch be situated in the wet lab or on deck for the deployment of the LEK 48 There was a problem with the 20t winch during the trials period at the start of the cruise All hydraulic power to the winch was lost during the deployment of ARIES This was traced to a faulty boost system relay Further trials of the winch were carried out in sheltered water using the trawl warp and chain clumps prior to heading for the work area 11 5 Storage systems and sheaves The 10t Sto
189. uired to titrate 5ml of the in house prepared iodate standard and of the difference between duplicate oxygen samples over the course of the cruise Titre volumes are the mean of five determinations and the error bars are one standard deviation from the mean value Text section 7 1 Fig 18 Nitrate baseline Digital units N and Si calibration coefficients bits mM Fig 19 Time series of the nutrient auto analyser baseline values and calibration coefficients for nitrate silicate and phosphate Text section 7 2 2 20000 4 19000 4 18000 4 17000 4 16000 4 15000 4 14000 4 13000 4 12000 4 11000 4 10000 Time series of instument baseline values ME e99 999 Lr 0280008 Silicate E e Nitrate gE Phosphate 4 f oe 82 o e LI Ooo mm o o ga 6900 6700 6500 6300 r 6100 9900 r 9700 5500 5 Nov 10 Nov 15 Nov 20 Nov 25 Nov 30 Nov 5 Dec 10 Dec 15 Dec Date Time series of instrument calibration coefficients 200 4 B giai 700 Ooo n OBB 20880 190 2808 Ha oeeo n 600 J 180 1 4 tn 4 4 500 170 E t t e 4 A 400 J 160 i 300 150 4 z g o 200 140 T 130 3 e 100 e t 120 T T T T T T T 0 5 Nov 10 Nov 15 Nov 20 Nov 25 Nov 30 Nov 5 Dec 10 Dec 15 Dec Nitrate Date Silicate o Phosphate Phosphate and silicate Phosphate calibration coefficient baselines Digit
190. uring each 7 day period On the front maps darker lines represent stronger or more persistent fronts P Miller Composite front maps for improved visibility of sea surface features on cloudy SeaWiFS and AVHRR data Submitted to JGR Oceans Table 17 below lists the relevant SST images showing features of interest made available in near real time to Discovery 258 and the MarProd programme Table 17 SST imagery for Irminger Sea and Iceland Basin Nov Dec 2001 Single day images Composites SST Composites frontal analysis 15 Nov 14 20 Nov 15 21 Nov 20 Nov 19 25 Nov 19 25 Nov 29 Nov 5 Dec 29 Nov 5 Dec 6 12 Dec 7 13 Dec 7 13 Dec 8 14 Dec 8 14 Dec more easterly coverage from Iceland Basin to Rockall Faeroes and northern Scotland An unusually cloud free image for this area in winter 52 The late November SST images were relatively clear for the Greenland shelf adjacent to the Irminger Sea and also provided patchy coverage to the south of Iceland Fig 26 They showed a system of frontal structures running from Cape Farewell to NW Iceland with temperature changes of several degrees over a few km eg from 4 to 7 C at 64 N 37 W This information was used to help plan the sampling strategy for leg 2 of the cruise Future users of the SST images should note that the colours represent different temperature values on each image chosen to enhance the visual representation of the structures present Peter Miller St
191. ve SOC UKORS mechanical Wynar John SOC UKORS electronics leg 1 Eric Armstrong John Dunn Chris Hall all FRS Aberdeen and Andrew Brierley St Andrews also joined for the first two days of trials on leg 1 Other personnel above participated in both legs except where indicated BODC British Oceanographic Data Centre FRS Fisheries Research Services SOC Southampton Oceanography Centre UKORS UK Ocean Research Services Plumley Robin Sarjeant Peter Oldfield Philip Hood Michael McGill Ian Royston James Harnett John Slater Gary Stewart David Searle Peter Drayton Michael Harrison Martin Dickinson Robert Allison Philip Thomson lan Buffery David Rowlands John Haughton John Harford George Duncan Andrew Ship s personnel Master Chief Officer Second Officer Third Officer Chief Engineer Second Engineer Third Engineer Third Engineer Electrical Engineer ETO Motorman 1A CPO Deck PO Deck Seaman 1A Seaman 1A Seaman 1A Seaman 1A Seaman 1A Shipboard Catering Manager Chef Mess Steward Cohn David Steward Link Walter Steward Acknowledgements This cruise was made possible by the excellent support services provided by the NERC Research Ships Unit SOC Ocean Engineering Division UK Ocean Research Services SOC George Deacon Division and the Fisheries Research Services Marine Laboratory Aberdeen Many other groups organisations and individuals contributed to its success with speci
192. vers for shallow and deep depth location respectively of towed gear and the lowered EK500 To deepen the interior a panel has been welded round the centre line of the fish so towing of new shape is untried The zero depth of the Scanmar pressure transducers was calibrated during a pause in TEK trials by hanging them over the side at exactly 1 m depth 18 10 New ARIES A new ARIES system constructed by FRS Aberdeen under contract for the NERC MarProd programme required ballasting trials Because it is not fitted with the 60 bottle rosette ballasting is likely to be different from the standard ARIES This ARIES was deployed over the stern using the A frame and trawl winch This worked very well There is just enough lift to raise the rig clear of the deck leaving little pendulum System towed well Further deployments will be needed to test adjusted ballast as pitch of 11 is too large To transfer gear from the hangar to the stern two heavy duty plastic pipes have been laid along the deck to provide a track These will act as guides to prevent the vehicles slipping far sideways if the ship rolls 19 20 CTD and EK calibration On completion of the ARIES trial vessel proceeded to anchorage in Brodick Bay east of Arran A test CTD cast station no 14190 was completed without incident firing all bottles at 10 m for sampler training for salts and oxygens Meanwhile the TEK was mounted on a calibration rig which has four arms each supporting a
193. y appended onto the absolute master navigation file and calculated the distance run from the start of the master file Output abnv2581 and abnv2582 gyroexecO transferred data from the RVS gyronmea stream to Pstar a nominal edit was made for directions between 0 360 before the file was appended to daily master files gp4execO transferred data from the RVS gps 4000 stream to Pstar edited out pdop position dilution of precision greater than 5 and appended the new 24 hour file to master files gp42581 and gp2582 glosexecO this was identical to gp4execO but transferred the RVS gps glos data stream to Pstar in master files gls2581 and gls2582 gpsexecO this was identical to gp4execO but transferred the RVS gps g12 data stream to Pstar in master files gps2581 and gps2582 ashexecO transferred data from the RVS gps ash stream to Pstar ashexec1 merged the Ashtech data from ashexecO with the gyro data from gyroexecO and calculated the difference in headings hdg and gyroHdg ashtech gyro a ghdg daily files ashexec2 edited the data from ashexec1 using the following criteria heading 0 lt hdg lt 360 degrees pitch 5 pitch 5 degrees roll 7 roll 7 degrees attitude flag 0 5 attf 0 5 measurement RMS error 0 00001 mrms 0 01 baseline RMS error 0 00001 brms 0 1 ashtech gyro heading 10 a ghdg 10 degrees The heading difference a ghdg was then filtered with a running mean based on 5 dat
194. y with little or no hysteresis Good correlation to the Seatech LSS Seatech LSS Performance generally good However on several upcasts eg 14231 the signal appears to drift for a period for no apparent reason ie there is no corresponding change in the transmissometer signal This was found to be a function of the leak having occurred in the BOB Performance was fine afterwards RDI 150kHz LADCP Data was collected and processed by science personnel From an operational point of view the instrument worked well although problems were experienced with the battery chargers These issues were resolved for leg 2 RDI 600kHz WHLADCP As above It was noted that the star cable arrangement modified to allow use with the Wynall chargers has live male pins on the charging and data download cable Care must therefore be exercised when connecting and disconnecting this cable During leg 2 the star cable connection leaked at the WH bulkhead connection This appeared to be the cause of split data files collected occasionally The cable was replaced and the problem did not re occur Benthos altimeter Performed quite well Usually a stable reading was obtained from about 30 m from seabed but sometimes as high as 70 m max range being 100 m For this reason it has been standard practice to use the pinger and PES for seabed approaches Terry Edwards John Wynar leg 1 Jeff Benson leg 2 13 2 2 CTD salinity calibration including ARIES
195. yll analysis 6 3 Phytoplankton studies Oxygen nutrients and SF6 27 7 1 Dissolved oxygen 7 2 Nutrients 7 2 4 Performance of the analyser 7 2 2 Bulk concentration and nitrite column efficiency 7 2 3 Duplicate samples Tables 5 and 6 7 2 4 N P ratio Table 7 7 3 SF6 Table 8 Floats Iable9 a 33 Underway data 35 9 1 Thermosalinograph and SurfMet data 9 1 1 Instruments Table 10 10 11 12 13 14 9 2 9 3 9 4 9 1 2 9 1 3 9 1 4 Flourescence calibration of underway data Processing Salinity calibration of underway data Navigation and vessel mounted ADCP 9 2 1 9 2 2 9 2 3 9 2 4 9 2 5 9 2 6 9 2 7 9 2 8 Introduction Navigation Heading 150 kHz ADCP 75 kHz ADCP Processed data handling On station profiles Depth of penetration Fast Repetition Rate Fluorometer FRRF Precision echosounder PES data FRS towed zooplankton net systems Sampling summary 10 2 Deployment 10 1 10 3 Results 10 4 Technical problems and solutions Mechanical systems Gantries Powerpacks PES winch davit and powerpack 11 1 11 2 11 3 11 4 11 5 11 6 11 7 11 8 11 9 300 kW Powerpack 20t and 10t Cobra unit Storage systems and sheaves Non toxic water system Workshop Winch control cab Crane for TEK deployment 11 10 Clam system 11 11 CAMM 2 engraver Shipboard computing systems Level ABC logging Email system GroupWise and Arcserve Data processing Hardware problems DartCom
196. ytoplankton physiology using FRRF and determination of 3D abundances of the copepod Calanus finmarchicus other mesozooplankton and their main invertebrate predators using ARIES Dual Methot and Ocean Sampler net systems also lowered and towed scientific echosounders The cruise was divided into two legs The mid cruise port call at Reykjavik allowed for some personnel changes and for discussions at the Icelandic Marine Research Institute Good coverage of the ocean areas of interest was obtained despite unworkable weather conditions for around a third of the cruise and other downtime and passage also around a third including a medical evacuation Provisional data from the Optical Plankton Counter on ARIES indicated that Ca lanus sized particles occurred throughout the water column with a maximum between 500 1500 m Depth integrated densities did not show much geographical variability Subject to post cruise OPC calibration they indicated that C finmarchicus winter abundances in the Irminger Basin region were lower than had been expected on the basis of summer upper ocean data and winter full depth data from other parts of the species range KEYWORDS ADCP SYSTEMS ARIES SYSTEM CALANUS FINMARCHICUS COPEPOD CTD OBSERVATIONS DISSOLVED OXYGEN DUAL METHOT NET EUPHAUSIID FRRF SYSTEM GLOBEC ICELAND BASIN IRMINGER SEA MARINE PRODUCTIVITY THEMATIC MICRO PLANKTON NORTHERN NORTH ATLANTIC NUTRIENTS OCEAN SAMPLER OPTICAL PLANKT

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