A productive start and middle to the week. I have been carrying on with my core logging - 8 have now been logged, only 27 to go! I gathered some push core samples as well based on various needs for the project to take up to the USGS at Santa Cruz next week. I'll be there from Tuesday to Thursday getting training on the grain size analysis machine. I'll be heading back up there later on it the project to run my full set of samples based on the work I am doing now. Both of my mentors are now on a cruise for the rest of the week and the following week so i'm glad I have enough to be getting on with!

Looking forward to getting out again this weekend and watching the US follow the English football team and win their second match (wishful thinking for the English I think!).

It's been a good week so far. Our lab met together to figure out the final details of our projects. I'm going to be studying the behavior of Histioteuthis, a midwater squid with a crazy eye dimorphism. It has one huge eye that could be optimal for staring up toward the surface where downwelling light is coming from and looking for silhouettes of animals above, and it has a smaller eye that could be for detecting point-source bioluminescence off to the sides and below it. It's thought to position itself in the water column with the eyes facing these directions, but no one has ever looked at their behavior on the ROV footage to see what they are doing with their eyes. I will be looking at their behavior in the video database, as well as collecting eye samples to take back to Duke with me so I can look at the spectral sensitivity and optics of each of their eyes. This week I've started looking through all the Histioteuthis annotations in VARS and started learning how to use the video lab and and VARS.

This week I have been getting into the preliminary project work. I am working on a guide for lebensspuren (life traces, such as footprints) at Station M, using photos from the time-lapse cameras and the rover. I hope to add images from the ROV, too. From looking through the images I will get an idea of which lebensspuren are more visible in images captured with which techniques. I am going to use the guide to assess the lebensspuren at Station M (diversity, densities and seabed coverage) to get an idea of the activity of the benthic animals down there. Many animals are deposit feeders, so studying their traces may give us an idea of what they are eating and when.

This week I have continued work on the MBA exhibit. I have designed more structural components for the suspension system, as well as modeled other components such as the motor. I also learned the procedure for submitting projects to the machine shop and have placed orders for the first set of structural components to be built. After submitting the project online, I took my component drawings down the the machine shop and discussed the design with the machinists.

 I also was a part of the biggest Costco purchase I have ever seen shopping for the BBQ on Monday, and had a lot of fun grilling burgers and sausages out in the sunshine on Wednesday. I heard a lot of people saying they liked our BBQ also so I think we all did well! Congrats everybody!

Haven't had much time at my desk this week, but, when I do, I am watching holo videos and reviewing larval development. At this point, we are just trying to get an idea of the community structure and determine the best way to view the images.

It's been a busy week on the social front at MBARI. Despite that our team managed to squeeze in a conference call with a collegue in Mexico to finalise the details of my project on the faults along Alarcon Rise. We discussed some common ideas, data limitations and work to progress. In theory I could study the entire ridge but time constraints mean I am splitting it into sections, pulling data from each section in turn, and if I complete one section I'll progress to the next.

So my week has involved a lot of staring at computers, which I have enjoyed.

Out of MBARI hours I've now arranged a lift for downtown after work, so I'm a happy bunny because I'm traning in Aikido once more.

This week has gone by so fast! I was able to sit down with the post-doc that I am working with in my lab and plan out a detailed schedule of my project. My project that I began with soon turned out much more complicated and time consuming than I had realized. Before I begin the actual experiment, testing the phosphorus depletion levels of the phytoplankton Ostreococcus, I will have to figure out which media they prefer (what I am currently doing) and what the optimal cell density is of each culture. After the meeting and planning out everything that needs to be done I feel alot better about what I have to complete in 10 weeks. And now two weeks in to the ten week summer I feel comfortable working with everything in the lab.

The BBQ was amazing and was a great great break from lab work.

My project is finally starting to take shape! This week, I did research on a squid photoprotein known as Symplectin. I BLASTed the Symplectin sequence against the transcriptomes for 5 different squid species and one nudibranch species. The transcriptome for Dosidicus gigas returned a very promising result (suggesting a Symplectin homolog in the species). I'm going to rerun the majority of the other alignments because our transcriptomes are going to be updated over the weekend. For now, I'm moving forward with the Dosidicus hit and will attempt to design primers tomorrow.

Both my research mentor and post-doc are headed to Sweden for a Bioluminescence conference, so I'll be lonely next week and everyone should come visit me!

A very busy week this has been with all the conferences and BBQs, but alas our work is always waiting for us.

As Katie T. mentioned, our lab has at last begun finalizing our projects, ironing out all the ideas and what not. I'm hoping to conduct a community analysis of the common and/or uncommon fauna found in Monterey's mid-water (~200-1000 meters down). MBARI's data compilation is so massive I struggle to keep my head on straight.

In other news, coming from Hawaii (-3 hour time difference) and being a naturally borne night-owl, I often find myself habitually staying up late (I also blame my friends back home). The coffee here has been a lifesaver, but I am resolving to sleep early from now on (on weekdays at least), especially now that my project has kick-started.

Pneumonia aside It's been a good week.  I got all the cool matlab toolboxes I wanted but somehow my computer doesn't have enough memory to run any of the cool included functions.  So I think I'm doing it all myself.  I spent this week trying to tackle the first problem -- a very uneven background.  My first solution took a test frame every n frames and subtracted it from the frames n...2n.  This basically assumes the test frame is a good match for the background (i.e. no jellies).  Unfortunately there are jellies in some of the test frames.  My next solution builds on the first.  It still takes a test frame every n frames but for the next m frames it averages the subsequent frames to to get a better measure for the background and uses that average to subtract from the frames (flattening the background).  This reduces the negative effects of chosing a test frame with jellies in it.  I am now performing grid searches to find the best values for n and m.  The error function I am using is very simple.  It averages the intensity of each frame and the higher the average the higher the error.  This error function assumes there are no jellies in the frames so I am using a specific segment of video with no jellies to try to find the optimum n and m.  In the future I hope to optimize n and m and then use blob analysis to actually pick out the jellies in the foreground.  I anticipate problems optimizing because my error function only attempts to flatten the background and not find jellies (ostensibly the best noise reduction would be n = 1 and m = n but that would reduce my frames to nothing).

A suggested topic for discussion for Monday's meeting - how to delete edited confluence comments

Overall had a pretty productive week. The week's highlight was a presentation I gave during a meeting with the LRAUV group and collaborators for Oregon State University. I presented my recent progress in locating LRAUV malfunctions in historical data (~6000 hours) and talked about the mathematical theory behind the machine learning binary classification method I hope to apply for real-time fault detection. Surprisingly, it actually went ok and we were able to agree on a general plan of action. It was truly great to meet new collaborators which I'll be in touch with on a weekly basis from now to the end of the summer (and hopefully after that). This week I finished writing code for consolidating all the data I'll be using for my analysis - now that I have it I'm really looking forward to see what I can do with it!

This week was hectic to say the least. In the beginning of the week I was fine tuning my project, and yesterday I worked on designing the ENTIRE experimental procedure for the summer, and worked on planning out the rest of my time here at MBARI. Right now my work time is booked with sampling, growing cultures, determining growth rates, making artificial sea water and media, inoculating cells with media, and the list just goes on and on. My project this summer will primarily focus on what the range of nutrient stoichiometry of carbon, nitrogen, and phosphorus (C:N: P ratio) for two strains of Micromonas (PCC 299 and CCMP 1545). This will hopefully provide much needed empirical data that is currently lacking in the field.

This project is challenging, but I'm looking forward to learning new molecular techniques, as well as enhancing old ones. I'm also excited to do my own little project for once, and to be apart of the full process,  including experimental design, data analysis, trouble shooting, and all the technical work in between.

Still busy hunting genes for population genetic analyses in my deep sea mussels. I have managed to run the first sequencing reactions and expect some preliminary results within the next week.

I want to take this opportunity to thank everyone once again for their help with the BBQ! I apologize if I may have been cranky on the day of, but I am so glad that it went so well! That, coupled with the many other activities this week, has made my project productivity level dip, but, as of today, it has significantly rebounded.

I have ironed out the last details that have thus far prevented me from collecting data! Let the fun commence! While there are many caveats to using ROV footage to document behavior, I have a feeling that the results will be interesting nonetheless. Figuring out a way to quantify the interactions that I will be witnessing is my main challenge at the moment. I will tackle this challenge by moving back into the video lab for the summer!

Another good week, and I'm only 18 hours late in posting this as, opposed to several days like last time. One of my dominant thoughts for the week has been, "With all these things going on, how does anybody get any work done!?" It's an interesting balance for myself as I recognize I should jump on the unique opportunities that aren't [strictly] internship-project-related (e.g. chatting it up with Board members), and the place I hold as a results driven engineer. I knocked out a handful of small electrical/mechanical things earlier in the week that will allow me to get the float in the tank, nothing worth writing home about, but I did learn how to make nice bends on SS pipe for Swagelock systems. The highlight of the week was the meeting Gene and I had with Steve Rock yesterday, talking about model and system dynamics. We touched on overall approach, possible sources of marginal-stability we're observing in the model, and a host of other things.

I feel I've got a clear trajectory for the short and medium term, and some ideas about what I want the final product to be (which will also depend on some of the results that I generate in the short term, regarding the suitability of one or more control algorithms.

Time to get cracking!

I have finished calibrating the pH sensors for my project (after many hours on Excel) and submitted an informal "proposal" to those at Hopkins that are overseeing my project (it is happening on their shore). Those two hurdles have been jumped and are good markers of my progress. Wednesday's BBQ was a blast! Thanks to all who made it so delicious, especially Ben B. for leadership on both menu planning and event coordination. I learned that my lab will be hosting a BBQ a few weeks from now...at about 8 members (as opposed to about 20, George included) we'll see how that goes...it may get hectic but at least I have a precedent to follow. The lab meeting on Wednesday was great, because I finally met everyone working for my mentor (Dr. Chavez) and got to give an informal presentation on my project (practice helps!) and ask some questions about others' work. Finally, looking forward to the weekend, especially Sunday as it will be my only day to relax - hiking, "football", and world-cup-watching are all on the agenda.