Summer Interns 2014 : 12-June-2014 This page last changed on Jun 12, 2014 by mage. just scroll down to the bottom where it says add comment - and add your update Comments:
Other than the usual intern orientation I was able to get going with my project straight away. In April, Charlie Paull and Esther Sumner (mentors) were on a cruise (I was supposed to be on it but I a fresh pin in my wrist and was in cast!) that collected 35 vibracores in three transects across the canyon from thalweg to flanks at ~600 m, 1000 m, and 1200 m water depth. My task is now to graphically log all of them to understand the deposits. That's probably 35-40 m worth of logging to get done. I've done three of them so far... The USGS up at Santa Cruz published a paper this year on grain sizes above the centre of the canyon from sediment traps to understand turbidity current thickness and behaviour. The second part of the project will be to sample cores at the same level as the sediment traps from the flanks of the canyon and compare with the USGS paper grain sizes to gain information on turbidity current thickness. That means I will be going up to Santa Cruz later on the project for a week or so to use the same machine for consistency. I feel quite lucky that I have been able to get in the lab almost straight away once let lose on Monday. Hopefully that wasn't too boring for you non-geo's! The facilities here are great! It's a much nicer room than I have at Southampton (although I have a bit of a walk to get the cores here)- I get it to myself! Posted by wsymons at Jun 11, 2014 20:36
I am excited to be getting started with my project this week. Linda has been generously spent several hours with me showing me how to use VARS. I met with Kathy, Ken and Chrissy to discuss the project focus; it will be something related to looking at megafaunal assemblages at Station M and their activity, likely using lebensspuren. We need to be strategic about the dives we use, and the imaging selected, so I have been reviewing images from the time-lapse camera, the rover and some from the ROV. Posted by jdurden at Jun 12, 2014 08:37
The first week of interning at MBARI was fantastic. Getting orientated and starting my project took up the entire short week. I decided to basically start a new project; I will summarize as "Visual Tracking of Jellyfish." My first week uncovered more problems than answers on the difficulties of computer vision and characterizing jellies. I started out my code developing in matlab. I am still in the incipient stages. Deciding what specific toolboxes I will need is an effort when considering if I buy them they are about 2 grand a pop. This decision making process is complicated more because I am not sure if matlab is the best way to start answering this problem. I have also uncovered some previous work on visual tracking of jellyfish and will explore this before moving on with the matlab code. Overall I have found a couple of ways that computer vision will not work at identifying and tracking jellies -insert quote from Thomas Edison and light bulbs- so at least it's a start. Posted by jsteck at Jun 12, 2014 08:55
First week - check. LRAUV group was very welcoming. With the support of my mentor Jim Bellingham and other members of the group I was able to set a few well-defined goals for my project and launch off with some first steps. My project will revolve around cataloging LRAUV malfunctions associated with vertical control, performing statistical time-series analysis of preexisting data (6,000 hours of LRAUV operations!), and finally, developing a classifier for vertical control malfunctions which will be integrated into the vehicle's autonomy software. First on the agenda - learn LRAUVish! This week I learned how the LRAUV communicates with its operators and developed a Linux based set of commands to extract communication strings containing critical malfunction messages from the LRAUV historical database. By the end of this week I'm hoping to finish writing a MATLAB script that will use the time stamps of malfunction communication strings to pull relevant data of the server for analysis. Right now we're getting ready to go out to sea to retrieve one of the vehicles - more next week! Ben Posted by byraanan at Jun 12, 2014 09:11
This has been a significant week of "firsts" for me. From being the first time moving out to California, to meeting everyone at MBARI, it has been a very exciting time. Starting off the week, the Bruce Robison lab was able to go board the Carlson for 2 back-to-back day-long research cruises. Using the massive ROV, the Ventana, we able to complete multiple respirometry experiments, run multiple video transects, as well as capture several juvenile octopuss'. Interestingly enough, our mentor (Dr. Bruce Robison) was kind enough to allow us to select our own research project, giving us time to explore our options until now. So today, I hope we can solidify our ideas and have a productive summer! Posted by wtruong at Jun 12, 2014 09:44
I'm working in the same lab as William T. so I've had just about the same week. This (thursday) is actually our first morning working in the Robison lab, because we went straight to sea for 2 days after orientation. The first day we deployed the midwater respiration system (MRS), which can capture midwater organisms (in this case, sergestid shrimp) and measure their oxygen consumption while left at a mooring. The next day we picked up the MRS and also did some video transects with the ROV at various depths in the midwater, 50m down to 1000m. We say some neat organisms and are now in the process of planning out our summer projects. I am interested in the behavior and distribution of deepwater bioluminescent cephalopods. Posted by kthomas at Jun 12, 2014 11:54
The first week has been great so far! I have started working on the MBA/MBARI AMP Exhibit, in which a model ROV, with a projector attached to it, will be suspended from the ceiling of the exhibit. It will then rotate/tilt to project and interactive video of marine life on a wall of the exhibit. I have started working on the design of the suspension system to allow the model ROV to safely hang from the ceiling while still being able to perform the necessary rotation/tilt movements. So far I have made a few digital models/drawings using solidworks for some of the basic components of the system. On Wednesday, Laughlin and I went through the orientation to use the model shop and we got to have some fun with the machines in the shop, using the mill, lathe, and band saw. I also went up to Santa Clara University with my mentor and met with associate professor of mechanical and electrical engineering Dr. Christopher Kitts and got to see some of the cool robotics and ROV projects that he has been working on. I have really enjoyed my fist week here at MBARI and am looking forward to the next 9 weeks! Nate Posted by nreed at Jun 12, 2014 12:14
What a week! I finished up my exams, moved out of my dorm, and had my first day at MBARI all on the same day. I'm loving the experience so far. The community and the building themselves are so stimulating: the Wednesday seminar was fascinating, and I keep on getting distracted by the posters on the walls. My mentor, Rich Henthorn, has so much to teach me about software engineering, approaching and designing projects, and testing out the ROVs themselves. I'm excited to help him out with the rovers next week. We decided on a project from which to start: improving the image analysis of the Sedimentation Event Sensor. I love that I'll be able to make something that MBARi can use. Posted by cordelia at Jun 12, 2014 13:09
This is really Lisa Ziccarelli's comment Danelle, John and I have been discussing possible project ideas. We will be using LISST-HOLO data to explore associations between the zooplankton and the environment. Posted by mage at Jun 12, 2014 13:43
Like Will T I have been given the pleasure of planning my own research project. Due to various members of the team being busy elsewhere I have until Monday to bring something together. I have been studying the data of the Alarcon Rise and become very excited about various fissures, pillow lavas and sheet flows. (Mostly the fissures, I like faulted and fissured rocks.) The deep water biologists would be delighted with the wildlife around the vents, but it's the geology around this wildlife sits on which has my interest. I have been reading papers to establish what work has been done here and elsewhere on the East Pacific Rise. I have also been looking at the seafloor maps and getting used to the wonders of 1 metre resolution. Posted by kwillis at Jun 12, 2014 14:03
Like Will T I have been given the pleasure of planning my own research project. Due to various members of the team being busy elsewhere I have until Monday to bring something together. I have been studying the data of the Alarcon Rise and become very excited about various fissures, pillow lavas and sheet flows. (Mostly the fissures, I like faulted and fissured rocks.) The deep water biologists would be delighted with the wildlife around the vents, but it's the geology around this wildlife sits on which has my interest. I have been reading papers to establish what work has been done here and elsewhere on the East Pacific Rise. I have also been looking at the seafloor maps and getting used to the wonders of 1 metre resolution. Posted by kwillis at Jun 12, 2014 14:19
While slightly hectic, this week has been great. I have thoroughly enjoyed meeting you all and am looking forward to a great summer! What a great bunch of people... the cream of the crop! It was great to get out to sea on the Carson this week and round up some Sergestids for the MRS deployment. While out at the shallow MRS mooring, we couldn't help but notice the abundance of Octopus rubescens and collected a few (some accidentally). They are now in a tank in the seawater lab if anyone is interested in seeing them! They are small, active, and hungry and have prompted me to explore the possibility of an alternate project as opposed to the one I had already planned. However, I think I will likely stick to my original idea of Dosidicus interspecific communication and foraging behavior at depth. Who is excited for the BBQ next week? How about a trip to Big Sur? The possibilities are endless here. Posted by bburford at Jun 12, 2014 15:06
I had a great first week at MBARI. After having discussed the goals for the internship project with my mentor (essentially clarifying relationships between vent mussel populations in the indo-Pacific and developing molecular markers), I have started some PCRs in the lab to identify which genes might be useful diagnostic tools. I am excited about seeing how it goes on! Posted by cbreusing at Jun 12, 2014 15:40
My first week at MBARI was amazing! Finally after 4 days I can navigate around the building without looking completely lost. This week, I worked alot with the post-doc in my lab, Amy Zimmerman, learning how to make media and work the flow cytometer. The information I have learned has been extremely overwhelming, but in a very exciting way. After a long meeting today with the two post-docs in my lab I have a better understanding of what I will be doing for my project. Next week I will begin to test which media the picoeukaryotic phytoplankton, Ostereococcus, prefers. After this I will begin to test what the ranges of nutrient depletion of picoeukaryotes are. I can't wait for the weeks to come. I am loving it here and it has been fun meeting all of you. Posted by zjensvold at Jun 12, 2014 16:55
My first week at MBARI has been both exciting and eventful. This week was basically an introduction to the lab, learning how to do certain laboratory techniques as well as doing some background reading on my project topic. Today I spent most of the morning with an REU intern who I will be working closely with as well as with two post-docs that will be mentors for my project. My project will focus on nutrient stoichiometry and how it affects the growth conditions of different strains of phytoplankton. We are going to start culturing strains next week and will collect data to determine what the growth curve looks like for the cells. This will be a good starting point for our project. Posted by amaitland at Jun 12, 2014 17:01
I've had a great first few days at MBARI. With the help of Jules (in Francisco Chavez's lab) and of course Dr. Chavez's guidance, I've been learning about how to calibrate temperature readings from a logger board. I've also made a good deal of progress figuring out the question I will ask. It was a busy week, but definitely productive. I really like the environment at MBARI. Whenever I need a short break, the pacific room is often open, so I can attempt to see whales feeding and/or breaching. It's been about 50/50 so far...good odds! Posted by jlafian at Jun 12, 2014 23:26
Sorry for the delay in posting! My first week was really interesting. After a lot of background reading and discussions with Dr. Haddock, I've decided to spend the summer comparing the luciferases in five different species of squid. It looks like I'll be doing a lot of work with the many different transcriptomes Dr. Haddock has access to. I'll also potentially get to do in-lab experiments if we manage to catch some of the species I'm looking at. On Thursday, we went out on the Rachel Carson and collected quite a few different ctenophores and siphonophores. All in all it was an exciting first week! Posted by thersh at Jun 15, 2014 19:11
A good first week - lots of meeting new folks, getting settled into my workspace/computer setup. Immediate goals for this week (and next) are to get the test tank prototype profiling float up and running. To do so I need(ed) to make a couple of hardware modifications, some of which I knocked out Wednesday/Thursday. Have some stainless Swagelock to bend/modify, and then a PCB to remount. Should be able to close up the float (hopefully) at that point. Have to learn C#, which is on the list of things to tackle this coming week, along with the above mentioned hardware mods. I should also be getting to the more exciting modeling/dynamics/differential-equations stuffs that is in my opinion, the exciting part! Looking forward to next week! Posted by lbarker at Jun 15, 2014 21:05

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