Well this week I have been doing plenty of reading and catching up on the things I didn't know about sea cucumbers. I also learned the basics of the VARS program and started some work with annotations. Next week I believe I will be doing more reading and more annotation work.

Well, fast and busy week. Kind of feeling time is flying.Great pleasure to work with everybody.

First week (June 13 to June 16)__Work done:
1. Set up the private account in MBARI, find the work space, install the computer and build the personal homepage.
2. Hold meeting with mentors and talk about the schedule & plan for summer intern period.
3. Meeting with Mentor Wayne, got the hardware Beagleboard C4 and all related cables, start to setup them. Install linux system and eclipse software, got C++ codes.
4. Meeting with Mentor Gene, got the proposal for my work project, got database in MBARI data drive. Install Matlab 2011a. Start to download the data and read MATLAB codes.
5. Study the first seminar on June 15th.

Second week(June 20 to June 24__Work to do:
1. Monday meeting on June 20
2. Meeting with Mentor Wayne, talk about the Beagleboard C4 and make it work. Try to run C++ codes based on eclipse and figure out the errors if it has. Start to order some instruments for the project.
3. Meeting with Mentor Gene, talk about the MATLAB code and the huge database, and figure out how to start working on the analysis for acoustic data.
4. Meeting with Mentor Charles, understand the big direction for this project. Work as a team.
5. Meeting with Linda, schedule the plan for Open house on June 25.

REFERENCES AVAILABLE UPON REQUEST

I went to sea this week to collect sea urchins for my work. it was fantastic. really interesting to learn how they collect urchins. we managed to collect sea urchins from three depths. now we are in the process of analysing them. also we are analysing water samples too.so i got a chance to familier with analysis of certain water quality parameters. Next week seems to be more interesting. I 'm planning work with some live sea urchins. trying to figure out a method for inducing their spawning. also I 'll be going out  sea to collect some more urchin samples. 

Well its been an exciting first week and I am slowly becoming assimilated to my surroundings at MBARI. Today was the first day that my key card actually let me in the doors of MBARI, so I feel as if I officially belong here! I feel extremely lucky to be here surrounded by brilliant minds, plus the view isn't that bad either.

Currently my mentor (Francisco, who heads the Biological Ocean Group) myself and our group are waiting to receive an integration kit from the company Liquid Robotics, which designs the Wave Glider ASV. The funds for the grant have been bouncing around but it appears that a PO has finally been sent from MBARI, so we should be receiving the kit in a few days!

Wave Glider is sending us a hollow shell that I will fill with a variety of Ocean Acidification sensors, specifically a pCO2 sensor that was designed in house.  My job is essentially a big electronic and plumbing puzzle. This week I have studied up on how the different OA sensors work and have discussed some possible integration solutions with Gernot Friederich and Chris Wahl who are both part of the Biological Ocean Group. Many trials will need to be run in our test tank before the integration can be complete, so the sooner I can get to putting the parts together the better our result will be.

Next week we should have the integration kit so I will be busy putting the pieces together so that test runs can began as soon as possible. I also may have some sea time with the JOHN MARTIN which is deploying sensors in Monterey Bay for the next week.

This week I have been going over a few things with regards to a project plan with my mentor Danelle and Erika Montague which will be suitable for the 10-week time frame. As the EITS data set is large, we had to critically evaluate an appropriate sub-set chunk of video-data to work on which will both help develop the AVEDac program and hopefully turn out some interesting results in terms of faunal behaviour!

Next week I plan to start pulling the data and process it through AVEDac and then begin on annotating some video-data.
Can't believe it's been almost 4 days already!

This week was spent primarily working with Thom Maughan (my official mentor) and the rest of his group (Kanna Rajan, Rishi Graham, and Frederick Py) establishing what I hope to accomplish this summer. My project is going to be finding ways to utilize control theory and AI techniques (e.g., Kalman filters, machine learning) to troll the data coming in through CANON to do automated detection of interesting "events" in the bay, such as upwelling fronts or chlorophyll blooms. Initially I will be tackling the relatively simple problem of just detecting upwelling fronts utilizing past water temperature data from Dorado and Tethys. This will then be built upon to include data from other sources, such as surface vessels, moorings, drifters, and satellites, as well as other types of data (salinity, chlorophyll, nitrogen) being received by CANON to do realtime detection of these upwelling fronts. The final step is to provide a means to generalize it so that the scientists can determine the parameters of interest (so that it can find more than just upwelling fronts).

As a side project, if there is time, I will be developing a stripped down version of this system that can run in situ onboard the AUVs so that they can have the autonomy to decide to track interesting events as they detect them at, say, 3am.

This week was spent establishing the parameters of the project, gathering the first data sets that will be used, and exploring some possible approaches.

The next week will be spent constructing a couple of simple Kalman filters and applying them to a single Dorado data set with a very clear upwelling front to see how they perform and evaluating how to proceed based on success or failure. I am also currently scheduled to go to sea on Tuesday with the Zephyr to actually do a Dorado deployment.

It has been a fantastic and fast few days so far. Tuesday I literally jumped ship to the R.V Point Sur and helped a Moss Landing Marine Labs researcher pull a mooring and deploy the CTD. Yesterday I was lucky enough to sit in on the practice DOEST talks, and I spent a lot of time thinking about who will use scientific data. I have also been working on accessing and plotting ocean acidification data from two moorings in the Northern Monterey Bay. 

Next week I will help Heather with the CeNCOOS presentation to the DOEST on tuesday, then head out on the Point Lobos on Wednesday. I am looking at relationships between physical and chemical variables in the surface ocean, and will begin defining ocean acidification indicators.

This week has flown by - having Friday off helps a bit - and has been a crash course in engineering chemistry. I'm feeling incredibly lucky to be at MBARI and working in the Brewer lab, both Ed and Peter are incredibly brilliant and excellent mentors. I've learned so much already, and I've only just begun actually analyzing samples.

So far, the bulk of my week has been spent familiarizing myself with the lab setup, the machine shop and the Raman laser spectrometer. The latter is an ingenious laser system that detects the vibrational signatures of compounds in any phase. We use it principally to study gaseous and solid hydrates, which are entrapped within layers of sediment on the seafloor. Methane hydrates serve as a source of both potential energy and emitted greenhouse gas that can escape the ocean and enter the atmosphere, so they are of great interest to any scientist concerned with climate change.

I've not spent any significant time working with lasers or their mechanics prior to coming to MBARI, so all of this is new to me. It's been refreshing to spend time on chemical analysis outside of wet chem/hood work. Peter Walz and I have fully set up and calibrated the in-lab spectrometer (we have a deep ocean in-situ laser system as well, which we will be using extensively off the Northwest coast in August) and run a few test samples of gas mixtures. Today I hope to get through a lengthy list of samples obtained earlier this year and identify their composition. Next week, I will be out to sea both Monday and Tuesday on the Lobos repairing another facet of our project, FOCE (Free-Ocean Carbon dioxide Enrichment), which is essentially a large scale, in-situ ocean acidification incubation off the coast of Monterey. We have been having some mechanical difficulty with the various gears and chains required to maintain a more acidic environment in this area, and that expedition on the Lobos will be dedicated to repairing this system. Later in the week, Dr. Brewer will have returned from Hong Kong and I look forward to meeting him and learning more about this summer's work in the lab.

Congratulations to everyone for making it through their first week!

This week has been spent mostly settling in and working out the basics of my project. Unfortunately it is looking like the AUV deployment intended to collect images that I was going to use to examine cold-seep habitats is no longer going ahead. Thankfully my mentors Charlie Paull and Lonny Lundsten quickly came up with another plan.

So my new project involves looking at ROV data from the SoCal submarine canyons to determine if the faunal composition varies between active and inactive canyons. To accomplish this I have been taught how to use VARS (Amazing!) and have had to quickly reteach myself basic ArcGIS (Urgh!).

So far I've put together a basic map of the ROV tracks for each canyon combined with the available multibeam data so I can see where each 'transect' was taken and get a general feel for each canyon environment. I've then mapped the available Concept Name data from the outline VARS runs already performed on the videos by Lonny to get a general feel of what's out there. At the moment I am also putting together a species list to help with my identification while I go through the first tape of ROV video data. I am also in the process of annotating outputs from VARS with higher taxonomic grouping data to ease comparison of the mapped points.

Next week: Pt Lobos on Monday, video analysis all other days, finalise project.

This week has been a really wonderful experience for me. After the induction I spent a lot of time talking to the guys who I will be working alongside in the Haddock lab, and they have really done everything they can to make starting here as easy as possible.

My main accomplishments this week were tied to previous engagements, but I did get a chance to discuss with Steve Haddock about possible project directions. The project I am most likely to work on involves use of the VARS database to investigate the ecological interactions between gelatinous zooplankton groups. In order to accomplish this I was trained in the use of VARS, and I look forward to beginning forming queries for it.

The other possible projects are;

• Investigating the chemical basis of bioluminescence in the planktonic nudibranch, Phylliroe bucephalum
• Investigating the composition and features of the pneumatophore gas found in benthic siphonophores

I have successfully traversed the terrifying Lobos without feeling too bad, and I got to see my first gymnosome mollusc, physonect siphonophore and lobate ctenophore. All are truly wonderful.

Next week I will begin to run some preliminary tests for my project to decide which group would be best.

This first week has been very fun and exciting. I had the opportunity to go out on the Point Lobos twice. Tuesday I joined Gayani in helping to collect sea urchins with a fascinating suction device, and learned a tiny bit about controlling the main camera on the ROV. We also saw whales and dolphins!! Today Kristian and I got the opportunity to learn a tiny bit about how to control the ROV itself, or how to "fly" - it felt like I was flying through space. And we saw jellies!

Also this week I have been reading articles and learning about hydrothermal vents and tubeworms that live there, to get project ideas for when I meet with my mentor next week. I will likely do a project on the population genetics of a tubeworm from the genus Tevnia. This is what I will be figuring out next week with my mentor, and then hopefully I will be able to get started in the lab.

Sorry about being a little late on this - I didn't remember to do it on Wednesday and was gone Thursday.

Last week I started learning about the tools I will need to complete my project including: basics on how to use the Terminal, the Scala programming language, and CSS and Mustache (both web editing tools). After Brian taught me the basics of some of the code comprising the Deep Sea Guide website, I got to jump right into editing. I have completed some small (mostly layout) changes to the Deep Sea Guide and I am continuing to work on layout until my mentor gets back on Thursday. I also had a few meetings with staff from the video lab to learn how to use VARS and to discuss what they need done to the Deep Sea Guide that I can take on.

This week, Nancy and the rest of the video lab staff are finishing the details of what they want added to the Deep Sea Guide and presenting it to me so I can get started on my project. Last week, Brian and Nancy concluded that it will probably be a page that shows quality control data for each of the dives in the VARS database. I will know the specifics on Thursday.

I am also going out on the Point Lobos tomorrow and I am hoping I will be like Vanessa and not have a problem. I have never gotten sea sick in my life so we'll see...

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.

My first week with MBARI was nothing short of amazing! I was extremely lucky in that I was able to join the Midwater Lab on their 2011 Research Expedition aboard the Western Flyer. We had a fantastic voyage and observed and collected an array of organisms and behaviors. One animal in particular, the deep-sea jelly of the genus Atolla, was my primary focus as it will be the center of my study while I am here at MBARI as an intern under Bruce Robison. I will be studying the structure and possible function of Atolla's curious trailing or hypertrophied tentacle. Luckily I was able to bring back some specimens to observe and experiment with in the lab.

It will be quite an adjustment being back on land and not seeing Vampyroteuthis, Histioteuthis, munnopsids, tompoteris, and all the wonderous creatures as I have gotten to see on the Flyer, but I am nonetheless excited to get started on my project.