This past week I implemented a system that can go through Dorado data and find rising and falling temperature fronts. The next step is to apply it to salinity, density, nitrogen, and chlorophyll data to see if it works equally well. Once that is accomplished I will be integrating the results from all of these different types of data to generate a (lat, lon) range for where the upwelling front most likely is, as well as a confidence score to reflect the system's belief in its results.

 I also went out on the Zephyr on Tuesday for a Dorado drop-off. I did not get sick, but felt a little queasy at times. Given that I felt queasy the rest of the night, I suspect it may have been more related to the orange chicken I had the night before than to the boat ride itself. Sadly, the Steve Rock cruise on the Lobos was canceled. Hopefully it will get rescheduled.

Another good week here at MBARI. I really feel as if I am falling into a stride and becoming more comfortable in my new surroundings. The weeks are flying by already, so there is already lots to accomplish in the next 8 weeks!

This week involved a variety of things, including:

Monday- the Wave Glider ASV parts came in, most importantly the payload (the controls drybox which holds our instruments). Myself and Chris Wahl (an Engineer part of the BOG) discussed the best ways of moving forward. I met with Heather Kerkering (Shandy's mentor) and Shandy for a presentation about CeNCOOS and the different initiatives that program is involved in. I also began to look over the 1,000 pages of documentation that came with the Wave Glider. Just some light reading!

Tuesday- I resumed reading Wave Glider documentation. I went to Francisco Chavez's talk about CANON as part of DOEST day and I also caught the tail end of Heather Kerkering's talk about CeNCOOS. During the afternoon after reading most of the documentation, I realized it would be effective to learn SolidWorks to accomplish my project goal of integrating MBARI's OA sensors into the Wave Glider. I started the SolidWorks 2008 tutorials.

Wednesday- Went on the John Martin during the morning. Was somewhat of an uneventful cruise, however some water samples were taken for testing levels of Cadmium at different temperatures, salinity and chlorophyll levels. Was back on shore by noon. I resumed learning the SolidWorks program and measured the dimensions of the payload so that I can eventually design the payload box in SolidWorks.

Thursday- Installed SolidWorks 2011 and began new tutorials. Scanned our database for SolidWorks drawings that are applicable for my project and consolidated into one folder.  Reviewed notes on Wave Glider documentation and discussed next weeks goals with Chris. Leave for Mississippi for a wedding tonight and return on Sunday night.

Next week- We are still waiting on some answers from Liquid Robotics about the Wave Glider, so once we have reply we will be able to take some big steps forward. For next week I hope to start putting instruments into the Wave Glider payload via SolidWorks in order to make sure all of the instrumentation will work. Also on Wednesday I will be one of the intern's giving a brief talk to the visiting high school students.

This past week I met my mentor Shannon, who is really great, and got started in the lab. I extracted DNA on several samples of Tevnia tubeworms that were collected from various latitudes along the East Pacific Rise (EPR), and ran PCR for those as well as several other samples that had previously been extracted. I got good results for the mitochondrial genes COI and cytB, so I purified the PCR products and they are currently in the beautiful sequencing machine Lola.

I also attempted PCR for a few samples with several nuclear gene primers, but got no results, so I am repeating those reactions today with a different program on the thermal cycler. For these genes, we are starting by looking at the two populations that are furthest apart, because those are theoretically supposed to be the most different, and so that would give us some idea of the variation throughout all the populations along the EPR.

Next week I will hopefully be analyzing sequences if the results are clean enough. I also hope to get the PCR for the nuclear genes working, so I can get those sequenced and analyzed as well. If not I will likely extract DNA from more individuals and repeat this process for the mitochondrial genes while we troubleshoot the reactions for the nuclear genes.

This week I worked on more aspects of the Deep Sea Guide layout, mostly formatting it to make it look better (IMO and Brian agrees). I also went through a lot of different pages to try and catch any bugs in the programming and found a couple.

On Tuesday I went out on the Lobos with Liz; I felt sick a couple of times but managed not to get sick. Sleeping helped a lot, as did eating even though it felt like the last thing I wanted to do! It was a very long trip out to the FOCE dive site. We saw a few small schools of dolphins and a couple of humpbacks in the distance. They were going out to fix two of the chains that had come off the gears on the fans, and it ended up being very difficult. If I remember correctly, there were problems with the cameras and it was very difficult to keep the tool steady when the boat rolled, so many times the tool would miss the chain. They did end up fixing both of them. Then, just as we were about to start home, we got the news - one of our engines had broken, so we had to limp home very slowly. While we were out, we also saw a humpback that had gotten tangled in a crabpot and couldn't get the pot and the attached floaters off of it! It was really sad and we wanted to dive in and help it, but no one had a wetsuit. So we got home very late and missed the DOEST reception, which was a shame.

Today I am starting to write real code, instead of just changing the layout, in order to re-enable the Image Search page on the DSG (the group originally decided to delete it, then changed their mind when they realized it could be useful). So for the next couple days, I will be working on the code to get the Image Search working better than it did before. Next week I will finish the Image Search code and hopefully start working on a page of my own, once we figure out exactly what that is going to be...

On Monday I was out on the Lobos with Liz to charge up FOCE with some CO2 for future enrichment experiments. I spent the first 2 hours pretty much unconscious (totally missed the whales!) but was feeling okay once we made it on station. I spent most of the day sat in the ROV control room asking inane questions ("what does that button do?") and generally finding out how FOCE works and what it is intended to do. After filling up the CO2 tank we swung by the main MARS observatory, the central hub idea for adding experimental modules (like FOCE) is really cool.

Back on dry land I have been analysing the outline data from the SoCal canyon dives. The canyon data clusters really nicely and separately from the dives in the basin and on the slope. One hurdle I have come across however is that there is a very significant difference between the 2005 dives and the 2010 dives. I am currently trying to determine why exactly this is but is most probably tied to observer variation, water clarity, and differences between HD and SD footage rather than due to inter-annual variability. I'll be going through all of the videos for a more detailed run through with VARS and am also currently cleaning up the data to account for any variation caused by differing levels of taxonomic classification.

While going through the videos I will also be classifying sections into macro-scale habitat groupings as thus far I have only been comparing at the mega-scale (between canyons) and would like to further examine the effects of substrate and depth.

My life achievements this week include opening a US bank account (thanks to a super-efficient bank-lady) and getting my jacket shipped from Phoenix, AZ after a nice person handed it in to lost and found.

Next week I will hopefully be in the digital lab for the majority of the time to get a handle on what could be causing the discrepancies between years and then come up with a way to address this in future analysis.

Over the last week I have been to several meetings, done some data analysis, read about ocean acidification, and worked on defining my project plan. Monday, Tuesday and Wednesday were spent learning about CeNCOOS, about MBARI, and about the role I will play between the two. This morning has been entirely taken up with plotting data from two Ocean acidification moorings deployed in Northern Monterey Bay. The moorings are measuring pCO2 in the water and the air , and salinity and temperature. I'm looking to see if I could use that data to predict oceanic CO2 from a physical variable. So far so good; pCO2 in the ocean seems to be somewhat correlated with temperature and salinity. The next step will be to research other peoples science and see if my correlations match theirs. All of this is heading towards being able to predict ocean pH from something like wind strength (wind = upwelling = salty cold water = acidic water).

On the CeNCOOS side of my project I am asking questions about who needs to use this data, how they want it communicated to them, and if there are any products CeNCOOS could provide to the public. I'm concentrating on aquaculture and shellfish fisheries, and the ramifications of current and future ocean acidification. In the next week I will ask lots of people lots of questions about shellfish, aquaculture, and acidification. Lucky me, the week after I will go to a workshop with my mentor in Orange County , to learn about how all of things work together.

 I'm loving my project, really enjoying MBARI, and learning a lot from my mentors. I have trouble not thinking about work when I go home! 

Well it is the second week.  I feel the environment here and getting more comfortable with it. Think now I'm more comfortable with the climate. But I miss sun light a lot.

On Monday, I went to moss landing marine laboratory with Josi and observed EM pictures of some of sampled sea urchin test plates. I'm learning lot from Josi.

Unfortunately my second cruise on lobos was cancelled. Hope they will reschedule it.  Rest of this week I spend for reading and literature survey. Also I tried to induce spawning of few urchins but ended with no luck. Finally dissected some of them and it seems this is not the best time period for their spawning.

Also I met my mentor Jim Barry on wednesday , I'm looking forward to work with him on the project.

Open house on this Saturday, I'm so excited.

I can't believe our second week is almost over! I'm feeling increasingly confident with the Raman system and the hydraulics, optics and software required to operate such a complex laser system. I've developed a few protocols for its use, standardized them and begun producing some data sets. I'm traversing relatively uncharted territory, and it's been really exciting to explore the broad potential of the Raman system.

 Monday and Tuesday I went out on the Lobos to refuel and repair the FOCE system. Monday, with 10 foot swells and high winds (that Grant somehow managed to sleep through, impressive) was incredibly rough, and I was down for the count for the majority of our trip. I was really disappointed in myself and was determined to try again, despite the warnings of the Lobos crew. It turns out that Tuesday was much calmer, and I had a wonderful time running around the boat, observing in the control room and eating a lot in the galley - all activities I missed out on the day before. After a very stressful day for the pilots (see Erica's update), FOCE was fixed in time for the port side engine to blow. We limped back into the docks 3.5 hours later. It was a long trip, but absolutely worth it for the restoration of the FOCE system and my pride.

 The rest of the week has been spent in various meetings concerning our leg of the Northern Expedition. Dr. Brewer has returned from Hong Kong for a few short days, and as such planning efforts have been kicked into high gear. Several new instruments need to be designed and constructed before our departure in August, so I have been running in between lab and the machine shop, checking in on the progress of a variety of contraptions needed to track and capture methane hydrates in all their phases.

 In addition, I have been continuing my identification of unknown gas mixtures collected by the USGS and MBARI in Barkley Canyon last year and developing pressure/temperature profiles of known mixtures created in the lab. These data will be crucial to later analysis of samples collected in-situ in August. Analysis has been a combination of impure gas kinetics, a throwback my high school chem class, and the most advanced spectroscopy - needless to say, it's been fun to relearn the fundamentals of chemistry I loved in high school and apply them to situations I never dreamed possible. Looking forward, I plan to finish constructing these profiles and then use them to calibrate the in-situ raman system, DORIS, and testing several phase-dynamic hypotheses regarding solid and gaseous hydrates. There is never a dull moment, and I'm feeling only increasingly lucky to be at MBARI.

Week I have done much more video annotation. Ken and I had a meeting with Linda and redefined what we would be calling these squishy little buggers. The large pink/purple ish ones are going to be penioagone sp. A, the medium orange/ pink ish one is going to be the amperima-peniagone complex, and the tiny little white one is the peniagone sp. B. I have also added the scotoplanes to my list of holothurians to annotate. I want back through all the previously annotated video and renamed everything, then preceded on the the new video footage with the proper names for each cucumber. I finished dive 230 and have moved onto dive 231. I would like to have dives 231 and 232 finished next week but we will see if that happens. Next week I will also be adding measuring the annotated sea cucumbers, and that is probably the bulk of what I will be doing as soon as the annotating is finished.

I certainly never thought there would be so much to learn about a sea cucumber, but they are pretty complex for being pretty much one long fat intestine. I am loving learning all I can, and I am so glad that Linda is patient with me and answers all my questions so fully.

Oh, yes- I also relearned that hot glue is very hot yay open house!

This week (June 19 to June 25).
1.Monday, update meeting in the morning, assign the work and report the prior job done. Have a short meeting with mentors, talking about the update. Read technical papers, find out some useful information about signal frequencies and processing method.
2.Tuesday, listen to the meeting in DOEST and learn some ocean engineering-related presentation. A general idea about the MBARI past work and future plans. Working on the installment of McStar, sensors, circuit diagram and wire connection.
3.Wednesday, continue the McStar hardware research. Look at the acoustic data, make own MATLAB codes to analyze the spectrum (DONE), research on Mentor Gene's MATLAB codes and try to make it running. Listen to the weekly seminar from Prof. Young
4.Thursday, work on the Ubuntu- Linux system and Beagleboard C3&C4, set up the Beagleboard hardware and try to debug based on Cutecom and Eclipse platform, but so far not done. Also, self-study C++ and read codes step by step.(Feeling not too good, cost much time-input but no results-output).
5.Friday, will continue working on the linux system and debug Beagleboard, hopefully... and prepare for the Open House on Saturday.

Next week (June 27 to June 30
1.Monday, update meeting. 2012 Proposal process meeting at 11 am and learn about the related projects.
2.Continue working on the Linux system and debug Beagleboard C4, read and write the C++ codes on Eclipse platform, try to make it working by Wednesday.
3.Install Beagleboard into McStar instrument and wire all the sensors, batteries and machine elements.
4.More research on the MATLAB codes and run it with old acoustic data, make sure understanding all the acoustic spectrum.
5.Propose to do the tank test of McStar on July 8th (need to talk with mentors).
6.Try to help for June 30th UCSC interns visiting.

(THIS WEEK WILL BE A HARD-WORK PERIOD)

I am shocked how quickly this internship is going, seems only yesterday since the last confluence update!

This week Danelle and I have made significant progress in calibrating AVEDac to detect squid species (mainly Humboldt). We started off by re-annotating data that I had already analyzed last summer and extracting the extremely cool interactions on the artificial bioluminescent display imposed by Humboldt squid.

The plan is to tweak the automated event detection software in a way which will only pick up fast-moving organisms (hence squid), which seems to be a simple idea but is actually quite complex. If we get accurate and consistent detections, then we can run it through the rest of the very large EITS data set. Danelle has been extremely patient with my limited background in software programming, it is like learning a different language! Guess that comes with the collaborative package here at MBARI when working with people of varying specialist background!

As for the biology side, I met up with post-doc Henk-Jan to discuss the different behaviours displayed by squid in different conditions and has put me in contact with a couple of cephalopod specialists outside of MBARI. I had a couple of questions regarding the somewhat antagonistic behaviour I had documented which has raised several other exciting questions...to be continued.

Next week I plan to build up the image library for AVEDac to get greater variance of classes in the training libraries. Hopefully by the end of next week we can start to process a sub-set of the 'unknown data' in the EITS data. Baby steps at a time!

I began my week by meeting my mentor in person for the first time, and discussing potential ways to proceed. After this meeting I was introduced to matlab, which was not a pleasant experience. I have no experience with programming, and I know nothing about matrices making the use of matlab, as best, difficult. After struggling for some time, it seemed better to take a project in a different direction, and the change was relatively drastic. Instead of comparing the ecological interactions between different gelatinous groups, my new primary focus is to understand the chemical basis of bioluminescence in the planktonic nudibranch, Phylliroe bucephalum.

So far this week, I have determined that Phylliroe, like many other organisms uses coelentrazine as the substrate for its luminescence. To get more familiar with these techniques I am going to perform similar analyses for Vampyroteuthis, Chiroteuthis and Octopoteuthis. Next week I will run these samples on a native gel so I can physically observe the luminescence, which should be good.

Also, a blue water diving trip is to be organised so I can encounter a number of the more common shallow gelatinous species in this area, which I greatly appreciate.

Week 2 was a whirlwind! After my lab and I unloaded the Flyer of all our specimens and belongings, I immediately went to work on keeping the Atolla jellies alive. After a few days of acclimation to the seawater in the wet lab and getting the flow in the kreisels just right, I finally added a total of 11 healthy looking jellies to three tanks. I spent most of the week hatching artemia nauplii to feed the jellies, which I think is going successfully. It is hard to tell if they are eating the brine shrimp, partly because they are too small to really see, and because the Atolla react poorly to light exposure, even red light. This makes it difficult to observe their behavior. In order to better observe them I have procured a night vision monocular! It has been working quite well, although I do think there are a couple of kinks that need to be worked out.

I attempted an experiment toward the end of the week involving the addition of fluorescein to a concentrated amount of artemia. After some trial and error we improved our technique and, using a small plastic pipette, I pumped the mix into each kreisel to see how the jellies respond to their feeding. I saw some interesting reactions, which has prompted me to continue feeding the jellies the fluorescein/artemia mix daily to monitor their reaction, until I am able to obtain live plankton (mysid shrimp ), likely to be collected next week!