LAB OFFICER'S REPORT

Roy Davis

Science Objectives

"Integrated Ocean Drilling Program Expedition 329 will core and log deep-sea sediment and basement at a series of sites in the South Pacific Gyre. The sites are characterized by different levels of marine productivity and different basement ages (6 Ma to 84-124.6 Ma). The primary purposes of the expedition are to (1) document the nature of microbial communities and test the energetic limit to life in the most food-poor deep-sea sediment and (2) test the influence of crust age and sediment thickness on microbial communities, availability of electron donors and acceptors, and the hydrologic evolution of crustal basalt. This project will address fundamental questions about the subseafloor biosphere," from the Expedition 329 Prospectus Abstract.

General Leg Information

Expedition 328T ended and Expedition 329 began with the first line ashore Papeete, Tahiti. Port call activities included a crossover, training and freight handling beginning on 9 October and ending when the vessel sailed on 12 October bound for the South Pacific Gyre. The vessel departed the last site on 8 December bound for Auckland, New Zeland with an ETA of 0600 on 13 December.

Port Call Activities Overview

Papeete

Offloading of

• Expedition 329 airfreight, one yellow box.
• Trash

Delivery and loading of

• IODP surface
• LDEO and Schlumberger freight
• Fuel
• Groceries

Auckland

Offloading of

• 8 Pallets of Core
• app. 10 Gas Bottle Racks
• IODP Surface
• IODP Domestic and Foreign Air
• World Courier Frozen and Refrigerated Samples

Lab Activities

Lab Safety

Daniel Manchaca, Radiological Safety Officer with Texas A&M's Enviromental Health and Safety Department gave a General Radiation Safety Course to the IODP ship's staff . The next day he gave the same class to the scientists who would be using isotopes on the Expedition.

Core Lab

The South Pacific Gyre expedition was geochemistry and microbiology intensive and most of the 'normal' catwalk and core lab procedures were set aside this cruise. Sampling and core lab activities were ever-changing from site to site and flexibility was key..

Paleomagnetics Lab

The lab was only modestly busy this cruise and was staffed by only one paleomagnetist. Only the cryomag, the Kappabridge and the new spinner magnetometer were used. A few APC cores were oriented with the Flexit tools when the sediment cover allowed

Curation

Samples-A total of 12,307 samples were taken from core material on Expedition 329. Of these, 8,856 were personal samples, and 3,451 were shipboard samples. There were 1,731 whole round samples taken. Of these, 428 were IW whole rounds. The remaining 1,303 whole round samples were for personal sampling. In addition 5,209 liquid samples were taken, including IW splits, and Rhizon sampling. The grand total of Expedition 329 samples is 17,516.

Thin Section Lab

There were 63 thin section requests of basalts fresh and altered, cherts and chilled margins. Routine maintenance and cleaning was performed as necessary and at the end of the cruise

Chemistry Lab

Expedition 329 was a heavy chemistry/microbio cruise. Several instruments were brought out from URI, to replace or augment IODP's instruments.

Microbiology Lab

Six Microbiologists participated in the expedition and free counter space was severely limited in the Lab. The PFT injection pumps in the pump room were extensively used. They were flushed with alcohol at the end of the leg.

X-Ray Lab/ICP Prep

Expedition 329 was a sediment and hardrock microbiology focused leg based leg with moderate hard rock and sediment recovery.
Analyses:
Total XRD: 61
Total ICP: 37 + standards

Micropaleontology/Microscope Labs

This is the first microbiology expedition since the ship's refit and the microscope lab was able to satisfy all requirements despite being only down to one (out of two) fluorescence microscope due to a compromised light source.

Information Systems

During Expedition 329 the Information Technology infrastructure was consistently operational with the notable exception of an incident during which files were lost from a folder in one of our Novell volumes. There were no major hardware outages. There were some changes to the computer systems, many of them involving the automation of certain cleanup and other procedures. A very active Teacher at Sea on staff engaged in ~25 successful educational videoconferences.

Developer

See developers report.

Imaging Lab

Expedition 329 was a fairly typical cruises as far as imaging was concerned. It consisted of checking section scans, PR photography, and close ups.

Underway/Fantail

Magnetometer deployment and data collection on first full, operational cruise was successful on all eight transits.
A site survey was completed at U1368, with the bathymetric software and thermal printer working well together.

ASSISTANT LAB OFFICER

Lisa Crowder & Tim Bronk

Summary

Expedition 329 ventured to the expanses of the southern Pacific to investigate the records from one of the most nutrient poor regions of the world's oceans. The port call and transit was spent moving unnecessary equipment out of the labs, setting up equipment and work areas for scientists and generally preparing for the cruise. The extensive organization of the supplies leading up to the expedition was extremely helpful. A substantial frozen/refrigerated shipment has been planned for (an estimated 200 coolers). Many samples will have radio and stable isotopes.

AMS/Inventory

Get the Crew & Cruise address list in AMS format early in the cruise and use as a basis for verifying addresses. This will make it much easier to upload the addresses in AMS. Encountered a problem trying to upload the addresses, which was due to the uploader not being compatible with the new version of Excel. The easy fix was to save the document to MS Office 2003 versions. The uploader is being updated to be compatible with new versions of MS Office.
Physical counts were performed in various locations.

Special projects

Core reefer: Converted the Core Reefer into a sampling laboratory. Tables, supplies and cold-weather gear were provided for the scientists. A laptop and Zebra printer were also installed. The hard shell glove box was relocated and set up. A nitrogen line was run to deliver nitrogen to the glove box and to flush sample containers. A biogas cylinder was also plumbed into the hard-shell glove box.
Additional gas cylinders were installed in the paleo lab, rad van, reefer and chemistry lab.
Microbio cold room: Most of the equipment was cleaned out for additional space and was used for the oxygen measurements.
Rad van: Weekly "safety wipes" was performed by the ALOs to ensure there were no radiation problems. The scientists performed spot wipes. No clean-ups were required.
Major shipment of frozen/refrigerated samples (including radio isotope samples). World Courier will provide coolers in Auckland as we did not have space available on-board. The WC coolers are slightly larger internally than a standard p-box.
Blank Page Core Lab
Kristin Hillis

Summary

The South Pacific Gyre expedition was geochemistry and microbiology intensive and most of the 'normal' catwalk and core lab procedures were set aside this cruise. Sampling and core lab activities were ever changing from site to site and flexibility was key. As the reefer was turned into a sampling area for the geochemists and microbiologists, additional core rack storage was needed. Several trays from one of the core lab racks were removed and placed on the core cart in the reefer to allow more core storage. Extra core tray storage was also needed in the cold room for oxygen analysis, so several of the Styrofoam holders from the metal core boxes were used.
Depending upon hole, cores were taken directly from the catwalk to the cold room for oxygen analysis or to the reefer for geochemistry/microbiology sampling. Temporary labels were placed on the sections on the catwalk. Once in the reefer for sampling, the remaining pieces of a section were kept together on a piece of split liner. We quickly realized keeping track of the section, interval, and also Working and Archive halves was going be complicated and important. We began by hand writing labels for each piece with the information, but developer Stephanie Zeliadt came to the rescue with the Advanced Bulk Printer program. This allowed us to scan the regular Sample Master labels used for d-tubes, enter the interval offsets, and print labels with all the information we needed (Figure 1). (Advanced Bulk Printer also has many other features, such as labels for a hard rock sample party and other temporary labels.) When remnants of a section came back to the core lab, the endcaps were acetoned on, pieces of a section that should be rejoined were with liner patch, and labels with appropriate intervals were attached (Figure 2).

Figure 1. Advanced Bulk Printer program used Figure 2. Remaining pieces of core section
to print labels with offsets and temporary labels.labeled and stored in half liner
Special care had to be taken when running the sections with multiple pieces through the whole-round tracks. To account for the intervals missing from microbiology sampling, core liner pieces were cut into measured lengths (10, 15, 30, 40cm, etc) and taped into place. This created a 'train' of continuous core and core liner to be pushed through the track (Figure 3). For the NGR, foam was used to take the place of whole-round samples.

Figure 3. Spacers used for running sections through whole round tracks.
When splitting cores that had been heavily whole-round sampled, extra care was taken to leave the appropriate vacancies on the sampling and description tables (Figure 4).

Figure 4. Split cores with intervals sampled for geochemistry and microbiology left vacant.

Equipment Performance Summary

All core lab equipment functioned without problems. The core splitter is making a louder squealing noise than normal from the actuators underneath. Perhaps Bill Mills can look into this during the Louisville cruise.
An MCS cart was fitted with handles and very helpful in moving core from one deck to another.
Imaging Specialist John Beck took photos of the reefer setup if needed to refer back to on future cruises.



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Physical Properties

Maxim Vasilyev, Zenon Mateo, Margaret Hastedt

Summary

The Physical Properties lab and the core tracks saw only moderate usage on this lower-recovery expedition. A new method for determining total potassium and thorium on the NGR was developed.

Problems Encountered

• "Banana cores" (warped liners) and other exotic Frankencores (recurated/reassembled microbio leftovers) would occasionally get stuck in the susceptibility loop. The motor was not torquing out as expected and would get hot if not caught quickly.
• The SHMSL suffered the same problem on one occasion. All tracks need to trap the error that they are not moving a distance as expected while in measuring mode or make use of the torque limit feature for the Galil motors.
• The pycnometer software caused the usual confusion with the scientists forgetting to save after runs etc.
• In this expedition, multiple whole round segments resulted from the extensive microbiological and geochemical sampling. In running the remaining whole round segments, empty liner or Styrofoam spacers were used in all the loggers and tracks. Consequently, there were several times when segments and the corresponding data points were not in their proper position.
  • This highlights the need for careful examination of the dataset, initially in LIMSpeak, especially before splitting.
  • In LIMSpeak, showing the symbols for each plot is the best way to view where data points exist.
  • A re-scanning of samples is the easiest way to solve such mismatches.
  • In cases where a re-scan is not possible (i.e., whole round has been split), cancel the old data, modify the original text files (from the local drive) to reflect the proper offsets, and then re-upload to the database.
• The Teka again had problems measuring sediment cores, especially ours which had large amounts of free water in them. Convection problems affected or even prevented getting any measurements from the instrument. See appended report with discussion from Teka.
• The P-wave caliper transducer would occasionally "forget" its programmed moves for no particular reason (just sitting around unused seemed to be sufficient excuse). We had to remind it of its programming by going into the Exlar software on the gantry.
• PWAVE gantry: there was one reported occasion when a discrete sample was to be measured but no wave was getting generated after the cube has been clamped by the transducers (read: the application was working just fine up to that point). A "shutdown-install Windows updates-start computer" procedure had to be performed (for the n^th time) and everything went back to normal.
• The PWL on the whole-round track also had occasional problems where the LVDT would fail to provide a distance to the data reduction routine, which locked the transducers on the core. There doesn't seem to be error trapping for this condition. The user has to abort the run and use the emergency stop button for the Exlar to get it to let loose, then go through some steps to clean things up for the next run. (see below in discussion)
• The SHMSL had problems measuring L* from our very dark brown-black cores. It would generate spuriously high (up to 250%) values.
• A number of tests were run on the SHMSL to ascertain the effect of Glad-wrap calibrations and illumination from the side of the integrating sphere. The results will be returned to the beach for discussion/evaluation by the PP lab-working group.
• Until such time as a fixed barcode scanner can be installed for SHMSL, the handheld scanner is set to read the reflection of the SHLF label from a mirror.
• The new Bartington MS probe in the SHMSL is very sensitive to how much contact it makes with the split face. It often needs to plow into the surface by about a millimeter in order to get values that are similar to the MS loop. As the pressure is often adjusted depending on the induration of the core material, the MS values also change. A better way to account for variability in depth/section-half thickness is needed without crushing the core material.
• LIMS quit displaying calibration verification data properly from the pycnometer this cruise. This is a formatting/reporting problem in Web Tabular.

Other items/Discussion:

• Another vacuum saturation chamber was set up for doing thermal conductivity on hard rocks (thanks, Mike Bertoli!). A pair of clamshell chambers has been ordered for Phys Props so we'll quit stealing them from the Chem lab or Thin Section.
• The pycnometer's UHP helium gas bottles were exchanged with Zero grade helium gas when they were empty after contacting the beach for guidance.
• The scientists noticed some GRA data that looked odd coming off the WRMSL. In LIMSpeak it displayed a distinctive saw tooth pattern from section to section:

There was a pronounced list to port at the time. The cores are stored in the rack with their tops to port, plus they were very watery AND had good-sized air pockets due to the optode sampling this cruise. This produced a double-whammy for the GRA as illustrated in the diagram:

The reason behind the drop in density about halfway through the section is that the GRA density calculation is assuming a full section's worth of material. The sloppy sediment, air gap and ship's list all combine to decrease the amount of material being sensed by the GRA in the bottom part of the section and lower densities are the result. Taking the same section, reversing it, and remeasuring confirmed this. The meniscus effect returned exactly as before.

Reasons for the PWL on WRMSL to not release a core

Problem: LVDT does not return a value to the program.  No value, no velocity determination good or bad, program is hung. (error not trapped properly)Possible fixes:a) Hit PWL emerg. stop button, force calipers open.  Reset emerg. stop button, abort WRMST program (Close all Apps button or force-quit w/Task Mgr).  Shut down (not Restart) computer, then cold boot again.  Let any Windows updates install themselves if necessary.  Try PWL again.
b) If the PWL does not run after restarting, open the Tritex.exe software.  In the side pane, there should be a tree node for PWL, if not, go to File > Recent Applications > and select the one named PWL.eapp.  Expand the Drive Networks tree node, then Modbus and there should be an entry for EM30.  It will most likely say it is DISCONNECTED and Disabled(unhomed) (in the Control tab).  Right-click on the Drive Networks node (you may have to select it with a left click first) and select "Scan and connect application drives...", then it will show a CONNECTED status.  Check the Control page by expanding the PWL > Pages Node and double-clicking the Control node.  The top message that previously read "Disabled(unhomed) should now read a fault.  Double-click the Diagnostics node to open the Diagnostics tab.  Click the Reset Faults button on that screen.  If you check the Control screen, it should no longer show a fault.  Close the program and restart the WRMSL software.  The PWL sensor should communicate after that.c) If problem persists, go into MAX and delete the  NI 5102 card.  Cold boot computer so it will redetect the card.  This worked earlier this cruise.
d) Suggestion from Trevor:  "Open the source code, find the waveform recording part and the LVDT volts part and go into the Scope Express VI and see if it works.  You may have lost the Task for the NI Scope.   You may have to recreate the TASK for the NI Scope functions.  Make sure NI Scope is installed, check the All Programs>National Instruments>NI Scope>NI Scope Soft Front Panel."

NGR report

NGR NaI detectors positioning study was done with the Cs-137 calibration source. Distributions are rather flat with maximum shifted on the level of 1-2 cm from calculated NaI positions. Exact knowledge of source positioning is critical in this kind of study. Recommendation is to make special collimating core and use it together with laser to perform that study on the required level of accuracy.
Absolute efficiency calibrations were conducted with Th-K standard. Detectors 1 and 8 have efficiencies 6-8% less than others. That information should go into the data reduction program, which is supposed to have the ability to accommodate it easily.
A calibration nonlinearity study with the Thorium standard was performed. For some detectors energy scales are not linear enough. In such case the low energy region will have a noticeable shift between experimental and Monte-Carlo peaks, while the higher energy region will show excellent coincidence. The hardware solution was found to be undesirable – affected detectors are very sensitive and already working at the lower limit of the HV (high voltage) supply region available for ORTEC ScintiPack HV modules. Software solution: uneven histogram binning. That method was tested during this expedition and proved to work fine.

K and Th concentration method development:

Absolute K determination in sediments and rocks was developed during the beginning of this expedition. Calibration with K standard was required as well as bulk densities measured by GRA. A basic program was written in Physical Analysis Workstation (PAW) to both visualize and give the possibility to easily adjust Compton continuum subtraction under the K peak. It requires some preparation of spectral files (deleting the header, leaving just channel information) as well as some post processing, which involves density information from GRA as well as corresponding depths from LIMS. The results of the calculations were manually uploaded to LIMS.
Correct methods for averaging densities were studied. It was found that just using reduced densities at the ends of core sections introduces artificial waves at the edges of each core section. Instead, using average densities calculated just inside the core section and applying edge correction afterwards produces no artificial structures at the end of core sections.
Calculating the weighted densities averaged with detector response function began. That should be important for rock sections and for sediment cores with gaps. Study of the method limits started. Large presence of U-238 daughters in the core material should be the main and most probably just one limiting factor. Initial Monte-Carlo estimations showed that even on the top of sediment with the highest presence of U-238 daughters but sufficient K presence (~1%, hole U1367B, U1369B) a linear approximation to Compton continuum is a valid assumption. But for much lower K (0.1%, U1368B) Monte-Carlo clearly suggests that linear approximation is not valid any more. On shore, more detailed study will be required to define exactly affected spectra and to make quantitative adjustments.
Absolute K concentrations were calculated for each site (so far) during expedition 329. For sites U1365 and U1368 included 2 holes – one with sediment cores and one with basement cores. Evidence of strong correlation between K concentration and rock alteration was demonstrated. Good agreement between K concentrations from NGR and LDEO downhole logging gamma ray tool was found for the only logged hole (U1368F).
A more automatic program is required to make K concentration measurements routine on the NGR. Towards this end the program was rewritten during the expedition from PAW to ROOT (from KUIP command processor language into C/C+) . ROOT is the C+ reincarnation of PAW and can be easily linked with an ORACLE database. Adjustment of I/O for MS Windows OS and a module, which will read densities from database and then finally upload results to LIMS still need to be written by application developers.
Method for simultaneous study and visualization of all measured quantities in PP lab was suggested and demonstrated with Ntuples available in both PAW and ROOT. Example distributions for exp. 329 were plotted. Such plots could be constructed automatically after the last measurement for a particular core section in PP Lab is finished. It could additionally enhance scientific support provided by IODP. More wide, event based structure TREE, which in addition to float numbers can link together vectors, characters, images and so on is also available within ROOT.
Monte-Carlo simulations for some holes were done. U/Th/K ratios for top layer and some lower placed sediments available. Ratios were also defined for manganese nodules from hole U1366C. Big enhancement in Th-232 demonstrated. On-shore chemical analysis with ICP-MS planned for validating the Monte Carlo-based ratios. U, Th absolute concentrations were estimated indirectly from these ratios plus experimentally measured K concentrations.
Limiting factor for Monte Carlo derived U/Th/K ratios observed – low concentration of 2 elements simultaneously comparatively to the third one, that gives the possibility to greatly vary ratio without any significant change in the spectra shape.
Absolute Th concentration measurement method was developed at the end of expedition with similar ideology to K measurements. Calibration with Th standard and densities from GRA required. Thorium absolute concentrations were calculated for hole U1369B. Comparison of these data with Th absolute concentrations extracted from U/Th/K Monte-Carlo ratios are now available and done for first 2 core sections. Rather good agreement between experiment and Monte-Carlo found. More comparison to come, depending on time availability.
Other NGR issues:
The NGR Analyzer program occasionally loses connection with the GALIL controller ~ once or twice per 12 hour shift. Simply pressing the restart button on the error message window, which leads to the new scan, of a core section label solved the problem every time.
Extremely rare strange output from data analysis program included in separate file ("NGR anomaly.xls"): It is not clear how both measurements were done in the same position. It looks from output that it was actually two separate measurements both in position 2. Not clear how it is possible within the existing software.
Samples measured as of report deadline:
MAD samples: 209
Sediment velocities (gantry): 65
Hard-rock cube velocities: 80
Thermal conductivity runs: 424
WRMST sections: 800
SHMSL runs: 619
NGR runs: 672
STMSL runs: not used.
Vane shear measurements: not used.

Teka

BabelFish translation of Teka PDF from Exp. 329 (with added illustrations)
Guesses on English translation in {italics}; minor grammatical corrections added by M. Hastedt
Thomas Gorgas, please clarify any mistranslations!!
We evaluated the accomplished measurements with TkGraph graphically and give for each measuring series in the following a short estimate. As in our email of 25.10.2010 describes, the encoding of some series of measurements (SECT2436121_75, SHLF2434621_100, SHLF2435301_75 and SHLF2435551_77) from us unknown reasons converted into UTF-16 and had to be back-changed to Windows ANSI and/or ISO 8859-1 (Latin-1), so that a treatment with TkGraph or a new evaluation with the mode of the TK04-Software is possible for evaluation.
In addition we give some references to questions, which are brought up for discussion in the passed on emails of the scientists and/or programmers. Generally we must point out however that we cannot take over a support for alternative evaluations, whose theoretical basis we were tested not to recognize not to be able and not by us. We refer however naturally to if obvious mistakes and/or knowledge gaps are noticeable to us
Macor VLQ vom 14.10.2010
As was to be inferred from the email of Maggie Hastedt, the tests at Macor are on behalf in order, so also these: In the Summary Plot is small the dispersion, the Contact values lie constantly with the default value 10, the LET values could when measurements of the laboratory standard be higher, are however ok, the same is valid for number of solutions, and the average value of the heat conductivity is scarcely under the desired value. Into the single Measurement Plots are the asymptotes something expand, but well recognizably and the evaluation intervals begin in front with 20 S. It is exactly the correct and also by us recommended procedure, for problems one To accomplish function test at the laboratory standard, around hardware defects or software nose {??} to exclude. There the measuring system and the site conditions (if the Macor was based on the same measuring position as the cores) correct is obvious, one should itself with de Error tracing next the sample preparation and the measuring parameters (in particular that Amount of heat) turn.















What good measurements should look like:
Good accuracy: Macor is 1.626 ± 2% W/mKLots of solutions for each testLETs should be high, >>10-20Contact values (CV)
should be similar for a seriesLow errors & variability `
Evals begin as early as 20 seconds, but some start later (green)
Normal, upwards asymptotes
Asymptotes separating slightly, but still OK.
SHLF2434591_95
Since only individual measurement is present, the Summary Plot says, LET not much is however in any case so small that the measurement is useless. With sediments the suspicion on bad contact is there always obvious. Interesting it is however that the number of solutions is also only easily increased also over 1000 pieces very highly and the Contact VALUE. With bad contact a low LET would be to be expected combined with a small number of solutions (under 100), the Contact VALUE would be usually also higher. In addition straight is good according to experience with damp clay/tone the contact.

Is informative in this case, the asymptote to regard (either in single the Measurement Plot or simply in the preview of the Summary Plot). Additionally to the normal, upward bending process (naturally because of the low LET value is only badly pronounced), one recognizes the beginning, quasi of a reflected branch bending downward. Then only bending a downward SHLF2435301_75 (see below) to have it, reflected process. Such effects (also laterally bending processes, partly employs, partly additionally to one " normal" Asymptote) are a practically safe sign for convection in the sample. NOTE: Measurements, with which convection arose, are without everyone Exception USELESS! Further notes for this see below (general to Convection)
Downwards asymptotes can indicate convectionSketchy upwards asymptote
SHLF2434621_100
Since only with one of the three individual measurings only one solution was found, one cannot draw further conclusions also with the graphic evaluation. It lies however near that convection is likewise the problem here.
SHLF2435301_75
The lower bound for LET was lowered when this measurement of 4 to 3, otherwise it would have likewise given no solutions here. Over the sense of this measure see below. Anyhow there are thereby relatively many solutions, naturally all with LET between 3 and 4, which downward forms bending asymptotes instead of upward. Thus convection is the cause here likewise.

SHLF2435551_77
The series of measurements is good: Dispersion small, CV-values even, many solutions, LETs high. Asymptotes well trained, start of the evaluation intervals in front.



SECT2436121_75
Since at all no solutions were found, no graphic evaluation is possible, be obvious-proved is also from convection as problem to be proceeded.
General to convection
With strongly aqueous samples the fluid contained in the sample can begin to circulate by the heating procedure. Depending upon strength of the convective heat transport the determined heat conductivity value can amount to then a repeated {multiple??} of the actual value, also to low values can occur. Measurements, with which convection arose, are useless without exception, independently of the used measuring or Evaluation procedure.
Countermeasure is first as low an amount of heat as possible, in order to avoid a mobilization of the water contained in the sample (power control at the lower bound, between 1.5 and 2.0). This was almost exemplary considered with all us available series of measurements. Then one should make certain that the needle probe is exactly perpendicular in the sample, in order to offer to the force of gravity if possible little attack region. If that should not help anything, one can try still another measuring position, in hope that pore conditions are somewhat different there, so that no convection arises. If convection cannot be avoided, no measurement is possible at this sample.
In order to prevent misunderstandings: Naturally one can with a conventional Evaluation procedures always any straight line by the measured values put to compute and from their upward gradient a heat conductivity. That does not mean however that this procedure supplies a correct value then despite convection during TK04 with convection malfunctioned. As soon as convective heat transport is present by fluid movement, the entire theory is no longer applicable for thermal conduction, and is valid for all measuring and evaluation procedures. The convective Heat transport exceeds the conductivity typically around several orders of magnitude. Since with sediments depending upon permeability the flow rates are small usually, the determined values are frequently not obviously unreasonable (we had however already 18 W/mK for a damp fine sand), but the error are as large, are completely unvorhersagbar with convection. The TK04-Evaluation procedure has from there particularly with convection opposite conventional procedures the inestimable advantage that one notices the problem at least, instead of storing house numbers as result.
General for lowering the LET limit
With some series of measurements the limit for LET is of 4 to 3 was lowered, this measure also into de E-Mails was discussed. Lets itself general say to changes at the evaluation parameters: If a measurement with the standard parameters no or no useful Ergebnise supplies, it is in such a way disturbed that possible solutions, which one by manipulation that Evaluation parameters out-lured, strongly faulted are. Lowering LET limit is here particularly unreasonable measure, because measurements, with which LET does not exceed values of 10-20, are completely useless already.
In the plain language: A disturbed measurement becomes better only by repair of the breakdown cause and repeating the measurement, because not the evaluation, but the heating curve is disturbed. That is valid naturally also for other measuring instruments/procedures, only one does not notice a disturbance there, as long as the value remains halfway in the plausible framework. Which concerns the technical problems with the new evaluation with the TK04-Software, she will function as soon as that inadvertently converting in UTF-16 was turned off or as soon as the files are back-changed again in Windows ANSI/ISO 8859-1 (Latin)
General to Kontakmittel {thermal joint compound?} with sediments
Of Maggie Hastedt we inferred from the email that obviously also the question was discussed, whether with the sediment cores contact means was to be used. The scientists are here in the long run at the correct conclusion come - no contact means - however one also more simply could: TK04 manual chapter 8,2 SAM-polarizes Preparation (VLQ). The same is located also in the data sheet of the standard VLQ; with the software one installs, and in the Application note SAM-polarize Preparation, which can be downloaded of our website. A short email inquiry with us would have likewise led to the goal.
General to alternative computations
We cannot express ourselves to alternative computations from the DWL files, whose theoretical basis we were not tested to know and not by us. In principle is valid however: If our algorithm does not produce results computed and no suppl. file, then, because it recognized the heating curve as strongly disturbed. From disturbed data in addition, with other evaluation procedures no unimpaired results can be computed (see above, general for lowering the LET limit).

Paleomagnetics Lab

Margaret Hastedt
Paleomagnetists: Takaya Shimono

Summary

The lab was only modestly busy this cruise and was staffed by only one paleomagnetist. Helen Evans (logging staffsci) filled in as needed to help cover the time when the Pmag scientist was off-shift. Only the cryomag, the Kappabridge and the new spinner magnetometer were used. A few APC cores were oriented with the Flexit tools when the sediment cover allowed

Problems Encountered

1. The compiled version of the SRM code had barcode parsing issues. It was not taking advantage of the new label format, which includes the original sample length, and was still attempting to look up the length information from the LIMS (a feature that was disabled prior to its being compiled). Dwight sent out a couple of iterations to fix the issue.

1. The cryocooler compressor shut down for between 12-24 hours one day before anyone noticed it, judging by the Dewar pressure and internal voltages. It may have happened due to an emergency generator test and/or air handler maintenance work at the time but we don't know for sure. Once again the compressor's switch was acting up and not latching. After several attempts the ET's got it started. Afterwards they dragged out the spare compressor to examine its switch with an eye towards ordering a new one, something I intended to do many weeks ago but had forgotten. Anyway, the spare compressor was found with no He pressure at all (should have read 250 psi static). The pressure gauge on the back panel had leaked, and it failed completely when we attempted to purge/repressurize the compressor. It will be returned to the beach for refurbishment if economical. In the meantime we harvested the switch in case we need it for the unit currently in use. Another compressor has been ordered as a spare and should arrive in time for the next expedition. Also, the Haskris reservoir temperature was lowered to 50° F and its supply hose to the compressor insulated to help minimize sweating. Doing so may reduce any shutoffs due to the compressor overheating.

While the compressor was off the cryomag flipped out in a manner I have never seen before. The symptoms were bizarre: all 3 SQUIDs were still superconducting, but none of the flux counters were working! So all you would get is the analog part of the signal, which is the very tiniest bit on everything except the weakest possible cores and/or trays. After a LOT of head scratching I got them working again, which may or may not have coincided with the compressor being back on again and cooling down the inner vapor-cooled shielding. But I can't say for sure, and to the best of my knowledge the two should have nothing to do with each other.

3. Spinner magnetometer: if using the automatic holder on cubes, make sure that the scientists know to keep the retaining screw flush with the sides of the holder whether there is a cube in it or not. Otherwise it will jam up when the instrument attempts a sample position rotation. Also, keep an eye on the holder when testing position rotations using the software as the instrument isn't quite smart enough to know if the actual sample part of the holder is in Position 1. It simply rotates the holder a certain number of degrees with each turn command. Verify it visually, and turn it to Pos. 1 manually if necessary then try the rotations again.


Samples processed as of this writing:

• Total cryomag section runs (all demags): ~2250
• Cubes measured (all demag levels): 667
• Cores oriented with Flexit tools: 23

CURATION

Chad Broyles

Summary

Samples-A total of 12,307 samples were taken from core material on Expedition 329. Of these, 8,856 were personal samples, and 3,451 were shipboard samples. There were 1,731 whole round samples taken. Of these, 428 were IW whole rounds. The remaining 1,303 whole round samples were for personal sampling. In addition 5,209 liquid samples were taken, including IW splits, and Rhizon sampling. The grand total of Expedition 329 samples is 17,516.
Shipments-
Core-There are 180 boxes of archive, and working sections (90 archive, 90 working) Core Recovery for Expedition 329 was 1,169 meters.
Hand Carry-Michal Szpak hand carried a portion of his samples.
Residues- The residue distribution is as follows:
ALKFerdelman
CELLKallmeyer, Morono
H2Smith
HSGCR
ICPMurray
IW (Squeeze Cake)Murray, Robinson, Spivack
IW (Liquid)Various shipboard geochemists
IWSSpivack
MADC(Sediment PP)Hoppie, GCR
MADD(Basalt PP)Evans
PALZarikian
PFTUniversity of Rhode Island
PMAGShimono
RZSpivack
TCH4GCR
TOCGCR
TSBGCR, Smith-Duque
XRDGCR
Frozen & Refrigerated Shipments-At this time we estimate 200+ boxes of frozen, and refrigerated shipments will be sent from Auckland, New Zealand.
Thin Sections-64 thin sections were made on Expedition 329, and described by the petrologists. All thin sections are being sent to the GCR for inventory, before they can be requested by shipboard scientists. The thin section inventory is attached in the same email as this report.
Smear Slides-Sedimentologists prepared and described 453 smear slides. The Smear Slide inventory is attached in the email with this report. All smear slides will be shipped to the GCR.
Core Flow Activity and Sampling
The following is a general representation of how each site was handled, and processed. Actual examples are given of sites that followed.
U1365A-"Oxygen analysis and Sedimentology hole"
Site U1365A was the first hole drilled on Expedition 329. U1365A was a hole mainly dedicated to sedimentology, and preserving a permanent archive half. One of the primary objectives of this cruise was to measure oxygen in the core. Two scientists were dedicated to taking this measurement via optode and electrode analysis, in the cold room of the Chemistry Lab. Therefore no whole round samples were taken from this hole. This hole was processed normally with one exception. Once received on the catwalk, we sectioned the core, taped on endcaps, placed temporary labels on the sections, and immediately delivered the sections to the cold room in the chemistry lab. When the optode, and electrode scientists were finished taking their measurements, the core sections were delivered to the core lab for routine processing. When the sections were split, archive halves were described. Shipboard, and personal samples were taken from the working halves.
U1365B-"Geochemistry hole"
U1365B was processed quite differently. Once the core was sectioned (without acetone or tape) on the catwalk, it was immediately delivered to the Hold Reefer. In the Hold we set up a make shift lab, and sampling area. A hard shell Augmentix laptop was set up in the reefer, with a Zebra label printer. A team of scientists then took many whole round samples from each core section. They carefully labeled each whole round piece that was remaining with the appropriate Site, Hole, Core, Section, and Interval information. Half liners were laid out on the mobile sampling table. Individual whole round pieces were place in the liners corresponding to the section and interval they came from. At times the remaining pieces were sent to the optode and electrode lab for oxygen analysis. Once all samples had been taken, and analyses performed the cores came back to the Core Lab for additional processing. This is explained in the "Reconstruction of Cores" section of this report. For later sites, the Geochemistry sample plan was modified to include catwalk IW samples from the bottom of each section of core.
U1365C-"Microbiology hole"
U1365C was processed similarly to U1365B. However, there was a completely different sampling strategy that was developed by the microbiologists.
U1365D-Additional hole
U1365B did not recover a full core 2. Sedimentation rates in this part of the ocean are very slow, on the order of microns per year. As a result, a significant geologic time span was lost. It was decided to take a few cores from U1365D to obtain this time span. These cores were reserved for microbiology samples, and some additional IW samples. If recovery was sufficient on later sites, the additional hole was not cored.
U1365E-RCB Basalt Hole
For Site U1365E, we drilled down to 71 meters and then began coring. This interval was denoted as 1-1. The first core we received on deck was core 2R. For 2R, we hoped to obtain the sediment basement interface. We did not receive any sediment from this core as it was washed away. Core processing proceeded as normal on the catwalk for basalt recovery. Since this was a microbiology expedition, we attempted to keep the core as cold as possible. As a result, we measured the original "created" section lengths, and printed labels as fast as possible. The labels were printed on pre-split liners. We delivered the core sections to the hold reefer as soon as this was finished. Once in the reefer, we shook the sections from their original liners into the pre split labeled liners. The petrologists then did a quick core description of the whole round core. The core sections remained in the reefer until a group decision between the petrologists, and microbiologists was attained. The group agreed upon a place to take the microbiology samples. This consisted of whole rounds that were not to be returned. Before removing the sample, the photographer took a picture of the sample labeled with core section and interval. A white foam whole round spacer was put in place of the removed sample. This foam was labeled with the type of sample that was taken (MBIO), and the interval in centimeters. Once microbiology sampling was complete, the core was processed as normal when obtaining hard rock core. More information on this matter can be found in Curatorial reports from Expeditions 324, and 327. This MBIO sample was entered into the database after the core had been completely curated, and split. Since there were only two petrologists onboard Exp. 329, processing of the core was a very slow process. We had shipboard sample meetings at noon, so both the curator, and petrologists were present. Once all of the basalt core had been described (including thin section description, and XRD/ICP analysis) we had a sample party for the petrologists, and other interested parties on a transit between sites. The same process was implemented for sites U1367, and U1368 with slight modifications.
Site U1366
Site U1366 presented its' own set of challenges. This site was estimated to have a sediment thickness of 17m. This resulted in only receiving a few cores from each hole. U1366B is the first hole that we received sediment core from. This core had a split liner and was deemed unworthy for optode-elecrode oxygen analysis. Since oxygen measurements were one of the primary objectives of the expedition, Hole C was used for this purpose. With such a thin layer of sediment, Core 2 from Hole B had already been shot by the time this decision was made. Therefore U1366B was used primarily as an auxiliary sedimentology hole. U1366C had far less damage and was processed in a similar manner as U1365A. U1366 D was processed as the "geochemistry" hole. There were problems with drilling for U1366E, and only one core was shot. U1366F served as the "microbiology" hole. Manganese nodules existed throughout most cores from this site. Basement was recovered on U1366F, and a large piece was processed for microbiology. RCB coring was not performed on this site.
For the remaining sites, a similar scheme was followed with minor modifications by the chemistry, and microbiology groups.
Reconstruction of Cores, Description, and Sampling
We reconstructed cores after extensive whole round sampling. Early on, I was very clear that I did not want to receive unknown pieces after sampling. Both the chemistry, and microbiology groups were instructed to label left over pieces clearly, and precisely. When we received the remaining pieces of sediment whole rounds, we continued processing them. The developers created a section label software that allowed us to label all pieces of sections (both working and archive) with their appropriate intervals. Sub sections were individually labeled with Exp, Site, Hole, Core, Type, Sec, Half, Interval. For sub sections that directly fit together, we took off endcaps, and melded them together with liner patch, and acetone. Sometimes it was necessary to use the sonic welder, when the acetone did not hold the sub sections together well. Subsections with gaps in between were treated individually. Whole round pieces of empty liners were taped in between gaps, where core material was missing. They were then run through the whole round tracks. Once all whole round data had been recorded, and uploaded the core sub sections were ready to be split. We then split all pieces for each section, in tandem, and laid them out on the sampling, and description tables in their appropriate intervals. The new system was good at helping keep track of these things. For imaging, foam spacers were used for missing parts of the section. Each spacer was labeled with the type of sample removed from the original core section. The majority of half round samples were taken from the "Sedimentology" hole. There were times when recovery was limited for certain intervals. We then filled in the gaps with leftover material that was returned from the "geochemisty", and "microbiology" holes. Split sub sections were placed together in their appropriate section half D-tubes.
Hard Rock Sample Parties
The first hard rock sample party (U1365, U1367) was done on the 3 day transit between U1368 & U1369. The procedure was the same as described in Curatorial Reports from Exp. 324, and Exp. 327. The second hard rock sample party (U1368) was held between sites U1370 and U1371.

Action Items

Routine Microbiology Sampling (RMS)
For each site, we collected several RMS samples for the archive. These samples will be sent frozen to the GCR. These samples will be available for post cruise microbiology sampling (stored at -86 degrees C at the GCR), if requested. Once the sample moratorium has ended, they will be made available to the scientific community at large. For all of these samples MBIO_RMS was entered in the Name field. A search for this name in Web Tabular Report will yield a list of these samples.
Thin Sections
All thin sections made on board Expedition 329 will be sent to the GCR for inventory. Once received, and inventoried by the repository they may be requested by shipboard scientists during the moratorium period.
Computer Software This expedition was unique in many ways. We reconstructed cores from remaining pieces returned after extensive whole round sampling. The following programs were created by Stephanie to help us with this challenge.
Advanced Bulk Printer(ABP): Stephanie wrote a new label program (Advanced Bulk Printer) that is able to print section half labels with any interval. The user can scan section half labels, enter the interval the sub section came from, and print the section half label with the appropriate interval. There is also the option for creating labels containing just the site, core, and section. These are placed at the top of core sections to help identify them when several sites, or holes are laid out at one time. This is extremely useful for sample parties.
Curatorial Oddities Report (COR): Stephanie provided a new web report for curation. The Curatorial Oddities Report lists all samples that are taken outside of the range of the section length. This is a very useful tool, as the sampling program allows you to enter samples outside of the range of the section length. The COR report allows you to search on Expedition, Site, Hole, Core, and Section. It then lists all samples taken outside of the range of section lengths. This report has not been put in to production but may be found at: http://ararat.ship.iodp.tamu.edu:8080/UWQ/
Curator Report Modifications: The Curator Report had been listing a subset of samples qualified as (none). It was then adding this number to the total number of samples taken. Further investigation indicated that samples labeled as (none) included chemistry subsplits, shipboard samples where the test field was left blank, and other unclassified samples. For reporting purposes on the ship, we need a list of samples taken either as whole rounds from sections, or discrete samples from section halves. Stephanie modified the Curator Report to include only these types of samples. It also was modified to list all samples listed as (none). This provides an excellent source of information for error checking on all entered samples in the database.
Web Tabular Report Name Field Search: A very useful search for sample "Name" in Web Tabular Report is now available to all users.
Latest Version of Sample Master: The latest version of Sample Master on the ship as of Expedition 329 is v2.1.1.4. The curatorial staff in the GCR needs to ensure that this is the version installed on all workstations in the repository.

Problems encountered

Piece entry in Sample Master
We experienced several errors when uploading pieces in Sample Master. Many times we need to enter piece lengths to the nearest half centimeter. This is necessary so that core images match entered piece lengths in the barrel sheets. Many times the piece length entered differed from the observed piece in the core image. We found that the program was rounding piece intervals when half-centimeter lengths were entered. When the numbers were uploaded in the barrel sheets, significant gaps appeared, and did not match the core image due to rounding errors. The developers were able to modify the program so that it was not rounding to the nearest centimeter. This seemed to correct the errors in the barrel sheets we were observing. The recalculate offsets button in Sample Master was designed for section entry. In the piece tab, this button was not functioning properly for piece entry. The recalculate offsets button in the Piece tab was modified, and now recalculates piece lengths.
Parameter Search and editing in Sample Master
The parameter search in Sample Master remains unstable. It will crash at random times resulting in "the red X of death". You then have to restart the program, and begin again. The Parameter Search feature is vital for editing bulk samples, and this problem needs to be addressed with Jim Rosser, and the development group. One thing I have noticed is, if you are performing a Parameter Search on Site, it is essential to have the Expedition included in the Search Criteria. I find it is best to close the entire program, after making bulk edits in Sample Master, before beginning a new Parameter search. At the beginning of the expedition, the Edit function was not working at all for editing sample request codes, and numbers. Towards the end of 329, Stephanie was able to resolve the issues with editing capabilities. Copy, and paste capabilities still do not work for editing in the Parameter Search tab.

Chemistry Lab

Lisa Brandt, Mike "Curly" Bertoli, Dennis Graham, Nicholette Zeliadt

Summary

Expedition 329 was a heavy chemistry/microbio cruise. Several instruments were brought out from URI, to replace or augment IODP's instruments.
General Note from Dennis:
As a one-timer temporary tech I'd like to make a comment on the lab layout. Change it if you ever get the chance. With any more than two or three people in the lab (including microbio) the flow does not work. The walkway down the lab is too narrow and is constantly blocked. I would take out the interior wall if at all possible and open up the entire floor but keep the x-ray and thin section as separate labs.

Sample Summary

URI Alkalinity Autotitrator

Alkalinity was measured by acid titration. A Metrohm 809 Titrando from the University of Rhode Island performed the titration. The main difference between the 809 Titrando and the IODP Metrohm Titrino is the size of the dispensing burette. The 809 Titrando is fitted with a 2ml burette, the Titrino has a 20ml burette. This volume of acid increment is more precise with the smaller burette. The Titrando is controlled with Metrohm Tiamo software. For an alkalinity standard we used CRM Batch 94 from Andrew Dickson's lab at SIO. Overall precision of measurement was ~+/-20micromolar alkalinity.

URI-IC

The University of Rhode Island participants on this cruise brought a Metrohm 861 Compact IC for the measurement of sulfate and chloride. It was necessary to measure changes in chloride content on the order of 2-3% down hole. We used a MetroSep A Supp 5 column with a Supp 4/5 pre-column. The IC was equipped with a suppressor module (MSM II), 853 CO2 suppressor, conductivity detector, column heater, pulsation dampener, high-pressure pump, peristaltic pump, and injection valve. The overall precision of replicate measurements was better than ~0.1%. Forty liters of eluent, (3.2mM sodium carbonate / 1.0 mM sodium bicarbonate) was prepared at the start of the cruise to minimize differences in batch runs. Also 20 liters of a 50:1 mix of de-ionized water (18Mohm) to surface sea water was prepared. This standard was calibrated to IAPSO standard seawater. The seawater standard was run after every 4 samples. In addition a 50:1 mix of DI water to IAPSO was run 4 times with each batch. Samples were also prepared 50:1. Dilutions were made by dispensing 10ml of DI from a Brand Tech dispensette and pipeting 0.5 ml of IAPSO or sample from a fixed volume Eppendorf Research pipette.

URI-UV Vis

Nitrate / nitrite was measured on a Metrohm 844 ion chromatograph with a UV/VIS detector. This instrument was provided by the University of Rhode Island. A 10% sodium chloride eluent was used with a MetroSep A Supp 8 column and pre-column. The IC components were a high-pressure pump, pulse dampener, column heater, and UV detector. The VIS detector was not used. Nitrate and nitrite were measured at a wavelength of 219nm with a bunching factor of 3. A nitrate standard was prepared from powdered potassium nitrate. In addition, a liquid certified reference material (CRM) from SIO was measured. Overall, precision of the measurement was 1.3% nitrate. A large volume of standard and eluent were prepared at the beginning of the expedition to facilitate inter-batch consistency

Formation Factor

Formation factor was measured in the core lab using a custom made platinum electrode and a Metrohm 719 conductivity meter. A large batch of surface seawater standard was prepared at the start of the expedition. The standard was calibrated to IAPSO standard seawater. The electrode was two pieces of 2mm diameter by 5cm long platinum wire press fitted into a virgin grade Teflon block one centimeter apart. Temperature was measured with a Metrohm pt1000 thermometer connected to the conductivity meter. The University of Rhode Island provided this equipment.

Helium Sampling

Samples were collected for helium isotope analysis. Pore water was collected in a copper tube straight from the acrodisc filter on the squeezer. After the tube had overflowed for about 20 seconds the lower part of the tube is clamped with a refrigeration clamp. The tube was taken off the squeezer and then the upper portion of the tube was clamped in the same manner. Sample volume was 1ml. The samples will be analyzed in Dave Hilton's lab at SIO. A 20' van was mounted on top of the lab stack and outfitted with an squeezer for this process because the helium concentration in the lab stack was too high from the carrier gas output of the gas chromatographs.

Coulometer

We had issues early in the cruise with the coulometer producing low standard values when analyzing a 100% CaCo3 standard. We think this was tied to the new silver nitrate traps.
UIC has replaced their old Silver Nitrate trap with a newer model. Instead of a trap with a glass stopcock at the bottom, the new trap has two slender glass tubes separated by a glass frit. The frit becomes clogged easily, and is very difficult to clean. The UIC tech suggested we use household ammonia to clean the frit or exchange the tube with a KOH tube. We exchanged the new tube with a KOH tube. The dispersion tip was removed and the 1/8^th inch inlet Teflon tube was extended to the bottom of the dispersion tube. This works okay but it is not nearly as good as the sulfur scrubber used before the ship conversion.

Ammonium Analysis

Ammonium was measured at the last site using a Turner Designs Trilogy Lab fluorometer. The University of Rhode Island brought out this equipment. The method used is described in R.M. Holmes "A simple and precise method measuring ammonium in marine and freshwater ecosystems" 1999. We used Protocol B and adapted the sample size down to 0.5ml to 2ml working reagent. This protocol is good for 0.5 micromole to 60 micromole ammonium.

CHNS

No major problems encountered with the CHNS.

IC

IODP's IC was primarily used to analyze Ca, Mg, Na, and K. Initially the chromatograms showed a noisy baseline. We contacted Dionex tech support and they recommended cleaning the check valves. This improved the baseline noise. Later in the cruise, the peak retention times started to destabilize, so we replaced the cation guard and regular column.

DA

The DA was used for phosphate and silica analyses. While the scientist was happy with the sensitivity of the DA (much lower limit of detection than the manual spectrophotometer), he had many of the same complaints that have come up before in regards to the software. This software is the one that came with the instrument; it is not in-house software. Among the complaints: the sample entry screen is horribly user-unfriendly, and the data was not transferred to the reporter software once because a window had been closed. If the limit of detection had not been better than a manual spec, the DA would not have been used this cruise, due to the frustration of the software. A few hardware issues popped up early in the cruise. We found that when hitting "prime pump" no water was being dispensed through the probe. After conferring with the company, and replacing the tubing sets, we found that it simply worked better after taking the back pistons apart and putting them back together. We think the pump had become air bound and locked up. Halfway through the cruise, the diaphragm pump started making a loud buzzing noise. Also the wash/rinse station kept backfilling with water. This did not seem to cause any carryover in the data. The pump has been added to AMS and a replacement has been ordered for next cruise.

GC3/NGA

After an initial calibration, GC3/NGA were used sparingly. GC3 was used for total hydrocarbon (TCH4) analysis, but results were rarely, if ever, above background. NGA wasn't used at all, save occasional standard and blank injections.

ICP-AES

Also See attached Rick Murray ICP Note
The ICP ran really well this cruise. We performed both water and basalt (flux) analyses. Rick Murray modified some of the procedures to improve data quality. See attached ICP note for details.

PFT GC

The control panel for the auto sampler was damaged (during shipping, I assume) thereby rendering it inoperable. GC2, as of the x329 port call, had a Restek Rtx 502.2 column installed, and was running PFT_METH_329.M as the method. After determining a less-than-ideal response factor, and after further testing, we decided to swap out the column for an older HP PLOT column. A different method was created, based on the method used on x185 and x201. With a much improved response factor, GC2 was used quite regularly without any issues. The instrument has always performed; I attribute any error to user error, and do not place fault with the machine.
 

TOC Analyzer

On this cruise, we obtained a new OI Analytical TOC analyzer. There was minimal method development done on shore. We only used the instrument to run DIC. Instead of the auto sampler, the scientists decided to use a manual feed sipper. Everything ran smoothly, though data retrieval does not seem to be possible the way we have it configured, and at the beginning of the cruise we ran it as a stand-alone instrument, they did not want to bother with hooking it up to the computer. Basically, this instrument needs more method development and to have a manual written.

Support Equipment

Freeze Dryer
On x329, we discovered many of the connections (read: hubs/dials on the top assembly) do not produce a good seal, so that the vacuum doesn't drop to acceptable levels.

Notes on Operation of ICP-ES

Expedition 329, South Pacific Gyre Microbiology
R. W. Murray
rickm@bu.edu
Boston University
December, 2010

On this expedition we performed a large number of porewater analyses by ICP-ES, using the shipboard Leeman Prodigy instrument. Compared to the original JY2000 instrument that we installed for ODP approximately 10 years ago (Murray et al., 2000, ODP Technical Note 29), this instrument is faster and more stable. Moreover, the data reduction strategies described in the modern "ICP Operations Manual" put together by the IODP technicians has greatly increased the capability to perform routine analyses in the shipboard environment.
During Expedition 329, Lisa Brandt and I worked to improve some of the techniques and standard operating procedures. Several cruise objectives depended on generating research-quality data with as high (good) precision as possible. Thus, several of the below suggestions were developed in that context.
1.Gather data on each analytical line with four (4) acquisitions, not three. This greatly improves the precision (% rsd) of each analysis while consuming minimal extra time. The trade-off is well worth it. We tested gathering for n = 5, 6, 7....10 acquisitions, and found that 4 presents the best balance between improving precision and yet not taking much time (each acquisition is ~ 20 sec). In theory, precision should continue to increase as a function of 'n', but that is only if "all other things are equal", namely, that precision would only depend on 'n'. In reality, vagaries in pump uptake, electronics, etc., contribute to acquisition variability. In the end, performing four acquisitions was deemed the best compromise.
2. The dilution factor for the major element determinations should be increased from using 100 µL per 10 ml of dilution solution, to using 50 µL per 10 ml of dilution solution. We assessed linearity of the instrumental response and found that, while the linear regression equations would commonly yield correlation coefficients very close to unity (e.g., r = 0.998), there nonetheless was "rollover" in virtually all elements. This "rollover" means that increasing concentrations do not yield a commensurate increase in counts. This can be combated by increasing the dilution factor (that is, become more dilute). While it did not completely solve the problem, it greatly improved linearity across the range of expected concentrations. Even less sample could be used (25 µL per 10 ml of dilution solution), but at that level pipetting errors increase. If still higher dilution factors are desired, I would recommend using 50 µL of sample in 20 ml of dilution solution, and only using some of the final solution for the analysis (the autosampler tubes are ~ 10 ml in size).
3.Somewhat akin to #2, for major element determinations the drift solution should be made with 50% IAPSO, not the 100% IAPSO. This is because drift will appear to be artificially low in a solution with higher concentration and using a drift with high concentrations is relatively insensitive because of the non-linear response. Using the "50% IAPSO" solution provided plenty of counts to quantify drift, yet did not approach non-linearity.
4.We did not do any background corrections. We looked at some typical spectra and saw that the backgrounds amount to a significant fraction of the total counts (that is, the S/N ratio is rather low). In some cases, the backgrounds were 20% of the total counts on peak. Because there is uncertainty associated with the measurement of background (even if the %RSD is low, such as 0.5%), subtracting any value with uncertainty from a peak (which also has uncertainty) serves to decrease precision. We tried different ways to pick backgrounds (by looking at the echelle patterns via the histograms, as well as by using the 'profile' function) and found little to no difference in results. Because backgrounds will most likely vary as a function of matrix, and because the matrices in the porewater solutions were virtually identical (made even more so by #2), this was acceptable. Calibration lines remained linear, and precision was greatly enhanced.
5. Constraining accuracy for major elements, B, and Sr is straightforward, by comparison to multiple preparations of fresh IAPSO solution prepared and analyzed as unknowns in the run. Comparison must be made to IAPSO solutions (not the 100% standard for Ca, Mg, K, Na, although it is also IAPSO) prepared separately (that is, at the same time as the unknowns) and not included in the regression. However, there currently is not an internationally certified trace metal SRM for Fe, Mn, Ba, and other elements analyzed with the shipboard ICP-ES. Canadian reference materials (NASS-1, CASS-1, etc) do not present high enough concentrations to be of use for porewaters. IODP should invest in developing an in-house independent standard for trace metals in porewaters.
6. For the most precise and accurate results, because the ICP yields such a linear response overall, for the conservative species (Ca, Mg, K, Na, B, Sr) it is best to simply ratio the data to IAPSO when the data are expected to be near seawater values. Provided IAPSO is determined very precisely (e.g., prepared and run 4 separate times and run randomly through the run), the result will be better than calibrating against a line of 5%, 25%, 50% IAPSO, etc. Even though the response is strongly linear, no calibration line is perfectly precise, and thus errors in the measurement of these lower standards will propagate to the IAPSO-like concentration. If you're expecting either higher or lower concentrations of species, of course, then you will need to generate the line, but for many analyses a simple ratio to IAPSO will give more reproducible results.

XRD Lab

Eric Jackson

Summary:

Expedition 329 was a sediment and hardrock microbiology focused leg based leg with moderate hard rock and sediment recovery.
Analyses:
Total XRD: 61
Total ICP: 37 + standards

Equipment (work completed and problems encountered):

Bruker D4:
Several times while unloading sample the D4 Commander program aborted due to a break in communication. No reason has been determined. Grant Banta removed the Bruker internal XRD transit while upgrading then downgrading Windows 7. The MCS's were going to look into it and have removed the external camera software leaving the D4 without a camera.
ICP Bead Maker:
No problems encountered.
LOI Funace:
A maximum temperature of 960C was obtained and determined sufficient for the expedition LOI's.
Mettler Toledo Balance system:
The chem. lab balance broke at the beginning of the leg requiring extensive use of the XRD lab balance by all personnel. A lack of familiarity of the balance led to some calibration attempts while at sea by users.
Sample Prep:
Some cannibalization of Freeze dryer parts occurred between the chemistry lab and the prep lab. The chem. lab had vacuum issues requiring frequent use of the prep lab freeze dryer. No problems were encountered with the freeze dryer in the prep lab. The proper 90-degree elbows are on order for use of more connections. The large freeze dryer in the chemistry lab may need to be addressed for functionality and sufficient parts and connections.
Sample Prep Air: The breathing air quality is questionable as evidenced by the accumulation of very fine silica powder that accumulates on horizontal surfaces.
Special Projects:
While underway the running lights were compromised by the tying in of the prep area lab and xrd lab to the external lights. These were re-wired and now have an additional switch located on the starboard bulkhead of the prep lab. Flipping the circuit breakers while in transit is not required any longer.
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Microscopy Lab, Paleontology Prep Lab and Core Description

Zenon Mateo

Summary

This is the first microbiology expedition since the ship's refit and the microscope lab was able to satisfy all requirements despite being only down to one (out of two) fluorescence microscope due to a compromised light source.

*as of November 28, 2010

Equipment Performance Summary

Instruments:

1. During the port call in Papeete, Tahiti, an attempt was made to make the Opto-Quip controller functional for the Axioplan2imaging fluorescence microscope in the Microbilogy Lab. It needed a regular 15-pin cable to connect to the back of the power supply. However, this cable compromised the fuse. The ETs made a systematic troubleshooting of the problem, replacing some "hexfit" and resistors in the circuit board of the power supply. In the end, it was declared unusable, especially without the circuit diagram from the manufacturer. Without any back-up fluorescence light source, the expedition was down to only one functioning fluorescence microscope in the laboratory.

1. The need and eventual purchase of another fluorescence light source gives us the opportunity to evaluate other types, such as LED fluorescence light source. In talking to the microbiologists onboard, I will have to perform a more detailed market research after the expedition.

1. A mercury arc lamp was replaced once during the middle of the expedition. In the process, it was found out that not all of the lamps we have in stock have the same terminal diameter (particularly the base/larger end). Because we can't open all items for investigation, it is suggested that the terminal diameter be checked prior to installing a new lamp.

1. The Axiophot fluorescence microscope in the lab is normally fitted with a rotatable stage with a mechanical specimen holder. Because moving knobs would move the clipped slide up and down or in and out of focus, especially for high magnification observation of microbial specimens, they requested for an XY stage, which will also be more ergonomic for doing point counting using the DIFFCOUNT electronic counter. However, the XY stage for this microscope did not arrive in time for the expedition. The solution was to bring up the Axioplan2imaging from the Microbiology Lab, which has an XY stage. The HBO fluorescent light source from the Axiophot was transferred into the Axioplan2 imaging as well. This worked out well because it freed up some table space in the Microbiology Lab, which was cramped with materials and all the users for this expedition.

1. The SPOT Idea 5MP CMOS camera was re-installed in the lab. Initially, it still gave the error that the camera is not powered or not connected. A driver from the SPOT CD installers was needed to run this camera.

1. A phototube was also installed in the SV-8 stereomicroscope in the Smear Slide alcove. The Zeiss phototube was replaced with a smaller diameter tube in order to connect to a 0.55X CMT adaptor with a C-mount and a P-clamp from Diagnostic Instruments. Subsequent testing (albeit qualitative) by imaging some foraminifera showed that the SV-8 depth of field is comparable to that of the SV-11. Also, for better stereoscope images, the "Correct Color Technology" in the camera settings was not applied and sometimes, for high-relief specimens, covering either left or right fiber optic lights enhances textural features. For future expeditions with significant use of the stereoscopes, the users will need, at the start, some guidance from the microscope technician to determine the best settings for taking images.

1. Objective installation: When immersion oil is extensively used in a microscope and if the number of slots in the nosepiece turret allow, no other objective should be mounted right next to the oil immersion objective. This is to prevent accidental smearing of oil on dry objectives.

1. Fluorescence filters: Six major users of the fluorescence microscope examined a range of specimens from bacteria, archea and virus to discrimination against the mineral (non-biogenic) matrix. This made use of several filter cubes and gave us an opportunity to examine further the specifications of each set. A summary report will be created after the expedition and will be made available to future microbiologists participating in an expedition.

Paleo Prep Lab

1. This lab was converted into an extension of the Microbiology Lab. To make space for all the materials and supplies that the scientists brought on board, all sieves were boxed and kept in the IODP machine shop and the oven and desiccation box were stored away as well to free up some countertop for a flow cytometer, hydrogen measuring equipment and several other instruments. This rearrangement is actually a good model for future microbiology expeditions.
2. A very dilute HF was safely used in processing of microbiological samples.

Core Description and Reporting

1. The core description process went well during the expedition. There has been no sighting of the "big red X". All data have been uploading and downloading properly. However, workspace and excel back-ups were still created as a precaution. It was also emphasized to the users that once the data has been uploaded, the workspace and excel files became only secondary files and that any further edits will have to be done on those uploaded entries.

1. During the entire expedition, there were two isolated DESClogik issues:
   1. Selective value uploading at the beginning of port call was attributed to an old bug (inability to handle "&") that crept back into the code, but, after some systematic testing in the ship, it was resolved by Chris Bennight back on shore well before we arrived at the first site.
   2. There was one instance when data for a section was downloaded for editing in several tabs. It was later found out that those rows were entirely or partially missing in the database. We were able to re-enter the data because the entries were also saved in the workspace and in the excel back-up files. The cause of the problem is speculated to be due to downloading and editing of data (common denominator for all entries that disappeared) but was not subsequently uploaded to update the database. However, this cannot be replicated and the reason for the disappearance of the data cannot be exactly determined.

1. Strater2 was installed in all of the workstations that previously had Strater1. The new features of this version have made it more flexible to work with. Hole correlation diagrams were easily generated. Although specific annotations can also be drawn in the log panel, the users still preferred working in Illustrator, mostly because of user familiarity and preference.

1. Images in the Novel folders. The close-up photo uploader and Strater had problems accessing images from the network folder. The only solution for some time was to copy the images into the local drive and upload or display from there. The issue was raised to the MCS and to IT back on shore. Nobody could figure out why or expected this kind of problem. Goldensoftware came back with a few suggestions (i.e., permissions, security features, different drive names for the network, etc). However, on Nov. 16, for reasons unknown to me, things worked!

1. No thin section reports were generated in this expedition because the application has not been synchronized to deal with variations in data entry between expeditions. Several suggestions have been presented and the issue has been extensively discussed back on shore and will potentially lead to some directives from management. For this expedition, there were only two igneous petrographers and the thin section description, as presented in DESClogik in multiple tables, was enough. Consolidated Thin Section Reports are more crucial in parties where several scientists contribute to the description of one thin section and that a consolidated report is needed. Hence, this issue was raised mainly in preparation for the next expedition (330).

1. 11x17 inch printout of section LSIMG is another requested feature that X324 noted in their post-cruise evaluation for use in hard-rock expeditions. This is for the initial annotation of observed features prior to unit delineation and rock interpretation and data entry. Although it was not requested by X329 petrologists, the need for this feature was raised and a script was written back in the beach by David Fackler and Tim Blaisdell. It was tested during the expedition in order to find out the best settings. The script is saved in a folder together with the TIFF file generated by the SHIL. When run (double-clicked), it goes through and finds the .TIFF files that don't have an associated PRINTME.jpg file.

We experimented with a few values for the sigmoidal contrast, starting with the usual 2,10 for the JPGs that the SHIL produces, all the way up to the 7,10 from.  Good thing we also still have the igneous cores up in the core lab to compare with, and a few more trained eyes to view the printed images. For the vesicular aphanitic basalt cores with alteration halos, the igneous petrologist think that a sigmoidal contrast of 3.5,10% is closest to how the dry split face looks like. However, the scientists in 330 can settle with whatever values they think will be useful in describing their cores (i.e., with what they think brings out the features that they are after).
In printing, we had to use Photoshop because the Windows wizard defaults to automatically fitting the image to the page. The image has to be reduced to 7.5 % of the original size in order for a 75 cm half of a SHLF to fit in the 17" paper.
An obvious challenge though is the color printer. During the testing, it turned all the brown alteration into green! John will try to come up with a calibration file that can be used in the SHIL workstation and we'll also have the MCSs service the core_color printer to get rid of some printing artifacts. According to Lisa Crowder, we have enough onboard supply of 11x17 paper for X330.

DOWNHOLE MEASUREMENT LAB

Garrick Van Rensburg & Randy Gjesvold

Summary

This was a microbiology leg.

Downhole Measurements Lab

Broke out and tested APCT-3 and SET Tools. Trained on running the APCT-3 and the SET tools. Ran APCT-3 tool in hole 1365A cores 1,3 and 4. In hole 1365B core 4 and 5. In hole 1365C core 3 and 4. In hole 1370 D core 4. In hole 1370E Core 3,5 and 6. In hole 1370E Core 3,5 and 6. In hole 1371D cores 4,5,6,8 and 10. Trans Ocean installed the Load Pin cable and mounted it to the draw works. Data was backed up at the following location:
VOL 1 (
JR1) (T/ data 1/ Exp 329/ 14.1 Formation Temperature. APCT-3_SET_WINTEMP_TPFIT
Note: Tool 1858007C. One of the batteries in the battery pack came loose. Tightened the metal fitting that holds it in place by bending it back while the battery is out. There were no further problems.

Rig Instrumentation

Rig Watch: November 15 computer system froze. Required the program to be restarted at the server to clear it. Lost 1 hour of data. Trained with the Ops Engineer on how to run Rig Watch. Had the IT personnel install the Omega instruments programs on the ET Computer so we can communicate with the rig watch sensors. Omega Transmitter box failed during testing. Dec 03 Rig Watch computer system keeps loosing communications (X Bob fails). This results in the core line depth freezing up. Krakatoa was re booted and the problems remains. Continue to reset comms as required to keep the system running.














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Electronic Technicians Report

Garrick Van Rensburg & Randy Gjesvold

Summary

This was a microbiology leg.

Special Projects/Problems

ET Shop

Changed out the DVD CD player on the shop computer. Cleaned and adjusted cooling fan on Computer CPU.

DOE Van

Changed power plug on new freezer purchased in Tahiti. Allowed to run for 6 hours to calibrate.

CO-Chief's Office

Re routed cable for the TV into the wire ways and hooked it up in the TV receptacle provided in the office.

Paleo Prep Lab

Hydrogen Analyzer display faulty. Re seated pins on power connector to the display assembly. This worked for over a month. On Nov 22^nd the problems re appeared. Machine was disassembled. All the contacts and connectors were cleaned out and re seated.

Core Lab

SMSL
Found the rubber isolator on the SMSL had broken. Fabricated a new one out of thicker rubber. Fabricated a few more out of thinner rubber. Will test which one's work better. Found motor and Galil over heated. It appears the run program did not disconnect the drive and it sat trying to drive for long enough to heat up significantly. Replaced light bulb on the Orion light source.
Whole round logger locked up. Un-plugged the main power and the Galil still had an error fault. Unhooked the 100 pin connector to the computer and the fault cleared.
Cryo-Magnetometer.
Compressor started tripping offline again. It wasn't noticed for several hours so the Cryo-Magnetometer heated up. The breaker was re-set. Tripped off again but was noticed immediately. Takes a screwdriver to shove CB1 into the on position and have it stay in the on position. Working on an alarm indicator for when it powers off. Researched a spare Circuit Breaker. It's an AC3-X0-02-455-213-D Circuit Breaker manufactured by Carlingswitch, Inc. Replacements run in the $150 range. Margaret Hastedt is looking into having the spare compressor refurbished or replaced. The one under the stairs is no longer functional. The control valves have failed. A new replacement will run in the $5000 range. Dust Buster ceased to operate. The motor has destroyed the bearings. New one on order.

Core Splitting Room

Steinel heat gun just wasn't putting out enough heat. It turns out the company schematic has it wired to run on 220V. Modified it slightly to run on 110V. Still wouldn't put out enough heat in the core splitting room. When in the ET shop it would put out enough heat. It appears it's a problem with the ships wiring. Supersaw safety footswitch ceased to function. This was disassembled, lubricated and reassembled

Paleo Lab

Replaced MP3 jack. The old one seems to have disappeared.

Chemistry Lab

Aft microscope ceased to function. Light was replaced. No help. Found a pushed in pin on the DB 15 connector cable. This caused a short and took out the power supply. Purchased 12 IRF640N rectifiers in port. No spares were available on the ship. Found damage to the power source was too extensive. Dave Houpt is looking into purchasing a replacement or upgrading to an LED light source to avoid cooking samples. Cahn Microbalance balancing hoop broke off. Debris was removed and the hoop was soldiered back on. Speaker in the aft end of the lab was too loud for personnel working at the computer station aft. Speaker was re located. Heat Sealer would run on its own. Found the control board with the function switches had some kind of milky residue on it. Cleaned this off with alcohol, checked all components and re-seated all of the connectors. Modified the transformer for the Furnace to meet with ships electrical safety standards.

Thin Section Lab

Trouble light ceased to function. Found all of the insulating material at the base of the receptacle had crystallized and was now a safety hazard. This will need to be replaced. Second Trouble light switch ceased to function. The switch was bypassed and a switch manufactured so you can turn it on and off. Hot Plate temperature became erratic. Attempted to clean the contacts on the switch and bent the temperature arm in an attempt to stabilize it. It was still erratic. Replaced the switch.

X-Ray Prep Lab

Rock Crusher. Oiled bearings, cleaned switches and adjusted tension on the belt.

Rad Van

Airflow was tested on the vent hood and found to be low. Oiled fan motor on the vent hood. Fully removed shipping covers. Air Flow is now satisfactory. Installed a temporary vent line to exhaust the fume hood overboard.

Core Reefer

Ran Power to the Glove Box in the core reefer.

Gym

DVD player ceased to function. Re-set the TV to run from the DVD player. Explained to the crew how to set it up. Conducted routine maintenance on the Treadmill. Cleaned out the dust bunnies and oiled the bearings.

Science Lounge

Batteries to the remote controls evaporated. These were replaced. Found the Popcorn media player had no hard drive installed. Appropriated a 750G hard drive from IT. This should hold about 75 movies. Went on line to download the run program and installed it on the machine. Downloaded several movies so the machine would have some movie choices without installing an external hard drive. Re-installed LD player. Optoma Home Theater Projector ceased to function. It appears that a power spike may have taken out the power system. Sending back to IODP to be repaired again.

U/W Lab

Trained on Fathometer operations and Magnetometer operations with Underway Technician.

Fantail

Deployed Magnetometer. Removed up/down limit switch for the cable on the crane. Greased the crane. Cleaned off rust and wrapped exposed solenoids in Grease Tape. The crane was prepped and painted by the Trans Ocean crew. Applied grease tape to all electrical penetrators on the Starboard Reel wind.
Port Reel Wind: Cleaned and greased the slide bars and chain drive. Greased fittings. Applied grease tape to all electrical penetrators.

MGE UPS Systems

Comet 40-50 kVA UPS- Machine is located in the Koomy Room. Unit is giving a Communications failure indication. The Transocean unit display assembly failed the last trip. Unit worked, just had no indication. This was fixed at the port call by company rep. E-mailed the company for information on how to proceed further. Nico (Chief Electrician) recommended leaving it alone for now.
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PUBLICATIONS SPECIALIST

Jamie Smidt

Library

No books or DVDs were added to the shipboard libraries during this expedition.

Summary

Provided administrative, graphics and publications support at port call and throughout the expedition. Forty-two holes at seven sites were drilled, with total core recovery of 1168.81 meters (88.4%). Prepared barrel sheets for approximately 121 sediment cores from 32 holes and 73 hard rock barrel sheets from 3 holes (7 holes were drilled with no core recovery, for the purpose of establishing basement) and comprehensive core summaries/core recovery graphs for select sites. Assisted staff scientist, co-chiefs and science party members in creating graphic reports and troubleshooting various software issues.
Was responsible for all expedition paperwork, including documents for French Polynesia and New Zealand customs/immigration, wireless devices, communication policy, photo release form, copyright form, etc. Worked with the IODP travel and conferences administrator to coordinate hotel arrangements for the end of the cruise. Collected, organized and tracked all text, tables, plates and figures for the expedition volume.
Served as social events coordinator; planning birthday celebrations, holidays, parties, contests, expedition logo design, etc. Wrote weekly captions for each of the scientist/technician photos that appeared on the expedition family and friends web page.

Strater Update

This is the first expedition in which Strater 2 was used to create barrel sheets and other core graphical reports. Strater 2 is a vast improvement over the former version of the software. Several issues specific to IODP were addressed and new features were added allowing greater customization of scheme patterns/symbols and great flexibility in the layout, creation and printing of barrel sheets. These modifications make Strater 2 easier to use and ultimately, easier to learn to use. Encountered problems were quickly resolved, often with prompt help from Golden Software technical support.
One three-ring binder of barrel sheets was placed in the core lab and one in the science office. Both were updated as new cores were described. This nearly instantaneous production of visual core descriptions ensured the data was complete and was immensely helpful to the staff scientist and co-chiefs, as they referred to the binders to write reports and daily/weekly science updates.
Eighteen new symbols were created within the LithSymbol5 font set, at the request of the science party.

Special Projects

The yeop folder was reorganized to allow for easier access to important files. All the Strater information is in one folder and outdated Illustrator, Excel and Word files were updated to newer versions of the software.
Instructional manuals/tutorials for Kaleidagraph were added to the yeop folder, as well as a quick guide for communicating with Golden Software technical support and a detailed crash report of a common Strater 2 problem. Email communications between Golden Software and IODP technicians were also archived for future reference.

Thin Section Lab

Jacob Virtue

Summary

There were 63 thin section requests of basalts fresh and altered, cherts and chilled margins. Routine maintenance and cleaning was performed as necessary and at the end of the cruise

Special projects

None

Problems encountered

ET replaced switch contacts in Thermolyne hot plate.
One Magnetic wall lamp was decommissioned by ET, and the other had a faulty switch which was replaced by an external switch.

Miscellaneous

Epoxy bottles where cleaned and refilled on the 25^th November 2010.
Buehler PetroThin machine was connected to external vacuum.

IMAGING LAB

John Beck
Expedition 329 was a fairly typical cruise as far as imaging was concerned. It consisted of checking section scans, PR photography, and close ups. There were more close ups than anticipated and had I known the quantity I would have moved the close up shooting table back to it former location for reasons that have been discussed previously. Microscope use was minimal. Only one of the fluorescence scopes was used on a regular basis. The power source for one of the fluorescence scopes is being sent back for repair.
There was an update for the Hasselblad cameras that was downloaded and installed on both cameras. One camera when turned on gave a " Will not calibrate " message. I contacted Hasselblad service and after attempting several fixes it was determined that the camera back and body would have to be returned to Hasselblad. When attempting to use the other Hasselblad I noticed a large irregular soft focus area. On removing the back I found a large smear of some type on the IR filter that covers the sensor. All attempts to clean this failed so this back is being returned also.
The Epson printer, which had been left on by whomever used it last, had several of its print heads clogged. It took several power cleanings to correct this problem at the cost of a substantial amount of ink. Scientists wanted to print core images to the core lab color printer but the color was not correct. I produced an ICC profile for that printer and installed it on the computer for the core section imager. A profile was also produced for the plotter in the users room. This was done because Ocean Leadership had requested that Joe Monoco ( Teacher at Sea) have big prints made for port call tours. Since Joe knows nothing about how to do this I am doing for him.
A new Canon Video camera was received this cruise and it has been tested. As of yet no video has been shot this expedition.
The lighting on the close up station was put back to the standard copy stand configuration. The strobes on the close up station at times still only fire one side. This is very inconsistent. I did not change out the power pack because it happens so infrequently but you have to pay attention. I did not use the data entry at the close up station. I find it much easier to shoot to a card and process the images in the imaging lab and then up load later. Initially there were problems with the uploader but Zenon got this straightened out after several e-mails to the beach. Zenon has uploaded the close up files.

All other camera gear functioned with no problems to report. It is worth mentioning that this is the second cruise that we have run low on AA batteries.
There will have been 1016 section scans reviewed. There were several instances of multiple images of the same section and several of different sections having the same name. These were all identified and corrected. There were 82 close ups shot.

UNDERWAY GEOPHYSICS LAB

Kristin Hillis

Summary

Magnetometer deployment and data collection on first full, operational cruise was successful on all eight transits.
A site survey was completed at U1368, with the bathymetric software and thermal printer working well together.

Data Summary

Expedition 329 consisted of 8 transits, 7 sites, and 40 holes.
Transits:Tahiti → U1365
U1365 → U1366
U1366 → U1367
U1367 → U1368
U1368 → U1369
U1369 → U1370
U1370 → U1371
U1371 → Auckland, New Zealand

Sites/Holes:U1365A/B/C/D/E holes
U1366A/B/C/D/E/F holes
U1367A/B/C/D/E/F holes
U1368 A/B/C/D/E/F holes
U1369A/B/C/D/E holes
U1370A/B/C/D/E/F holes
U1371 A/B/C/D/E/F holes
WinFrog 1 was the primary computer used to collect navigation data. The 3.5 kHz was run on all transits.

Equipment Performance Summary:

Trimble/Ashtech GPS

The Trimble was the primary GPS used for the duration of Expedition 329. No problems were encountered. I believe a new GPS (to replace the Ashtech) was ordered prior to SPG, but did not make the shipment to Tahiti, so it may arrive in Auckland.

Gyro

The gyro from DP was used throughout the cruise without any problems.

WinFrog

WinFrog 1 was the primary computer used for Expedition 329. One crash was observed due to someone improperly closing the software. A cfg file was reloaded.
Something to note, I have not been able to display the magnetometer data on any computer but the master. On the smart remotes, I have enabled that field in the vehicle text, but it always reads '0.00nT.' I even installed a smart remote on the seismic computer, thinking perhaps I was configuring something improperly and would start from scratch. After setting it all up, it still reads 0.
We attempted installing WinFrog on the spare computer in the LO office, to run as another smart remote and to test compatibility with Windows 7. The software would not complete the install, recognizing it was a newer platform.

Bathy 2010

Bathy 2010 provided accurate depths throughout the cruise. It also worked well for the site survey we did for U1368. Enabling a thermal printer and marking events went well. We were also able to capture screen shots of the bottom zoom on the different lines of the survey to print out for the co-chief.
 

Magnetometer

This was the first complete, operational cruise for the SeaSPY. It was deployed on all 9 transits and functioned well. I have created a SeaLINK cheatsheet, which basically list all the steps for powering up and powering down the magnetometer on one page. As I was not always on-shift when it was deployed or retrieved, it proved helpful for the other techs as a quick reminder.
We did experience a problem with the GPS requiring a re-sync at midnight GMT. This was mainly a problem on the second and third transit. I contacted Mike at Marine Magnetics with screen shots of what was happening. He said they would try setting up a long term test, as most of their testing is not done over multiple days, and get back to me. I have not heard the results of the test, but the problem has not occurred in the last few weeks of the cruise.
Remote desktopping has also been enabled on the Seismic computer. The IP address to enter is 165.91.72.123. As we were not holding Underway watches, this allowed the software to be monitored from the LO office at midnight GMT. We also had the poop deck camera swing to the direction of the fantail crane, so we could keep an eye on it via the TV system.
Roy put a new 14'' block on the crane that hangs horizontally and allows deployment and towing to go very smoothly. The cable can be fed through the block, attached to the towfish on the deck, the crane extended out a little and the towfish placed over the side with no worries of it banging the hull. After deploying and retrieving it so many times, this was found to be the optimal way.

EPC Recorders

The recorder was used on a site survey for U1368. The site was in a shallow sediment pond and we wanted to ensure we were in the proper location. Printing and eventing from Bathy went well.

VSP

No VSPs were conducted on Expedition 329.

Items Ordered/Received

Items ordered during 329:
I've asked the Lab Officer to add to the cruise requisition a spare set (three total) tail fins and an extra nose cone for the magnetometer. As of the end of this cruise, the spare nose cone was not deemed necessary but two tail fins were ordered, to give us one complete set.

Misc

Karen Graber requested that I redo all the screen captures for the WinFrog Cookbook. An Ashtech Evaluate/WinFrog connection cookbook was also created.
Requisition made:

• Requested that a file drawer be found at TAMU surplus and brought to the ship so we can have a central place to store our documents, personal items. This will especially come in handy during periods of rough seas.

Data backups:

• data files for the Expedition were copied to:

\\Vol1\data1\EXP329\1.5 Ops Navigation
\\Vol11\data1\EXP329\1.6 Ops Bathymetry - PDR pulse depth recorder

FANTAIL

Roy Davis & Kristin Hillis

Summary

Navigation and Bathymetry data was collected during all transits. The magnetometer was deployed on all eight transits and data was collected.

Special Projects

Marine Magnetics suggested using at least an 8'' block, so a new 14'' block was added to the crane to allow for better cable handling and to avoid sharp bends in the cable.
The fantail crane was painted during the expedition.

Problems Encountered

None

Miscellaneous

The leads for towing the gun which where hanging on the port side were stored in one of the grey plastic boxes on the fantail so as to get them out of the weather.
The switch for preventing the crane from two blocking was jumped inside the rewind reel box for the switch cable. The switch is not used, as the winch cable is not run thru the main pulleys.
Two spare tail fins were ordered for the Maggie. We had one and needed 3 in all.

SYSTEM MANAGER'S REPORT

Matt Mefferd and Mike Hodge

Summary

During Expedition 329 the Information Technology infrastructure was consistently operational with the notable exception of an incident during which files were lost from a folder in one of our Novell volumes. There were no major hardware outages. There were some changes to the computer systems, many of them involving the automation of certain cleanup and other procedures. A very active Teacher at Sea on staff engaged in ~25 successful educational video conferences.

Special Projects

1. In order to provide space for ship tdb on host jenny, the disk drives were un-mirrored. The layout of disk c1t0d0 was left essentially as it was and c1t1d0 was reconfigured to provide 4GB additional space for swap and a 143GB partition mounted on /u03 for use by Oracle. The Oracle configuration on jenny was otherwise left untouched. A recommendation was made to purchase a Solaris file system iDA and Oracle iDA (CommVault) for jenny.
2. As opportunity presented itself, updated PC workstations to McAfee v8.70i. Not all workstations done due to system usage.
3. Embraced Skype for Video Conferencing sessions this expedition as implemented on prior expeditions. Noticed bandwidth consumption minimal and Skype session traffic blends in with other traffic. Held multiple VC sessions each week with no interruptions to regular internet users. Worked with Iocom on their new Visimeet software. Testing and evaluating ongoing.
4. An Augmentix laptop and Zebra barcode printer were set up in the reefer for this expedition in order to facilitate the core sampling process. This was due to the large volume of microbio samples and the requirement that they be handled in a cold environment.
5. The / filesystem on etna and pico have had a tendency to fill up due largely to the fact that they are both running CommVault media agents and the backup indexes are stored in /opt/galaxy/MediaAgent/IndexCache. To resolve this, additional SVM mirrored space was configured on remaining slice 4 (100 GB) and mounted as /space. The contents of /opt/galaxy was moved to /space/opt/galaxy and /opt/galaxy is now a link to it. This space could be used for other things as well.
6. Margaret noted that the Thermcon data files are created in unicode but TKgraph program can't open the files to process and display them unless they are in ansi format. Margaret is working with the vendor (Teka) to fix this bug, but meanwhile a couple of scripts were created that together will recursively convert all the specified files in a directory from unicode to ansi format. All the Thermcon files generated on EXP 329 have been converted to ansi and loaded into the asman catalog and there has been discussion of using these scripts to convert the data collected on previous expeditions as well.

Problems Encountered

1. Data Center Aux AC system – main fan motor for Aux AC system failed. Transocean replaced the motor, they have a spare one arriving for Exp330 portcall.
2. Sent parts order in for DVD optical disk and CPU heat sink from ET shop (PC51588). Put parts from spare PC51546 and are to be replaced on Exp330.
3. Motherboard on PC51586 Pub's Yeop PC failed. Unit to be shipped to shore for repairs. Need to purchase memory for it.
4. Swapped out Enterasys D2 POE switch in LT50 data center, packaged original for shipment to shore. Installed unit had an incorrect internal serial number which caused a licensing issue with the unit.
5. Discovered scientist's registration expiration, removal and cleanup set to 30 days which causes the scientists to have to re-register their personal laptop with Network Access Control (NAC) server, changed to 75 days.
6. Discovered no adequate tools for Novell to look at or manage open files by the users, especially Apple users.
7. We had an incident where many files were lost from the "Expedition 329 Reports" folder on Uservol. Inasmuch as was possible the files were restored from backup and a case was opened with Novell support. Backline support was brought in, diagnostics on the storage pool found no problems and nothing in the AFP, NSS or any other logs shed any light on this matter. The case remains on hold. Fortunately, the issue has not come up again. During this process it was discovered that the AFP log file on the node that was hosting Uservol had grown to ~1.5GB, possibly causing or contributing to this problem. The log file was truncated and set on a rotation schedule to control its growth in the future.
8. MGE UPS encountered a Communications Fault error message. It lost front panel and web interface access. Worked with the manufacture and Transocean to remedy but, unable to do because of hardware failure in the UPS. Transocean working with the shipping agent in Auckland and a local New Zealand vendor to arrange repairs during Exp330 portcall.
9. Replaced (failed) ViewSonic monitor 52034 in Science Office with 51506 from spares.
10. Replaced (failed) ViewSonic monitor 52049 in Telemetry lab with 52048 from spares.
11. Discovered Ararat iManager does not run. Fails on startup. Works fine on other nodes.
12. Encountered VBrick software not working on various Mac workstations. Research revealed that it is not compatible with any version of Safari on Snow Leopard or any version of Firefox above v3.6.3. VBrick vendor recommends that we upgrade our current installed VBrick server software since it is about 4 years old. Exp330 MCSs are to do.
13. It was observed that Google search on some of our systems were primarily discovering Canadian websites. This is apparently the result of Google's incorrect redirection, and "geolocation". It appears that Google uses more than just internet registries to determine the "geolocation" of an IP address or address range in order to "help" you out by providing relevant content (or, I don't know, maybe it's just for marketing purposes). Perhaps during the tie-up enough people on 165.91.150.x subnet used Google to check the local Victoria weather or buy ferry tickets to Seattle, etc. that Google reassessed the "geolocation" of that subnet as being in Canada. That may have been fine while we were there, but at the time this problem was observed we were southwest of the Cook Islands. There is a workaround and the problem was reported at the time to Google via their web page which said to expect results in about a month, and the problem does appear to be gone, now. Note that systems on our 165.91.72.* range (servers, MCS workstations) were not effected. We may see this again, especially during the next tie-up.

Technical discussion

GroupWise

• Inbound email size limit set to 5MB on Exp328.
• Webaccess hung several times and had to be restarted.

CommVault

• Moved IndexCache to another partition with adequate disk space. See Special Projects above.
• No issues with CommVault backup software, worked as configured.

Printers

• Black drum failed in Canon copier and required replacement. Noticed that all drums had been in use for over a year and had exceeded 100% usage. All drums were replaced in Canon copier.
• No problems with printers or print services.

Servers

• Encountered several AFP stoppages during the expedition. Each stoppage was successfully restarted.
• There are several notable cases on our Solaris and OES Linux systems where log files have been growing to unmanageable size (e.g., the AFP log noted above) or are being rolled over, but accumulating in numbers and taking up an increasing amount of disk space, ultimately requiring manual intervention to control. We have had occasions where these log files actually filled the / or /var filesystems causing problems with these servers. We have set up log rotation schemes for most of these problem situations, including Oracle (listener.log, sqlnet.log), Tomcat (catalina.out, catalina.log, localhost.log, manager.log, admin.log, etc.) and AFP (afptcpd.log).
• In addition to the log file growth problem, we are having a problem with an increasing amount of space being taken up in /var on the virtual SUN Cluster host web (usually on etna) by the Cumulus daemon, cumulusd. The symptoms of this were noted during crossover prior to this expedition, when /var was found to be 100% full, so we were keeping an eye on it. Until we determine why cumulusd is progressively tying up that space the workaround is to stop and start the web-cumulus-rs resource when /var begins to register as > 90% full.
• Installed and configured a disk space monitoring tool called SMELT on our OES Linux and Solaris systems. It is configured to run every 4 hours and check the disk space usage. If any of the filesystems register > 90% full an email alert will be sent to the jr_MCS email account.
• Raju Elumalai of RCI sent us a sql script that populates an oracle data table with information similar to the old JANUS dboverview. We modified it to set all the appropriate oracle environment variables and check to make sure Oracle is running. It is set to run under the oracle crontab every hour on both SUN Cluster nodes. The data are displayed by a web service that Stephanie built:

http://ararat:8080/jqGarden/lims/esh

• The Tomcat load balancer on web is configured and has been since Victoria. The load balancer is configured to distribute requests for all web services 30/30/30 between rainier, shasta, and ararat, however the web services themselves need to be pointed to the load balancer for service:

http://web.ship.iodp.tamu.edu/balancer-manager

VSAT

• Swapped RigNet loaner Codan radio in aft dome with our repaired radio from Victoria tie-up period.
• Conducted multiple tests on Cisco phone circuits via VSAT equipment due to problems encountered on shore calling the ship. As instructed from shore swapped circuits HWIC-2 and HWIC-3. This appears to have remedied phone access to the ship. No further actions taken this expedition.

Workstations

Pc

• Discovered a Compaq 610 laptop in MCS possession. After conversations with Margaret Hastedt onboard and Kim Lee on shore, this laptop handed over to MCSs. An image was captured of the laptop and it has been reconfigured for shipboard environment as a spare laptop.
• Installed Strater 2 and upgraded to latest version v2.2.351 on designated Strater stations.
• Installed shore based SRA from Expedition 318, captured an image of the system before installation.
• Installed new version of Sea Link magnetometer software on PC51646 in UWGL.
• The new TOC from OI Analytical came with a network card so that it could be connected with PC51450. The NIC was installed in PC51450 and configured with a private network for communication with the TOC. The TOC software has also been installed on PC51450.
• Encountered our first verifiable Microsoft security update that caused a host instrument software to stop functioning. Working with the vendor was able to identify the update and uninstalling it remedied the problem.
  • Update that crashed Ion Chromatograph software - Security Update for Windows XP (KB982802)

Mac

• Discovered various Mac workstations on different versions of Snow Leopard. Observed one workstation at v10.6.4 but not able to install this version from local Apple SUS server. Contacted Lamont for assistance and they remedied the discreptancy. However, Snow Leopard 10.6.5 became available during this process and Borehole IT staff attempted to push it out here, but it was revoked by Apple corporate in the middle of this. The result was that 10.6.4 was not available for auto pickup by workstations, and had to be manually installed. Eventually, v10.6.5 updaters were pushed to the SUS server by LDEO Borehole IT staff and client autoupdates to v10.6.5 are now working.

Network

• Observed possible compatibility problems between NAC and some (not all) laptops running Chinese and German language versions of Microsoft Windows OS. Vendor is working on making their NAC agent more compatible with international laptops. When encountered we have a temporary solution until the agent can be upgraded. However, the overall effect of the recent improvements to the NAC is that the self registration process is much more user friendly and it frees the MCS's to focus on other important tasks during the port call.

DEVELOPERS REPORT

Stephanie Zeliadt, Algie Morgan

Summary

This expedition presented new and unique challenges with regard to label printing, data collection and sampling.
There was major work completed on the new Depth project and the MADMax application as well as to SampleMaster, resteasy-lims-webservices, Web Tabular Reports and Lims Reports/UWQ. A new Advanced Bulk Printer project and a new NGR %K service were implemented to solve expedition issues. There were minor upgrades and fixes to MegaUploadaTron, Excel Uploader, CloseupCapture, resteasy-printing-services, resteasy-asman, VirtualPhotoTable, LIMSpeak, and LIMSOnLine. The WRMSL is in progress but remains ongoing for the next expedition. Work on the GANTRY interface had been scheduled but was not able to be accomplished during the expedition.
Project Summary from beginning of expedition task list:

• Support needs of the expedition – goal met.
• SampleMaster modifications / enhancements – goal met and exceeded.
• Java Balance modified to work with Cahn Balance for Rad Van – goal met.
• MADMAX development – partially met, work continues to merge the .NET main application with the LabVIEW pycnometer controller.
• LIMSOnLine – minor improvements made, more work remains to make this production-ready.
• Source-code management / recovery-path plans – process was refined, documentation remains to be completed – overall goals met and exceeded.
• Change management process – implementation was problematic, still needs work, partially met.
• WRMSL/STMSL rebuild – this project was postponed, Trevor and Fackler have both made significant changes and have the technical knowledge to complete this project.
• GANTRY interface – no work done on this.
• Depth project – implementation complete to modified depth model – goal met.
• Operations Core Tech Report – goal met.
• Automatic Testing – JUnit test cases were implemented for all new service code – exceeds goals.

Algie Morgan experienced laptop memory failure which the MCS's were able to partially remedy by replacing the memory in his laptop with memory borrowed from an older laptop.

Environment Comments

The MCS are to be congratulated on a very quiet and well functioning Expedition. The systems have been up and responsive throughout.

Balance (for RAD Van)

The Java Balance program was modified to correctly interface with the Cahn balance.

SampleMaster

Several changes/fixes/enhancements were made to SampleMaster:

• Changed Sample Table sheet to display and validate against Parent Curated Length (x_length) instead of Parent Observed Length (x_curr_len).
• Changed Core Sheet to display rotary columns and Time on Deck for drilled intervals.
• Added new core catcher types.
• Added example Latitude/Longitude in header.
• Added ability to show tooltips on mouseover of header by adding a description attribute to the sampleMap.xml definition file and added tooltips for the Latitude/Longitude headers.
• Changed Sample Type and Request Code columns on Sample Table tab to be editable drop-down lists.
• Modified print dialog to print the number of copies selected for printing instead of just 1.
• Modified the Options Dialog to open to the currently visible sheet.
• Fixed validation of offsets and added Recalculate Lengths method for piece logging. This replaces the Recalculate Offsets behavior for piece logging.
• Added code to allow new lines and degree symbols to show in spread headers.
• Added a notification that depths have successfully recalculated if manually performed.
• Added new fields on the Hole entry tab for operations data: Spud Time, BHA Length, Sea Floor Depth, Mean Draft, and Bit Information.
• Changed End Drilling Time to match Time on Deck if entered instead of Start Drilling Time.
• Refactored upload code to make it more maintainable and reliable. Removed pieces of redundant and non-functioning code. Includes major modifications to uploading behavior to honor uploading/editing only changed data and all changed data.
• Fixed bug that prevented sections with comments from automatically printing labels.

Depth Project

Implementation of new depth model was completed in the web services and depths are currently being logged and updated in the tables. Viewing of the depths has been implemented in LIMS Reports/UWQ. JUnit test cases for insert/update of depths were added.

NGR %K Project

A new project was started with the collaboration of Maxim and the developers to meet the goal of automatically calculating K, U, and Th concentrations in the cores. A service was implemented, complete with JUnit test cases, to supply the average density over the range of each of the detectors in the NGR for calculating these concentrations. Maxim completed code to determine the %K based on the average densities and supplied the developers with these data, which were then manually uploaded with the Excel Uploader. More work remains to be done to make the process automatic.

Megatron Uploader (MUT)

• Modified the CORIENT class so that it would properly upload the data and associated raw files. This change was required because the Core Lab tech modified the software that generates the data and files.

Resteasy-Lims-Webservices and WTR Reports

• WTR – Core on Deck: added unit names to report fields.
• Modified cancel webservice to cancel all child samples/tests/results.
• Added code to automatically update x_sect_offset on change of x_offset
• Fixed recovery calculations to not include drilled intervals.
• Added new depth project implementation to the logging/update webservices.
• WTR – all reports: added sample name as a search parameter.
• WTR – xsl scripts: modified to use "top_offset" and "bottom_offset" results if "offset" is not present.
• WTR – Core Tech Summary: added tables to show rotary and piston core sheets separately in addition to combined.
• WTR – Core Tech Summary: modified to show new information entered on hole.
• WTR – Core Tech Summary: changed Grand Totals to Site and Expedition Totals.
• Modified logging/update services to automatically update the piece halves when a parent piece is changed.
• Added JUnit test cases for all new feature implementations.
• Modified WTR and logging services to remove rounding to the nearest cm and instead to the nearest mm.
• WTR – all reports: changed column names to be constants instead of static fields that were being modified, causing incorrect columns to display in the reports occasionally.
• Added automatic calculation of water depth on log of seafloor_drf and mean_vessel_draft
• Fixed bug in number formatting causing fields with 0 decimal places to be formatted with a trailing decimal point.
• Removed deprecated SUMADVANCE and SUMOBSERVE entry.
• WTR – Curator Summary: Modified to eliminate piece halves from total counts and added new experimental tables to show unclassified samples.
• WTR – Curator Summary: Removed "(none)" entry from tables.
• WTR – all reports: Fixed bug that didn't write close tags for table/div nodes, causing inconsistent displays.
• WTR – Hole Summary: Changed SQL query to outer join to allow holes with no ORIGDEPTH/LATLONG to display.
• Implemented new utility method isNumber and replaced local isNumeric method with it.
• Modified result logging to ignore canceled/rejected results when selecting the next replicate number/result value.

Java-Utils

• Moved java-utils project back to proper location in svn.
• Added isNumber utility method to determine if a string is a number or not.
• Added JUnit test case for isNumber method.

Resteasy

• Deployed a new version (2.6) which appropriately returns filenames with spaces in them.

Resteasy-Asman

Modified to use a new version of resteasy (v2.6) which appropriately returns filenames with spaces in them.

Resteasy-Printing-Webservices

• Fixed bug in printing services that would cause printing to fail if a text id or label id was supplied instead of a sample number.
• Fixed a bug that caused a label to print 3 times for each sample because the label id/text id/sample number was passed 3 times.
• Fixed error in label variable replacement routine and removed unnecessary code.
• Fixed casting error when passing a copies parameter to specify number of copies to print.
• Added new label types and handling for new variables.
• Added JUnit test cases.

Advanced Bulk Printer

The Advanced Bulk Printer was created to meet the unique label printing requirements for this expedition. It is a new interface for the Bulk Printer project that allows users to print information that is not currently in the database, such as intervals for sections labels and labels for sections that have not yet been uploaded in addition to the ability to specify a number of labels to print.

Excel Uploader

A large number of third party instruments were used this expedition, requiring much use of the Excel Uploader application and the need for the following enhancements:
Added "Analysis Instrument" column to sheet to allow specification of an instrument when uploading data.
Added another view that allows entry of Site, Hole, Core, Core Type, Section instead of Text Id, which was required for the data upload needs of this expedition.

WRMSL Logger Development

It was decided by Algie and Maggie Hasted, the Core Lab Tech, to postpone this project when it was discovered that implementing this required not only installation and modifications to the LabVIEW code, but some rewiring to handle a new track-motion system.

Data Issues

Most of the data issues were related to the MAD process. Several errors in volume capture were associated with problems with the Pycnometer and Balance container handling as discussed in each of those instruments sections. There were also the usual assignment errors from both Pycnometer and Balance results being assigned to the incorrect sample or test.
Several of the data issues were related to the scientist's decision to run the MAD process repeatedly on the same samples. This required canceling and resetting the various tests and results multiple times.
The data cancelation process was an issue this expedition. Often, cores were run through the WRMSL track multiple times without canceling prior runs which led to a problem calculating average densities for the %K project. This highlights a need for a well-defined process for and/or tools to aid in the effort of canceling data.

THERMCON

The Thermcon up-loader was modified to correct errors which occurred when the "normal" process was not followed. This normal process was shown in the documentation, but was not identified as the ONLY way that the software worked. The normal process is to (1) include a name in the base section of the TEKA program AND (2) to upload the results to the database immediately upon completion (before running another test). Deviation from this process caused the up-loader to (1) corrupt the data files through name/value substitution and (2) reassign all results to the last sample tested. Both issues have been corrected and a new up-loader released.
The following changes were also added to the Thermcon uploader:

• The version displays in the title bar of the application.
• Fixed an error in the calculation that occurs when the .erg files are not written by the Teka software.
• Added a test method to compare the calculated thermal conductivity values to the Teka software generated ones.
• Added a result instrument to the results to differentiate between uploader calculated thermal conductivity values and Teka software calculated ones.
• Modified to only upload the average and standard deviation for the first replicate.

MADMax

This is a new application, designed and built during Expedition 327. It facilitates the process of measurements known as MAD (Moisture and Density) in a single application (rather than three or four separate applications previously used). (See Developers Tech Report for Exp. 327 for a full description of the application.)
It should be noted that at the time of this writing, MADMax is not yet complete. The individual components; MADMax .NET application, and the LabVIEW PycModule are built and work as designed individually. There was significant difficulty in getting these two modules to work together, despite weeks of effort and considerable communication with developers on the shore we were not able to complete the integration of the LabVIEW pycnometer module with the main MADMax application. It is possible that the project to combine the two components may be complete by the end of port call in Auckland. Otherwise it will remain for the developers on Expedition 330 to complete.

GANTRY interface

There was not sufficient time to finish work on this system. New code was developed by Trevor and is available for testing, but has not yet been deployed or integrated with the existing system.

Virtual Photo Table

• Added the ability to change the processing interval from the GUI.
• Modified to cancel the previous COREPHOTO analyses on successful run.
• Added "Seconds until next process" to the GUI.
• Added start time to the GUI.

LIMSOnline

There were minor enhancements to LIMSOnline, mostly to add analyses which LIMSOnline can be used to view and edit. Considerable work remains to be done on this application before it will be ready for full production.

LIMSPeak

A new template, "NGR, %K", was added to LIMSPeak which shows the NGR data plotted next to the new %K values uploaded this expedition.

Application Deployment & Recovery

During the last tie-up period in Victoria, considerable progress was made in implementing a new software deployment process. The main components of that plan include reorganizing the subversion source code repository and defining a set of conventions for the developers to follow when deploying IODP software projects in the production environment.
As part of the process, all deployed code must be built on the "build" server (a computer outfitted with a full set of source-code compilers and IDEs for building and deploying all in-house software) prior to deployment. The complete process for deploying IODP software in the production environment is:

• Modify and thoroughly test code locally, including writing test cases where applicable.
• Check all code and dependencies into subversion.
• Increment the code version and tag as that version in the release directory in svn.
• On the Build Server:
  • Check the project out from the appropriate tagged release version in subversion.
  • Build the application with the appropriate IDE or build tool.
  • Deploy the application using the appropriate deployment process.

During this expedition Algie and Stephanie refined this process and instituted a backup and recovery plan by adding the following step as the first step on the build server:

1. Make a backup of the existing built version in production.
   • • For web services, copy the war file to the build server.

     • For client apps, create a Recovery
       [version] folder on the server and copy necessary files to that directory.

Each deployed package must have its own recovery folder, and any files needed to quickly restore a previous version must go into this folder. Both developers on Expedition 330 employed this recovery plan and found that it significantly reduces the anxiety of deploying new versions of any software and reduces down time due to introduction of unanticipated bugs with new features. The combination of having accurately tagged versions in the subversion repository and a recovery folder that makes it possible to quickly restore a previous version of a software package also satisfies a major requirement of the new change management process.

Microbiology Lab

Nicolette Zeliadt

Summary

Six Microbiologists participated in the expedition and free counter space was severely limited in the Lab and the small main aisle layout of the chemistry lab had lots of wasted time dealing with the heavy traffic flow.
.

Equipment Performance Summary:

• The cold room was used extensively for O2 analysis.
• The glove box had limited use but performed without problems. Some comments were made for a better vacuum evacuation system in addition to the scrubbers.
• The GC2. This is being addressed on shore by David Houpt and needs further attention. One of the issues was that the auto sampler was not functional.
• The furnace was used for sterilization and had heavy use by chemists and ICP preparation such that an additional furnace would have proved useful.
• The laminar flow hood was used extensively by all Microbiologists and was set up with a pedal controlled "fuego" gas burner "torch" fueled by camping style propane canisters. Initially a fire watch was used but eventually deemed unnecessary.
• The PFT injection pumps in the pump room were extensively used. They were flushed with alcohol at the end of the leg.

Special Projects

• The reefer was set up with the glove box and fitted with nitrogen and M-bio gas but only Nitrogen was used. It was noted that the low flow regulator from the cold room was moved to the reefer and would also have been useful to keep one in the Micro-bio lab. Extensive sampling was performed in the reefer.
• The laminar flow hood was set up and operated temporarily in the Thin Sections Lab and equipped with a torch for sterilization.

Problems/Concerns

• Scientists expressed a desire to have the anaerobic chamber outfitted with a vacuum.
• The 50 mL centrifuge tubes (Falcon conical tubes with blue caps) that were in stock did not withstand centrifugation at high speeds (4,000 rpm) routinely used by microbiologists. The Corning tubes with orange caps did not have this problem, but our supply of these tubes quickly ran out.
• The low temperature incubator (reefer) located in the center on the starboard side did not reach a low enough temperature (20°C) needed by one of the microbiologists. The ETs worked with this previously and have been notified of the issue.
• Small cryovials (1-2 mL) needed for long-term preservation of bacterial cultures were never ordered.
• One scientist pointed out a wasteful use of supplies (such as gloves, aluminum foil, and autoclave tape) by other scientists on board, and would have liked to have had a an initial, brief training session for all scientists on more efficient use of supplies.
• There were not enough pipetmen pipettors on board for everyone to use, and some scientists were concerned that the pipettors were not calibrated recently enough.
• A UV light bulb needs to be installed in the laminar flow hood for surface sterilization of materials.
• The microbiologists would have liked to have more gas burners available to use because these burners were in heavy use and frequently many of them needed to use the burner at the same time. They also would have liked to have a dedicated "clean" bench for this process.
• In the Micro Bio Lab hard rock samples were smashed with a piston crusher (hammer power) in a stainless steel "flame sterilized" box. This was quite noisy and a special smashing station with a heavy base but with dampening feet of stiff rubber would prove useful in the future.
• Heavy use of Denatured Ethanol (includes mixture of hexane, toluene, methanol, ethyl acetate) for sterilization had many Microbiologists complaining of headaches.
• The swing centrifuge located in the paleo prep lab did not have the original equipment micro centrifuge tube insert and a temporary one had to be made of paper.

Biology Lab Van

Roy Davis

Summary

The Biology Lab Van for isotope work was loaded in Victoria, B.C. It was placed on the Focsle deck just forward of the moon pool on the starboard side. Connections for electrical power, phone, fire alarm, and computer network were run. Wipe tests of the complete lab were done once a week during the Expedition. Log Sheets were maintained in the lab for the isotopes used. Lab liquid and solid lab waste were stored in the locked van at the end of the Expedition awaiting removal at a later port call. The unused isotopes were locked in one of the incubators till they will be shipped off at a later date. All in all the lab functioned well with no major problems.

Special Projects

An exterior sink was built and placed near the entrance to the lab. The exterior sink was installed with the idea in mind to keep the use of the sink in the lab to a minimum. The labs sink drains to a holding tank, which is tested for contamination. If the tank is found to have contaminated waste it is pumped to a plastic container and saved for removal as waste. The anticipated handling of muddy cores in the bio lab van did not happen. The cores were sampled in the hold reefer and only clean samples were brought into the van. This helped keep the van free of mud and liquid waste byproducts.
A Nitrogen gas bottle was installed it the room of the van housing the vent hood. A Chan Balance was installed for the use of the scientists using stable isotopes. Software for running it was installed on the laptop computer running the scintillation counter.

Lab Operating Procedures

Protocol of Periodic wipe test for the Radiation van

A thorough wipe test was conducted every week. A detail map and correspondent check list can be found in the Radiation Van Log binder in the van. The purpose is to check for any working area that is subject to contamination. The drain tank test was never conducted due to lack of usage of the sink.
Two sets of log sheets were generated.
One log sheet was for personal post work checking. This is a simple wipe test on the worker after they have finished the handling with radioactive material, and before they leave the van. Five wipes were commonly done, these includes sleeves of the lab coat, counter top surrounding the working area, and bottom of their shoes. This is to ensure the contaminant, if any, does not leave the van.
The second is the RAD disposal log sheet for each individual RAD source. It includes the type of isotope, the compound form it's in, batch number, catalog number, strength, and volume (in ml). This is the official disposal form submitted to TAMU EH&S the end of the cruise.

Handling of Samples containing isotopes

When the freezer/incubator was full with the inoculated samples a wipe test was performed on the samples before these samples were taken out of the rad van. An average of 6 wipes were done on the outside of and around the opening of the samples bags, and also inside the upper side of the Ziploc seam (with the bags sealed). These bagged samples were also sealed inside vacuum seal bags. These sample bags, once proved clean were then transferred to refrigerated or frozen storage.