My return to the sea on wednesday(albeit on a tiny tiny boat) was a welcome break. (I now think it was blue whales we saw, not fin whales.) I had run into a quagmire of data processing on tuesday and needed the time out to consolidate my thoughts. Liaising with other team members and building on their thoughts I now have worked out a system that is both:
a) systematic and.
b) liable to minimise any inherrent errors.
So today I was so happily lost in the data the next thing I knew it was half ten and I hadn't even finished my cup of tea.

I now walk around the building in my socks, switch commons for lunch every day to confuse anyone who is following me, worked out which are the best biscuits in the vending machine, and discovered that ten minutes on a bike has made my botty so sore that I'd rather have a black belt in jiu jitsu beat me up again than sit on the bike for the next week. Regarding the last point, it meant I wussed out of the Bike to Work Day.

I finally have gotten somewhere with my jelly tracking software.  After optimizing my background flattener my thresholding function is working well.  I added bounding boxes and completely cut out the computer vision toolbox from my code.  I also employed a "border filter" that really cut out the noise and false positives allowing me to lower my threshold and identify more jellies.  I plan on making some kind of predictive algorithm to allow the computer to identify the same jellyfish from frame to frame.  I may also be able to optimize my code further once I have finalized the general philosophy of the code.  In the distant future, I also plan on maybe making a new "edge detect" function which would allow me to tackle the problem in two parallel ways. 

 As Dilly mentioned I went out on the Rachel Carson and it was awesome.

I am going to be a good example this week and actually get this posted on time! This week has been hectic like always. I have determined my questions, how I will answer them, what data I will be looking at, collected my sources, started my paper, and I am about to finish setting up how I will organize and analyze my data. I anticipate spending a lot of time in the video lab next week as my data collection commences.

We are also in the process of planning an epic future weekend in July... more to come on that. Sounds like there are great plans for July 4th floating around as well. The interns are taking the ball and running (or dribbling [go USA]) with it! Trying not to think about how these weeks are flying by. Have to enjoy the MBARI experience  it while it lasts! 

This week I figured out exactly how I'm going to analyze ROV footage of the squid I'm looking at and what parameters I'm going to measure. I've started watching the hundreds of videos of the squid and that's pretty much where I'll be for the rest of the summer.

I am super jealous that y'all saw blue whales!

This week I got a lot done. I have made the media that I will be inoculating on monday, which will be the beginning to the first part of my main experiment. Everything is going very well, and the Rachel Carson trip on wednesday was a blast. We had perfect weather and saw too many whales to count!

Crossed some big ones off the list this week. No doubt my most notable achievement was barfing in the Rachel Carson's head! After years at sea I finally got schooled - guess it was bound to happen at some point. Also, got to go out on the Paragon and deploy a Wave-Glider (super cool and highly recommended)! Made some real progress with my project this week as well. I've been looking at lots of LRAUV data and so far have managed to find a couple of good predictors to plug into my failure classification model.

Looking forward to tomorrow's dive!

I went on a boat this week! (The rachel carson). It was CRAZY seeing the ROV launch. I didn't realize how huge it is (about the size of a medium-sized bathroom.) Marvelous. I also finished calibrating my pH sensors and drafting up an abstract for my project. Today I'm at CSUMB learning some GIS skills. Ideally I will be able to use GIS for my paper...so long

A ver... Things I accomplished this week: Troubleshooted (w/Gene) the Test Tank Prototype (TTP) and it's sensors. Got everything tested and communicating via VisualStudio. Encountered some odd behavior from a position sensor that sits on an SPI bus, but everything else more or less played along nicely. The TTP is filled with oil, and I will run one more test on Monday to make sure I don't explode an oil reservoir when the bellows retracts fully.

I'm familiarizing myself with the code in C#, and having to add/modify some things to get the TTP running. I took the opportunity to further establish my understanding of Git, and wrote a guide on using Git in a shared network repository environment which I'll be sharing with Gene and the larger engineering community at MBARI.

Next week I would really like to concentrate on finishing the code modifications, as the C# work is "perspiration" (Gene's words, which I agree with) and not of significant intellectual interest. I want to get the dang thing moving in the tank... and then dive deeply into controls!

I have the hypothesis that a pure PID depth controller is not stable for our non-linear plant (drag is proportional to velocity squared). Marginal stability is observed in our Simulink models (plant oscillates around set-point), so I have some significant exploration to undertake in the modeling/theory realm, and then hopefully apply to the control algorithm which actually controls the float.

This week, I continued going through the LISST-HOLO images to identify the zooplankton. I have been concerned about the limitations of the images and my ability to draw any concrete conclusions about the community structure using these images. I briefly spoke with JR during the big intern BBQ about these concerns and we will meet next week to further address them. We simply might alter the direction of our project. On wednesday, I had the opportunity to dive with George for inspection and maintenance of the swFOCE instrumentation at Hopkins. On thursday, I also enjoyed participating in the WATCH land use panel.

I finished the third week with an overwhelming appreciation for all the kind people at MBARI that seem to have endless time to help me out. It was great to get out on the Carson and see the ROV and rover in action (but being the third intern to go down wasn't great - glad it amused some!). Being in the control room on board was fantastic, as was the little Q&A session I had with Paul and Rich on the deck the day before.

I finished the draft of the lebensspuren guide for Station M this week, and am working with Linda to get it added to the Deep-Sea guide. Our lab group seemed pretty receptive to it, and gave me some ideas on how to improve it and apply it. Brian was also extremely helpful in sorting out some of my questions with VARS. So, next week will be all about implementing the lebensspuren guide and getting some data out of VARS.

Finally, it was great to meet some of the interns at other institutions around Monterey Bay - I had no idea that there were so many different marine-related organisations that had interns.

My week was ok. I have accomplished lots of work in the lab and have now a bunch of sequences to analyse. Let's hope that the genes are polymorphic!

Whoops, a little late on my confluence update. Right now my cultures are running me into the ground a little bit, I bit off more than I could chew with having a total of 26 cultures. 18 are for my Phosphorus/Nitrogen concentration experiment for RCC 299, 4 are for my temperature experiment for CCMP 1545, and 8 were for my dilution experiment for RCC 299. I know that's incredibly vague and you probably have no idea what I'm talking about, but I'll shed some light on these experiments next week and explain in a little bit more detail... depending on how the data turns out... Anyways, so far the experiments have been going well. Now I just have to manage to keep up with all the cultures I have going.. which includes me coming in on the weekends and on my off days . But I'm excited to start interpreting the data and seeing how everything works out. My mentor left for Germany on Tuesday, so it's been a little bit of "sink or swim" on my end of things, but so far I've been managing everything well. One of the highlights of my week was going out to sea and seeing the Ventana in action. I got some great pictures :^)

Sorry for the late post. Lots of stuff going on this week. Finally cracking into MABARI's database (not literally) and pulling data for my project. I'm gonna be analyzing 10 uncommon or "rare" species found in the bay and attempt to determine their distributional patterns based on MBARI's massive time-series.

During my data excavations, I found a few errors/inconsistencies in the VARS database. These errors include triplicated data points and misread oxygen CTD readings. I informed my mentor, so hopefully they can be sorted out.

Thus ends week 3!

A productive week, finally! I have managed to log about half of my cores and things seem to be falling into place based on my interpretations from them. The biggest thing this week was heading up to Santa Cruz from Tuesday to Thursday. Driving in the US went fairly well apart from a slight mix up on the way back from Trader Joe's one evening...Anyway, the set up they have at the USGS is so good. Nice big labs, new equipment and the technician that was showing me the ropes was extremely helpful! The grain size data that I got out of my time up at the USGS means I can now start some proper investigation. I'll have to head back up there later in the project to run my full set of samples but I now have an idea of how long it will take to run samples.

This (short) week will be spent logging and looking over the data from last week with Charlie and Esther now that they are back from the cruise they were on.

Super productive week! I designed a ton of primers for a bunch of different squid species and we were able to run PCR using Dosidicus DNA and my primers. The exciting news was that we got bands! But we also got a lot of nonspecific junk, so on Thursday I reran PCR using a range of annealing temperatures. Today, I'm going to run another gel and hope that at least one of the temperatures had better results.

A little late on this post but it was a very good week! The aquarium project is coming along very nicely. I submitted more drawings to the machine shop for fabrication an am continuing on to more components of the design. Last I heard the material for the first set of components has arrived so i should get to see my designs built very soon!

 I also got to go out to sea on the Rachel Carsen on Wednesday. It was really exciting to see the ROV being operated first hand. Also we saw more whales that day than I ever have at one time before. I definitely came back a little sunburned, but it was a great day!