if you click on the add comment tab (look below), you can insert your update and it will show up under your name.

Just learned how to add a comment on the confluence dashboard! Met with my mentor and discussed possible project ideas. I think I've narrowed it down to something very exciting that should keep me more than busy throughout the summer. I am finding it hard to differentiate my responsibilities with the STAR program and those expected of me through MBARI. There seems to be some overlap, so we need to find a good plan for me to meet all my requirements.

Wanted to get this in today since I will be out on the Carson tomorrow.

I hope everybody has gotten the first week jitters out of the way and are adjusting to life here at MBARI. I'd like to reiterate that if you need help with anything while you are here don't hesitate to email me, call, or drop by. This internship is an amazing opportunity, and I'm here to help you get the most out of it.

Since I wasn't there to meet you all on monday let me tell you a little about myself. I am graduate student in physical oceanography at Moss Landing Marine Labs, just up the hill from MBARI. My thesis is on internal waves in submarine canyons (which I'd be happy to tell you all about sometime). I worked with the Smith group last year writing a machine learning algorithm for the Benthic AUV that if implemented could correct navigational errors throughout the course of a deployment. I really enjoyed this project because while I had an interest in machine learning, and vehicle programming, I had no background in them whatsoever. This meant that I got to be very hands on and develop 2 new toolsets over the course of the summer, and see that work immediately applied.

This year I am staying a bit more in my wheel house and analyzing current meter data from the Rover, and nearby Camera tripod, both of which are deployed in the deep ocean at Station M about 200 miles SW of San luis obispo, and a depth around 4000 M. There are very few current meter records this deep in the ocean, so it will be exciting to describe the physical environment at Station M.

It's only the first week and it's been plenty busy (not that I mind at all)! Although I've read only a few papers, I've learned a lot about the project I'm a part of and have an idea on what my focus will be. MBARI seems like a really awesome place to be: right outside the window of the Visiting Scientists Office aka my unofficial office is the beautiful Monterey Bay and all the people working here seem to be really great!

I'm super excited to be working at MBARI this summer and am glad I have been given this opportunity to explore the field of marine science!I can already tell I'm going to hate leaving MBARI after summer is over...

First week at MBARI is awesome. I am still developing my research question as well as preparing the materials, methods, and plan that goes along with that. So far I think I will be researching how climate change stressors (low pH, high temperature, and hypoxia) will affect sperm motility using red abalone as a model organism. I may couple this research with how these stressors affect the egg jelly coat and fertilization kinetics.

So excited to dive into this project and to hear what the rest of the interns are taking on

We've only spent three full days at MBARI but we've already hit the sea swimming (sorry, had to). After orientation, I spent day 2 getting started with MatLab and beginning to familiarize myself with some of the principal data sets I will be studying this summer--my research question is still developing but I am planning to use the Monterey Bay Time Series data (Temp, Sal, chl-a, nutrients, etc) that my mentor Tim Pennington has helped to collect over the last 2.5 decades to look into the changing parameters of MBay. I am particularly interested in the recent warming events in the bay (the "blob" and the current El Niño) and comparing them to past years and perhaps other geographic areas (ie. the central Pacific or other latitudes of the west coast).
Bryce and I spent day 3 participating in the collection of the data we will be analyzing over the summer aboard the Carson with the "CTD Team." We stopped at three sampling sites including M1--MBARI's principal mooring station that is often used as a representation of all of Monterey Bay in terms of SST and other essential parameters. The CTD we sent down collects data on temperature, salinity, and depth in real-time and the water samples collected in a Niskin-bottle rosette are brought onboard, filtered, and then analyzed to determine chlorophyll-a, nutrient content, and the eDNA genetic material that Bryce is interested in among other measurements. So cool to be part of this time series legacy!

Countless trips to Phil's over the years have often involved walking past MBARI's grey buildings and R/Vs. Ever since I was a kid, I'd been curious about the goings-on here, wondering what it'd be like to be a part of such a prestigious place. Needless to say, it feels awesome experiencing this dream-come-true opportunity!

It's been a fabulous first week (bacon anyone?) with plenty to learn and explore. I'm still processing the heaps of information that's been thrown at us the past few days, but things have been falling into place. The MBARI staff has been welcoming and extremely helpful—the sense of community here is truly something special.

My mentor, Susan von Thun, pitched a great project idea that taps into my design and communications background. Broadly speaking, I'll be creating a content-rich interactive webpage that will feature a specific story or topic (to be determined**). The final product will be shared on MBARI's social media outlets and we'll assess the analytics and feedback (e.g. visitors, page views, shares).

I don't doubt there's plenty in store for the interns this summer; the excitement amongst us seems to be mutual. Looking forward to the coming weeks!

**Update: Looks like I'll be focusing on the Southern Ocean for my project! Totally stoked on this!

Monday (6/6/2016)

• Orientation and tour of MBARI facility.
• Met with Ginger from the Chemical Sensor lab
• Updated user password and checked email
• Setup workbench in lab

Tuesday (6/7/2016)

• Met with mentor, Gene Massion, and learned about coastal profiling float (CPF) project and the overall research mission.
• The research team wants to have CPF drift near shore, but not get too close and not too far away (it has to be just right!) so that they can measure temp, pH, nitrates...
• These are passive floats (very similar to the floats used in the ARGO project), they do not have propulsion systems to steer. To ensure that the float does not beach itself, we can use the internal pump system on the CPF (the "dive engine") to change buoyancy of the float and have it drift at a particular depth and catch an underwater current that would cause it move back into the volume of ocean we are most interested in measuring.
• But fist we need to locate these underwater currents and characterize their flow during each mission, so we would need a way to measure the drifting float velocity while it is underwater and out of communication with GPS.

• For the internship, I am tasked with trying to determine if it is feasible to use a small inertial measurement sensor (IMU) to measure the underwater drifting velocity. The sensor is small and cheap (you have them in your smart phones), but provide noisy measurements that result in accumulated error over time. The sensor measures accelerations that are then numerically integrated to get velocity, any error or noise is compounded during integration...yikes! So I will work to create a simulation model to predict the magnitude of the error that we could expect to have so that the researchers and engineers can determine if using these MEMS sensors is a worthwhile endeavor.

Approach (this is sure to change and evolve over time)
a. make a Matlab/Simulink model of a 9 degree of freedom (DOF) IMU and include mathematical models for accelerometer, magnetometer, and rate gyros
b. add error terms for drift, bias, white Gaussian noise, and cross coupling
c. write a program that inputs the floating buoy path and estimates the error in the predicted velocity based on the sensor model
d. validate the model with testing in the tank
e. if model is validated, test some simplifying assumptions Gene has about how the buoy moves underwater and characterize roll, pitch, yaw rates while buoy rises to surface.
f. if this all works, try an ocean test and see if we can measure the underwater drifting speed in the OCEAN!

• Met Jose, Tom and Jim from the Electrical Technician lab. Was shown how to use the soldering equipment and fabricated a wiring harness for the IMU sensor that I will be using.

Wednesday & Thursday (6/8 - 6/9/2016)

• The rest of the week was spent learning to use Microsoft Visual Studio to program in C# ("cee-sharp") programming language.
• Working to write drivers in C# so that we can communicate with the BNO055 IMU and read the sensor values over I2C bus lines.
• I am learning how to use this programing language and also how to write drivers to interface different pieces of hardware together.

Goals for next week:

• Finish writting the drivers for the IMU and start reading sensor data to SD card to verify it is all working as expected
• Start working on the Matlab model of the IMU sensor
• Create code to take accelerometer data and numerically integrate to obtain velocity estimate.

My mentor is out of town this week but a post-doc who works under her has been here showing me the ropes and my mentor (Monique Messie-didn't know how to get the accent mark over the last 'e' sorry!) has been super helpful over emails sending papers and example MatLab scripts to look over! I have been messing around with one example to run for different variables at different time periods that were recorded on the Dorado and that has been pretty interesting. This project is open ended so I am still trying to figure out what my exact project will be, but I will be discussing it with her when she gets back next Tuesday!

First week is going well; It has included a lot of (interesting) reading so far, and yesterday Ed and I successfully mucked up the MATLAB installation on my lab computer, forcing Peter to do a clean install for us this morning. It seems to be in working order now though. We've been doing some prep work for our trip out on the Rachel Carson on the 23rd, setting up a capture system for midwater jellies that we can flood with Argon to get a clean Raman signal. I've been learning about the DORISS II setup and operation, both the advantages and disadvantages, and the hopes they have for the DORISS III system currently in development. Still working on a specific research question for the summer, but it's looking like it will involve setting up processing software for data obtained with the DORISS III setup in such a way that we can make meaningful comparisons to the spectra already collected with the earlier systems.

MBARI is pretty much a dream land for nerds(me). Everyone is so friendly and helpful even if they don't know you, I got lost yesterday, of course and met Jim Montgomery from Wisconsin who's an electrical engineer here and he was more than happy to show me the way. Everyone smiles even when its early in the morning!

Tuesday I met with Dr. Chavez and came up with my research project which will focus on eDNA to determine if the high population of anchovies in the years 2012, 2013, & 2014 was due to a preferable zooplankton species being present. DNA extraction and PCR are two lab techniques I will most likely be using to analyze data from samples. Dr. Chavez gave me a proposal to read as well as a lab protocol. Yesterday I was fortunate enough to go out on the Rachel Carson with Zi and Gabriela using the CTD. We collected chlorophylls and filtered eDna using a .2 micron filter. Today I will be working with Kristine Walz in lab getting eDNA from the Gulper(an AUV) samples and finishing reading materials.

First, let me just say that MBARI is basically Willy Wonka's chocolate factory for science majors!! This place is incredible and I am so happy to be here! So far this week I have been working on forming my research question for my project, as well as getting familiar with the software that the deep sea lab uses to analyze data. I having been using the VARS software mostly, which allows you to annotate imagery collected at Station M over time. I think it is awesome that the software was developed here at MBARI, by Brian Schlining! My focus area for my research project concerns Echinocrepis rostrata, which is an unusual looking sea urchin species that is periodically present on the deep sea floor at Station M. This species has been found to be a good indicator for impacts of climate change within the ocean, specifically within the deep sea community. I am currently going through imagery collected at Station M and observing the moving/behavioral patterns of this species, as well as trying to determine whether there are differences in such patterns when comparing individuals of different color and age. Aside from that, I will be going on a cruise next Wednesday with my mentor and the rest of the crew from the deep sea lab. We will be going on the Rachel Carson, and I can't wait! I am excited for what is to come and ready to learn!

Cool first week at MBARI! I spent the first half of the week researching different potential projects, but as of late yesterday my project is ironed out. The LRAUV operators write mission scripts in a clunky language called XML. It has its uses, but for the operators wanting to quickly define a new kind of mission, it's very cumbersome. I'll be spending the summer developing a domain-specific language (DSL) for them to use for writing mission scripts. A DSL can be cleaner and less clunky than XML because it's single-domain: it doesn't need to support the same wide-range functionality that a language like XML does. After developing the DSL, I'll work on a translator from the DSL back to XML so that new code they write is compatible with the old stuff. Next week I'll continue to familiarize myself with the XML schemas used to write mission scripts, explore language parsing for the eventual translation, and meet with LRAUV operators to hear their thoughts about which parts of XML work for them, which parts don't, and what their ideal language would be like.

Have a good weekend all, see you on Monday!

I'm finding that I very much enjoy working at MBARI! Everyone is extremely friendly and helpful, and it feels as though I am quickly becoming a member of the MBARI family. I have been working hard with the Haddock lab to prepare for our upcoming week-long research cruise (leaving tomorrow - yay!!). We've been loading up the Western Flyer with the gear necessary to track and collect organisms that emit bioluminescence. I will be performing assays on the luciferins (light emitting compound)/luciferases (oxidative enzyme) found in bioluminescent ctenophores, radiolarians, doliolids, and more to determine the biochemical processes that characterize each organism's light emission. Joining us on board will be a BBC camera crew to document the cruise's finds and compile them into a film on bioluminescence. This will be my first overnight cruise, so this should be very fulfilling and exciting!!

It's just the first week but I know I'll miss a lot this place. I made a big big travel for being here and at first I was so afraid about being so far away from home, talking and listening another language and just being surround by strangers. But I couldn't be happier right now. Everyone (interns and people from MBARI) are so nice and very patient with me and my english.
My mentor is not here until next week but I have like another mentor and she's very nice with me all the time. Also my lab is very international, there's people from France and I think there's someone from German I can't remember but I feel like I'm not the only one with some difficulties with the language. All of them seems very smarts and they're working on really cool things so I hope I can learn a lot of things from them.
We're working with micromonas (picophytoplankton) and what we wanna do this summer is find out if micromonas are myxotrophis or not. For this week we have been doing some new cultures and measuring them using a very cool machine called The accuri and today for finishing the week, I did it by myself for the first time!!!
I find everything very interesting although we're still not doing so much things, just like the introduction so I really wanna see what we're gonna do next week!

I also met a women called Katie Loweth. She's from England and she can talk a little bit of Spanish so that made my day!!

Have a nice weekend

Orientation day was mind blowing as we got a glimpse of the projects that MBARI is capable of doing! I unfortunately had finals and had to leave after orientation but I did get a chance to meet with my mentors - Aric Bickle and David Anderson. We brainstormed some ideas for what I will be doing for the internship. Part of the CENCooS monitoring program include looking at ocean acidification and we want to write a story on how ocean acidification will have an impact on humans. Our current idea is to interview scientists and businessmen in the areas of aquaculture and looking at it from both a scientist's angle and from a business prospective.

I will start working officially tomorrow! Today was a great day aboard the Rachel Carson

This is very late as far as "Thursday Updates" go but I've just arrived at MBARI and am really excited to get started with everything! Last week kind of went by like a blur, taking finals and packing my apartment and walking at graduation, but now I'm ready to be here instead. There is a ton of stuff that I'm not sure about and I haven't really done anything worth updating on yet, but I did install a mouse onto my computer and fix a tax form so at least I have accomplished something. Hopefully by Thursday I will have more to report on!

This week has been very exciting for me, so I'm posting my confluence update a day early (I'll be gone tomorrow). On Monday, I had the privilege of joining Dr. Stephanie Bush on the hunt for the opisthoteuthis sp. flapjack octopus! I was told to not get my hopes up as they are not always successful, but opisthoteuthis was the first thing we saw as the ROV hit the bottom. The first 30 minutes were really exciting and then the next 8 hours of sea sickness made the trip a bit less fun, but I had a blast and I'm really glad I went. Tuesday was really interesting, since I'm ahead of schedule on my project, I got to sit in on the presentations during the DOEST board meeting. I was able to gain a better working knowledge of my own project and the role our project plays in the future of MBARI. I was also happy to finally talk to someone in my own field, Microbiology and Clinical Laboratory Science (Dr. Norman Pace). Finally, on Thursday I get to go to SLAC and tour the particle accelerator lab and make contact with other STAR members. I was really excited to nerd out this summer, but this week has been exceptionally geeky. (FYI- Jen and Alaina are pool sharks, proceed with caution)

This Monday I had the pleasure of being invited on the Rachel Carson to seek out opisthoteuthis sp. (flapjack/adorabilis octopus). Getting a chance to see the MB Aquarium folks in action/behind the scenes was such a memorable life moment as I have gone to that aquarium since I was a little kid. Such a great crew, group of scientists and fellow interns to talk to and learn from. Seeing the ROV vacuum arm collect benthic creatures was too awesome. Maria took a great video of flapjack if anyone wants to see.

On the work side of things, I have just been continuing to prepare for my experiment. Aileen and I purchased 3 M/F abalone from Davenport Abalone Farm and our mentor instructed us in abalone husbandry so that we can keep our animals happy until our individual experiments. Excited to continue!