Dear MBARI diary,

Day three, I am becoming more excited about my project as I start to outline the process and set up a few experimentation days. My first experiment with abalone is next Wednesday, so I have been working with Dr. Jim Barry on figuring out the logistics of how we are going to run the test. I'm also going to be working in the Barry lab soon where I will be messing around with carbon dioxide to make the pH of the bay seawater increase and decrease in order to prepare it for my test tubes – and I get to use stunning machines to manipulate chemistry...(cue mad scientist laugh). I've also been speaking with many people in my respective field who have brilliant perspectives and astounding approaches to problems I am only beginning to understand. Nonetheless, I am eagerly awaiting the launch (lunch) of my abalone project and am hopeful for the rest of this summer.

Best fishes,

It was really cool going on the beach right in front of Pacific Forum during breaks. I cleaned up the cabinet and came up with questions for Chad to clarify specifications for the project that I will be working on this summer. I was introduced to the FOCE project lab, the EE tech lab and EE lab. Chad went over what I will be doing this summer today and I did some research on the 4-20mA current loop. I have decided on using XTR117 for the current loop transmitter and started the software flow diagram for the terminal that I will be using to test my instrument simulator. I can't wait to test the circuit and work in the FOCE lab!

Week 1:

I am working this summer on gathering dissolved oxygen datasets with the hope of looking at trends in the central and southern California region.  There is some indication that dissolved oxygen levels are decreasing in the California Current region, especially some indications from observations from the CalCOFI repeat hydrography program.  Changes in dissolved oxygen may indicate changes in climate, currents, biogeochemistry, and even biology in the ocean.  Dissolved oxygen is one of the oldest parameters used by oceanographers.  It tends to indicate the "age" of a "water mass."  The lower the dissolved oxygen, the longer the water has spent away from a well-mixed surface layer of the ocean.  (Respiration decreases the concentration of oxygen, and outside of the euphotic zone there are few sources of oxygen).  Lower dissolved oxygen in the California could be the result of many things, including increased atmospheric CO2/climate change.

This week, I set up my computing work environment including a CeNCOOS workstation and my personal laptop.  I also started a list of datasets with dissolved oxygen.  I downloaded data from CalCOFI and determined that CeNCOOS shore stations would not be applicable to my project. I also worked on my model output data, updating my dataset to include 2011-2015.  For fun, I'm helping to deploy the wave glider on Thursday June 11.  Tom O'Reilly keeps me company in building G and kindly gave me the opportunity to volunteer.  I get a chance to be on the Paragon.

This summer I would like to learn Python; I'm an intermediate Matlab user.  I'd love to improve my Matlab skills, and I should actually be learning Fortran.  The list of things to do is always endless, no?

Week one so far has been an outstanding experience already. Everyone is so friendly and helpful which makes me feel really welcomed. On top of that, I'm really enjoying the project that I'm working on so far. Granted this is more of a prologue since I'm learning IPython Notebook at the moment which will be used when I really start my project. It's actually not that bad of a language since it's basically Python (which I'm familiar with) with some new preloaded assets such as matplotlib, numpy, scipy, and other libraries. Everything is so far so good and I think that the summer here is going to play out just as nice (if not better than it already is).

Larvacean Log, Week One: Over the past two days I have poured over hours of video of the bathochordaeus (which I still have not managed to spell correctly without looking it up). We are investigating the kinematics of these organisms, both when they are swimming freely and when they are swimming in the "houses" that they construct. The swimming mechanism is different for each of these cases. When they swim freely, they send a traveling wave through their tail, propelling them in a direction. However, when they are in their houses, the wave does not seem to propagate through the entire tail; instead, it stops slightly past the midway points and sort of hinges off. The question of why the swimming mechanism changes is of great interest to us.

While the videos are very high in quality (and quite beautiful), both the camera platform and the organism are moving during all of them. This makes the kinematic extraction much more difficult, and out of the range of things I have ever attempted. Therefore, my Matlab skills will need a serious boost to figure out a method to manipulate the videos to keep something still. Luckily, Kakani taught me a few new tricks with video processing in Matlab. Hopefully, by the end of next week I will have developed a protocol for measuring the waveform. 

MBARI is even more spectacular than I expected it to be and I can't wait to see more of the bay and surrounding areas. Plus, we start scuba diving certification tomorrow! 

Week 1:

This summer I will be working on a project in Ken Smith's lab assessing the enteropneust population at Station M (~4,100 m). The lab has been collecting data at this location for the last 24+ years and is one of the few abyssal plain locations in the world that has long-term data. I will specifically be using the time-lapse images at this site from 2006 to present in order to execute this project. While I am looking at the images I will take notes regarding their feeding patterns and if there is time after I have processed the population results I will look further into their feeding ecology. Additionally, I will also look at the ROV transects fr closer images of these organisms. Linda has indicated that these ROV images show enteropneusts with eggs and potentially associated organisms so I am very excited to get a closer look at these fascinating creatures. Anecdotally the population has increased due to an increase of food supply at this site so I think it will be very interesting to quantify their population.
So far this has been a busy but amazing first week. It is really wonderful to be surrounded by people with different research interests but are each incredibly passionate about their work and other hobbies! I really enjoyed the Wednesday lecture on biomimicry and I can't wait to attend more.
Cheers,
Jessie

P.S. If you are interested in finding out more about deep-sea enteropneust here is an excellent paper about their diversity. Linda is one of the authors so you should definitely check it out! http://rspb.royalsocietypublishing.org/content/early/2011/11/10/rspb.2011.1916

Osborn, Karen J., et al. "Diversification of acorn worms (Hemichordata, Enteropneusta) revealed in the deep sea." Proceedings of the Royal Society of London B: Biological Sciences (2011): rspb20111916.

11 June 2015 (Thurs):

Week one has progressed smoothly. The facilities are comfortable with a plentiful amount of coffee, support, and excitement. I've thoroughly enjoyed the intern activities so far such as the seminars, cookie break, and orientation. I was taken back about how social all the workers are here and their willingness to strike conversation with me, but I have learned to embrace the acts of friendliness.

This week my mentor Jenny Paduan introduced me to the Sample and Expedition Database, both of which I'll be working on this summer. She told me the background context of the information provided by the databases as well as the issues that occurred after switching the server from Typhoon to Wind. My current objective is to identify errors present in the databases on Wind and if an error is found, search through the code to find the problematic code. My other two mentors Joe Gomez and Rosemary Martino-Rodriguez have been assisting me with any server or coding issue I need help with.

Highlight(s) of My Week:
Seeing a sea otter.
My first time fixing a few lines of code for the Sample Database.

Orientation on Monday was busy and exciting and left me very excited for the rest of my summer at MBARI. Unfortunately I won't be able to return until next week due to school finals, but every day I've been thinking about how fantastic my first day was! I enjoyed meeting the other interns and especially enjoyed meeting Ed Peltzer and Peter Walz, two scientists with whom I'll be working in the Brewer Lab. During my couple hours in the lab on Monday, I learned about my project using Raman spectroscopy to study gas samples evolved from oil collected in the deep sea. I practiced compressing gas, which enhances the signal from Raman and which I'll be doing with all the samples. Peter also gave me a brief lesson and demonstration on Raman, showing me characteristic peaks in the spectra for seawater and ethanol.

End of week 1:

This summer I am working on getting free food as often as possible as well as validation and optimization of a low cost chemical sensor developed by an intern in 2013. So the plan is, first, look into replacing some of the current components with less expensive alternative. Second, build another sensor so I can collect field data over long periods of time and run controlled lab experiments at the same time. Finally, compare the field data with the experimental data and compare the results. This will be done under the supervision of Ken Johnson, with help from lots of the people in the chemical sensor lab.

Week one is coming to and end and it has been a great one. This summer I am working with Brett Hobson and many others to determine the orientation of jellies in relation to ocean currents. As many of you have probably heard from me it involves a lot of Matlab, which is not one of my strongest skill sets, but I will survive. I have received help from many people already which makes me very comfortable knowing everyone is here and willing to help. Overall I am still trying to get my bearings and work down my list of things to get done for the week. However, I did get to drive a crane yesterday which was awesome and I am hopefully going to watch the launching of the Wave Glider today (fingers crossed). I cannot wait for what the rest of the summer has to offer!

Acoustics Week 1:

 My first visit to the US and that too for working on applications of oceanography couldn't have asked for more.  The jet lag did kick in but it vanished on my first visit to MBARI , the tour all of the all the labs, facilities, watching the auv's and the rov's, free food and not to forget the limitless pacific ocean does put my mind to peace. Its amazing to see how seminars, activities, cookie breaks,barbeques etc are put together so that people can get out of their cubicles to socialize and exchange ideas.

My project here at MBARI is all about playing around with the acoustic signals of the underwater mammals( blue whales, Risso's dolphins, beaked whales etc.). My task is to design a classifier that can automatically distinguish between these creatures(blue whale? or beaked whale? or dolphin ? etc) based on their acoustic encounters with the MARS observatory using a hydrophone in the real time. To distinguish between any two things( in this case underwater mammals) it is important to find out  common features based on which they can be distinguished , so that's what I am working on currently i.e the extraction of  acoustic features(Energy, auto-correlation,MFCC's,entropy etc) from the already collected acoustic data ( dataset provided by the Scripps Institute of Oceanography) of the various species.

Both my mentors Danelle Cline and John Ryan are really enthusiastic about the project which makes me work even more, I am really looking forward to this summer for work and enjoyment!.

Week 1

It is hard to believe that my first week at MBARI has already come and gone. While it has been a whirlwind adjusting to a new schedule, and orienting myself to a new building (albeit not so very far from my office) it has been an incredibly rewarding first week. I have spent the bulk of this week working with Richard Henthorn ona program for the benthic rover that scans the data files it creates (syslogs) for important information.

As we have heard this week ship time is very expensive, and it is important to work as efficiently as possible. When the Rover is brought aboard the ship, the team used scan through the syslogs by hand.

These files look like thousands of lines of:
013-06-19T16:27:01.68,Aanderaa,_ Obtained data port_ref_optode: o2=291.99,sat=92.85,temp=15.02
2013-06-19T16:27:06.50,Aanderaa,_ Obtained data port_ref_optode: o2=292.26,sat=92.96,temp=15.03
2013-06-19T16:27:11.42,Aanderaa,_ Obtained data port_ref_optode: o2=292.49,sat=93.05,temp=15.04
2013-06-19T16:27:12.90,Launch,_ Optode baseline reading is 93.05
2013-06-19T16:27:16.44,Aanderaa,_ Obtained data port_ref_optode: o2=291.98,sat=92.91,temp=15.05
2013-06-19T16:27:21.46,Aanderaa,_ Obtained data port_ref_optode: o2=292.03,sat=92.95,temp=15.06
2013-06-19T16:27:26.49,Aanderaa,_ Obtained data port_ref_optode: o2=292.25,sat=93.03,temp=15.0

What my program does is scan through each line and looks for 3 things. Firstly it looks for "propulsion motors on" which will tell us when the rover starts a move. Secondly it searches for "favorablecurrent behavior" which tells us when the rover starts looking for favorable currents to move, and eventually how long it performs that behavior. Finally, the program searches for "difference between current and desired heading.This tells us how far off the rover is from its prescribed path. It then drops the lines matching the above behaviors into their own files so the team can instantly see how the rover is performing.

Finally, the program takes the time stamp at the beginning of the line(see above) and converts that into the number of seconds elapsed since the start of the deployment. This is way the team can see exactly how far into the mission things are happening.

I have already improved greatly as a programmer, and can't wait to improve on this project. The rest of my time has been spent preparing for our cruise next week, which I am hugely anticipating!

Week one:

This week has been very exciting, MBARI is such an incredible powerhouse of research and everyone I have encountered has been very welcoming and helpful. To be quite honest, I am still working on getting my bearings on both navigating the building and further understanding my project. I am working with Brett Hobson and a number of others in the Long Range Autonomous Underwater Vehicle lab, my project is to develop an improved ballasting procedure which could increase the range and improve the dynamic control of the LRAUV. Throughout the week I have been reading through documents and speaking to others in the LR AUV lab and other labs to gain a better understanding of the LRAUV itself, as well as ideas on potential methods to accomplish an improved ballasting procedure. Looking forward to the weeks to come, as I am excited to work with everyone I have met (and will meet) to make progress on my project.

I cannot believe my first week at MBARI is coming to an end! It frightens me how quickly this summer might go. On my first day here I felt like a little kid visiting Disney World for the first time. I was very impressed with the facility, the amazing technology available, and very friendly staff here at MBARI (oh and the amount of free food, especially cookies!). I can already tell it is going to be very hard for me to leave when my ten weeks are up.

My project here is working with Brian Schlining and Kathy Dunlop on photogrammetery in the deep-sea. MBARI has years worth of videos recorded by a camera mounted on the ROV Doc Ricketts at Station M (~4000m at the Monterey Deep-sea Fan) and since 2006 scientists have measured megafauna body size through these videos on the Video Annotation and Reference System (VARS). They are able to so with the ROV's two paired lasers, which are always 29cm apart and acts as a scale bar in the recordings. However, for maximum accuracy the organism of interest must be oriented horizontally across the same plane the line the lasers make. If the organism is oriented vertically or horizontally across this plane it can still be measured but with a bit of error.

This is where I come in! I have to find a way for correcting these measurements. So far, I have thought about measuring the percent error and precision of measurements starting horizontally across the primary point (basically the midpoint between the lasers) and then measuring the same from angles increasing by 10 degrees from the horizontal line. Today I found out that VARS does not tell you the angle in which a line is drawn so I am currently thinking about doing the same but instead of increasing by 10 degrees, increasing by a certain number of pixels. Once I figure out how to do that I will use VARS to make measurements on a color calibration board and then I will physically make the same measurements on the physical color calibration board. Then comes in a lot of math and I am sure more factors I haven't thought of yet (such as the height of the camera above the bottom of the seafloor and angle the camera is looking down from the horizon).

Week 1: June 11

I spent a lot of time this week downloading software and familiarizing myself with Mathematica, R, and 3D geometry. I'm working with Steve Haddock, and my project is trying to find out how radiolaria form their intricate glass spherical colonies, starting by modeling the structure and then thinking about how the organisms might handle the process, so I've been modeling spheres formed by subdividing faces of polyhedra (octahedron and icosahedron are the stars for now). Whether or not the method of subdivision is possible with tiny glass rods, and how they might do it otherwise are the big questions. I also have to read up on silica deposition to see what methods of growth have been observed in other organisms.

Because it takes a while for the computer to compute the shapes (5 subdivisions took at least 30 min to plot), it looks like I'll also get to work in the lab helping with genetics work. Working on the cool structure problem and also getting to learn PCR and DNA extraction etc, I basically get to have my cake and eat it too!

Added by Lisa Ziccarelli , last edited by Lisa Ziccarelli on Jun 10, 2015
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We're having a great start this week and I'm happy to see everyone is settling in alright and getting excited for the summer. We've organized an open water dive class for several of our interns that starts this weekend. Meanwhile, I have been working on 3 projects. The first is conducting the quantitative phytoplankton counts for CANON15 day cruises via epifluorescence microscopy. Unfortunately, the microscope has been under repair for about a week, but Kurt is working on it and says it should be ready by the end of this week. The second is working with the Chavez N15 data. To this end, I have begun learning MATLAB from square one. It's a great deal to learn in just a few weeks, but I've got some excellent teachers, including Brian and Reiko. The third project is learning how to process eDNA samples. While Kris and Kevan are finalizing the protocol, Shannon has taken me through extractions.

Week one:

This exciting experience in MBARI will be better than I thought. I started meeting so many people who received me very kind and friendly, and eager to learn Spanish. Knowing all MBARI and enjoying its majestic scenery.

My work this week has focused on knowing and learning how to handle the Video Annotation and reference System (VARS), a very useful tool for summarizing the cruises made by MBARI. Also, I started to explore the videos from a cruise in Isla Tortuga South, Gulf of California, 2015. I have been seeing and identifying amazing organisms with unique features and adaptations that allow them to live at great depths. On the other hand, I am very surprise to notice that people from MBARI are using my work to identify these organisms; even regardless of my work is in Spanish.

I am very grateful for this opportunity and also to the people who work in MBARI, including all interns, for making me feel at home. (GRACIAS !!)

A little late but here we go,

When I mentioned to the older researchers at my university that I will be doing a summer internship with MBARI via the CSUMB REU this summer I must have been told a dozen or so times about how fortunate I am to have this opportunity. As joint CSUMB/MBARI interns Madison, Robert, and I are able to benefit from the weekly skill building workshops designed by the REU while also working at a world class institution with mentors that are very invested into our projects. I am working with Dr. Charlie Paull and his research assistant Dr. Roberto Gwiazda to try to determine the implications behind what we believe to be whale created depressions on the seafloor in a remote part of the Canadian Beaufort Sea.

Like many others here I am using VARS to annotate ROV data. The videos that I am looking at were taken from multiple dives spanning from 2010 to 2013. When Charlie and others first explored this part of the Arctic they were originally drawn to the location by using sonar to locate high reflectivity spots of the ocean, with these reflective hotspots indicating that some sort of gas was seeping out from the seafloor (later identified to be methane). They were surprised to find the frequent and large depressions that existed around the methane seeps and it would be a few years after the first expedition before marine mammals and specifically whales would be seen as the cause for the depressions.

As a first order analysis I am looking at the ROV data and using VARS to note whale marks whenever I see them. Using the distance between the two beams shot out from the ROV as a measuring tool I am also taking note of the width of the marks and other characteristics (i.e mark pattern, visibility, impact on surrounding) to match what whale type/types could have created the depressions. This will eventually lead to the question(s) of why would this whale type be feeding on the bottom of the ocean in this high of abundance? Has this been seen in other places? Is there a direct correlation with the methane seepage seen in this area and the whales' decision to feed in these places? I think I'm off to a pretty good start and I'm excited to see where this project will go. Hopefully I will produce something useful out of it at the end of the summer but you never really know...