woohoo!
you're in the right place to post your first weeks' update. How are things going? what are you doing? what is working and what isn't working? thoughts? concerns? put up whatever you want and we'll discuss these updates and much more on Monday at our meeting.

Things are going well. My mentor Nancy Barr has given me two and possibly three projects to work on: Iceberg AUV with Ken Smith, Brett Hobson, Alana Sherman, and Steve Rock. They are all very excited to have me on board to illustrate their research on free-drifting icebergs in the Southern Ocean; Seafloor Chemistry with Peter Brewer, Ed Peltzer, and Peter Walz. We are formulating our ideas based on their Laser Raman spectroscopy of methane and sulfate cold water seeps; and Global Floats by Ken Johnson.
I really hope there is time to work on all three projects as I find all of them equally fascinating and challenging.
If any of you are involved with any of the above projects I would certainly welcome your insight.
Thank you.

After one day of induction, I was trained by Dr. Linda Kuhnz on VARS software to annotate ROV images taken at Station M (4,000 m). The aim of my project is to look at the distribution, frequency, size and habitat of Paradiopatra (Annelida:Polychaeta:Onuphidae) tube worm patches from 2006 to 2012. This second day was also the opportunity to get familiar with the Deep Sea Guide and set up all computer settings. Wednesday, the project started. I looked at the four first tapes for my project, getting familiar with my tube worm patches, looking what features I should annotate. In the meantime I have started reading related papers on Station M.

This week has been primarily meeting with my mentors, both Jim Bellingham who is overseeing the entire project, and my more day to day mentor, Julio Harvey, of the Vrijenhoek Lab.
With Julio I am working on the methods for the sandwich hybridization assay (SHA) to detect target organisms by their rRNA. So far it's mostly been training lab methods and safety, as well as preparing the probes and reagents needed. We're hoping tomorrow to start running a plate with actual samples in it.
While I haven't worked much with Jim this week, we have been discussing some of the potential ideas to test on AUV sensory system. I may be working with the laser optical plankton counter (L-OPC) and comparing it to the molecular probe testing done with Julio.
Both projects will involve working with copepod and possibly barnacle nauplii cultures, and eventually using whole water samples. Specific experiments haven't been pinned down yet, but I'm hoping to figure that out in the next day or so.

So far, so good, and I'm looking forward to joining Jim Barry's group on the Carson cruise Monday.

This week has been highly productive for me, and I've learned some new lab/culturing techniques for my project, so it's been really exciting. The part about productivity is a bit of a pun, in that I hope my algal monocultures take off and grow. I have been working with Sebastian Sudek in the Worden lab, getting oriented to the ins and outs and using their lab equipment to create culture media. I also learned to use the autoclave the other day, that was neat. Yesterday we added five strains of phytoplankton of interest to my culture media and set them up with favorable light intensities in the incubator. We also set up and tested the fluorometer yesterday, and set up a test for bacterial growth in the culture media. Today I will get a refresher on DAPI staining, and we'll take a look at how the monocultures are coming along. Next week I will begin measuring growth at the same time every day or couple of days. I'm really enjoying this project and spending time in a lab getting my monocultures ready to test on the vehicle sensors. My project plan builds off my data analysis project from last year, characterizing plankton communities using multiple sensor data from the AUVs. The project this summer is to create monocultures representative of the range of sizes/species of algae we see in the bay, and run them on some of the sensors from the AUVs. The challenge will be to ensure we have pure, healthy monocultures, and to set up a system where we can run the lab samples through the sensors in a way that can most effectively reproduce conditions encountered by the vehicle in situ. I'll keep you guys posted on how it comes along! The latter half of the summer I anticipate to be more data analysis heavy, integrating the data sets to answer my thesis questions.

Oh yeah, I also got to go out on the R/V John Martin with Kendra, Nick, and two teams deploying/retrieving wave gliders on loan to MBARI from Liquid Robotics. That was really cool to see and learn about. We also saw a bunch of dolphins, which was just delightful. One of the cool things about this trip is the wave glider was deployed just before the Dorado AUV (my favorite AUV, don't tell the LRAUV folks) was deployed off the Carson, and as I understand it the goal is for the glider to detect a front and track it, and then to tellthe AUV to get in there and collect more data with its larger suite of oceanographic instruments. I would love to get out on a Carson cruise to help with a Dorado deployment. Did I mention we got to see Julie Packard christen the boat last summer during MBARI's 25th anniversary celebration? That was really cool.

Finally, I almost have the intern blog ready to share with you all, it just needs a bit more style modifications and then I'll share it with any and all who are interested in sharing their summer intern experiences.

In addition to general intern orientation, this week consisted mainly of familiarizing myself with the resources and databases utilized by the Haddock Lab. I was given a tour of the VARS system and its database, which I will be later using to analyze temporal, seasonal, and environmental effects upon diversity and abundance of midwater zooplankton and invertebrates. I have begun to examine automatically generated plots of ROV data for a series of potentially interesting taxa provided by Dr. Haddock. I am in the process of familiarizing myself with the Deep Sea Guide and a series of Python scripts that allow flexible data retrieval from the VARS database. I hope to narrow down our focus to a few particular taxa next week, when we can begin retrieving/considering actual ROV data. My time at MBARI has been great so far, and I'm looking forward to learning more as the weeks go on!

First week at MBARI, as an intern under Jim Barry, was absolutely AMAZING!  With the guidance and help from Jim Barry, Patrick Whaling, Kurt Buck and Chris Lovera, I learned an abundance of new and valuable knowledge related to the marine world.  Future projects I will be potentially working on this summer include testing and observing the response of small marine organisms to Ocean acidification. Specifically, I will be observing physiological and/or behavioral effects relating to hypoxia, differing pH levels and/or respiration and pCO2. This week we collected intertidal crabs (Hemigrapsus and Pachygrapsus) from the Monterey Bay area and Elk Horn Slough (Kirby Park). These little guys will potentially be the organisms I may be observing for my project. 

Things are going great. I've been helping set up the new database server I'll be working on and I've started playing with some of the software I'll be using on the server once it's up an running. Along with that I've talked with my mentor, Mike McCann, about some of the details of what I will be doing and could be doing this summer. Since the server has a lot of things that tie into it I have quite a few option for things to work on.
One other cool thing I wanted to throw up here is that I suggested the name Kraken for the new server and it was chosen to be the servers name.

Things are going well. I returned from the week-long midwater ecology research cruise with my mentor, Bruce Robison, on the Western Flyer Monday evening. What a great experience! Although I have never been on a research vessel before, I found that I quickly adapted to the daily schedule and tried my best to be a sponge and soak it all in. It was so cool to be surrounded by and learn from experts in the field of midwater ecology! While on board, I spent my time helping with loading and unloading the ROV, Sorting through and dissecting animals, observing and participating in the collection and observation of midwater animals in the control room during dives, finishing schoolwork (as I left school two weeks early to go on the cruise), fishing for squid, hanging out with the crew and scientists, helping anyone who would let me with their data collection, observing birds and marine mammals, and (most importantly) spending a lot of time discussing and investigating possible research topics for this summer with the scientists on the boat. I cannot thank Bruce and the rest of the midwater lab enough for this wonderful experience! Aside from that, I have been playing catch-up with getting situated here on dry land, as I missed the orientation day (and meeting all of you guys :/ ). I think my project will revolve around the behavior of adult and juvenile Chiroteuthis calyx squid, most likely examining their color change, postures, inking, and mimicry.     

Things are going well. This has been an introduction week. First day, an introduction to my mentors and all the utilities needed to work in MBARI and the second day, an introduction to my project.
I've been discussing with my mentor Tom O'Reilly and my co-mentors Kent Headley and Duane Edgington, the main goal of my project here, and how to start working on it.
On this week Tom has been quite busy with wave glider deployment on Wednesday, so Kent helped me a little bit more with my doubts and problems on these first days. He also explained me the main projects that they are developing actually.
Today that I have a little more knowledge of my work on MBARI and I have started working on it, I will do another meeting with my mentors, at lunch time, in order to discuss about my principal doubts on the project.

This first week as and MBARI intern has been really amazing! The first day was a little tiring from all the talks, but that just lets you know were you're standing and all the stuff that has to be done by the end of the week. VG and I were sharing a place, but then we got transfered downstairs in building B; now we don't know what to do with so much space!

I met with my mentor Francisco Chavez on monday and then again on tuesday to discuss where my project will go. We've decided to continue the work we started a while ago, and finish it. We have CO2 fluxes all along the western coast of the Americas, from Canada to Chile gathering the first 100km offshore. We will try to explain the flux pattern based on preformed nitrate values on three different scenarios.

On the other hand, I'll meet with Monique Messié, who works with Francisco too, and I'll try to learn some of the Matlab stuff she's so great at.

Oh, and I have also been checking out the Canyon Head, 'cause there's so much stuff to see!!! I'll try to modify my web page later in the day.

So far this week with MBARI and the other interns has be great! My mentor has been gone all week, so I've pretty much been on my own.  I was able to come in a few days last week to figure out the scope of my project and the things I need to do to start it. I'll be working with Bill Kirkwood on his Shearwater project.  Shearwater is a new AUV design that will have aerial capabilities enabling it to fly out from a facility to a target area and land in order to submerge and conduct testing.Specifically, this summer I will be focusing on the development of the propulsion system. I was able to do a lot of research last week on some technologies that we are thinking about for this design and have been focusing on the calculations needed to determine overall power needed for both hydrodynamic and aerodynamic flight modes. Once I have this information I can start looking at propulsion options for both modes.

I'm looking forward to Bill being back on Monday, so we can discuss things now that I've had time to wrap my head around this project.

This has been an exciting and information filled week! My mentor, Connor, and I started by discussing potential projects I could be involved in.  These include updating the aquarium exhibit "Mysteries of the Deep", planning the Open House social media component, and of course, the Earth Conference in July!

I began by reading MBARI's Strategic Plan other documents about the institution's collaboration with the aquarium.  It gave me a better idea of MBARI's view and goals in terms of education and outreach, as well as the differences and similarities between our objectives and aquarium objectives.  I spent much time talking to my office mate Nancy who is a wealth of knowledge about the different projects in the department. She has been amazing about letting me spout my ideas, and directing me to those who have the expertise in particular subjects.  I was exploring an idea about interactive lesson plans for teachers so I talked to George.  I walked out with information about a newly developed national curriculum, inspirational education success stories, and a cool iPad app called Ocean Science. I connected with Connor again today, showed her my ideas, and am developing some new ones!

Orientation was amazing, the tour was the highlight to be honest. It still feels like a labyrinth but I am sure I will be able to find my away around. On day one I was given a tour by my mentor, Dr.Francisco Chavez on the AUVs and LRAUVs, their specification, limitations and the various sensors and equipment on them. Like Alba mentioned, we now have a large desk space and it is a little overwhelming. I had some account hiccup on the first day of my attempt to access Atlas, and I had my account locked for more than 3 times; eventually I got in towards end of the day. I needed to get a Physical Oceanography data analysis text book from the library at MLML, so on the way I brought Alba there and gave her a small tour around the lab (hope she had fun).

My mentor introduced me to Mike McCann and Steven Haddock to talk about AUV and LRAUV data sets, and the possible data trends I can find in them.For the first part of my project I am cataloging the AUV and LRAUV data from 2003 to 2012 (for now), to narrow them to the months of September-October and look for patterns in backscatter. I am hoping while going through those data sets I will develop thought process that link certain variables.

Have a good weekend guys!

Since orientation, Gene and I have jumped right into defining a project for the summer, and started some initial design work. I will be working on redesigning a ballast engine and controller for a coastal profiling float. My primary focus for the first two weeks is to quickly address some design flaws in the existing model, and fabricate a new pressure housing for the benchtop model. After that I will look into modeling relationships between pump efficiency and pressure, and use these results to update the mechanical model for the system.

This week has been mostly trying to figure out how the Co2 sensor works, all the programming that is behind it in  order for it to work. My mentor and I got it to transmit data and measure temperature, Co2 concentration, and RH. In addition I mostly did some research on how the microcontroller that we are using works. We put the clock of the circuit together and make it run to give measurements of time.

The next task will be making the Co2 to give measurements every certain amount of time. And after that hooking it up with the microcontroller and periodically setting up the clock, the external memory and the relays.

Afer getting settled into the lab I began working on a fluorimeter in order to use it for micro- to nanomolar concentrations of ammonia. We had issues with the sensor being maxed out on all solutions but have resolved this problem. After reading a number of journal articles on ammonia fluorimetry we will be focusing on creating protocols.  A side goal is to use a 6-way injection valve to increase reproducability and utilizing python to streamline data logging, ideally offering real-time graphical output.
Patrick and I went on the slough Thursday in order to change batteies, download data, and collect water sampled from LO1.
Next week we aim to have calibration curves created for the current fluorimeter set-up. We will also be tagging along with a cruise on Thursday.

Monday's Orientation was an exciting day. It was exhilarating to see some of MBARI's newest equipment being tested, see some of the deep water video footage in the video lab, and listen to Stephan's research presentation on pore fluid flow, a topic somewhat related to the project I'll be working this summer. I met with my primary mentor, Peter Brewer, my secondary mentor, Ed Peltzer, and the Brewer lab tech, Peter Walz. They showed me around the lab. The Brewer lab was representative of interdisciplinary nature of MBARI as it looked like half a chemistry lab and half a machine shop. I saw the Raman spectrometer equipment that is loaded onto the ROV sleigh. I helped Peter with some calibration and trouble shooting work (by help I mean I was an extra set of hands!).
I had to return to UC Davis the remainder of this week to take final exams. Since finishing Thursday evening, I've been reading a number of journal articles on Raman spectroscopy. I'll be graduating this Sunday and returning to MBARI on Monday morning. I'm looking forward to hearing updates from the other interns at our weekly meeting.

Added by Larissa Clary , last edited by Larissa Clary on Jun 13, 2013 - posted in next week's update
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What a whirlwind of a week! Between the orientation, seminars, and starting my project there has not been time to actually grasp just how amazing it is to be working at MBARI. I definitely appreciate how helpful everyone has been towards the interns. I know I could not have made it through this week without all the smiling faces. I think Claire and I ran Linda ragged with all of our questions yesterday! I have started looking at and measuring holothuroids (those are sea cucumbers for those who do not know) using the VARS annotation system. For my project, I am going to be determining distributions and the biomass of these holothuroid populations at Station M. Due to the long time series of data at Station M (this is a 4000 m deep site), I am going to attempt to detect changes in the distributions and biomass over time. There is definitely a lot to do in 9 weeks but I always like a good challenge.

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