Hi everyone,

Well this week was a bit of a letdown, starting with our Western Flyer trip being cancelled mid-travel after spending 1/5 nights at sea.  It wasn't a complete fiasco since I saw my first wild whales, ate some great food, and controlled the ROV's arm, but I mostly feel bad for my mentor Dr. Peter Brewer since that was his last Western Flyer expedition.

I thought this trip would provide some data that I would be able to talk about for my project, but alas we had to make some adjustments.  I'll be working with a desktop Raman spectrometer and shooting a laser at sea water inside a pressure cell.  This will measure the effects of salinity, temperature and pressure on the hydrogen bonding index and velocity of sound.  I thought it sounded cool, but not extremely relevant to 'the bigger picture' initially, but my mentor told me that this work is extremely important for the NAVY to find out how deep submarines have to travel to be undetected by the enemy (but not too deep), but still able to communicate.  I'll be collecting a ton of different data to map somewhat of a 'ocean temp/depth' profile while most likely keeping salinity constant.

Other than that, the aquarium VIP tour was awesome (watching the 'vegetarian' sea turtle eat the fish and seeing the sheer size of the tuna were highlights) and trivia was quite a success (shout-out to Rachel for the closest guess to the number of goats in the Netherlands; that was gnarly).

 -David

Aloha everyone,
This week was interesting. I feel I took two steps back, three to the side, five forward and one in the air. I made some progress on getting interviews scheduled for HABs water sampling, SPATT and mussel sampling at the Santa Cruz Wharf as well as water sampling at the Monterey Wharf. I got the green light to change any of the educational resources on the CeNCOOS website and my mentor and I discussed re-organizing the layout of any and all HABs resources. I got to spend 2 hours speaking with Dr. Brewer who is most interesting, helpful and experienced. No question I asked could stump him. I was there when David saw his first whale in the wild, it was a pretty exciting moment and I shared with him the first time I saw a whale in the wild. I was really lucky to get to know the Brewer lab even though we only did a short day trip out to sea. I would love to come back! I also got to speak with Ed Peltzer, who was also very interesting and helpful. I have a ton of work to do as I am sure you all do. So good luck and eyes on the prize!!!
Alia

And I'm off to the races!

Last Thursday I talked to Larry Bird about Dr. Benoit-Bird's hydrophone and worked on getting the blog live. Yay!

Monday was EXCELLENT. I had so much fun, and I had no idea how rad tunas are until I saw them. Nature is wild. Is it too late to change my career path to become a tuna aquarist, ha? Highlight of that trip was the tuna and the hammerhead shark. They're so cool and graceful. Afterwards, I wrote a blog post about the MBA tour (which is online now) and features some great pictures of everyone, plus a video of the tuna thrashing (S/O to Alia for editing that video). I'm really happy with it, although I'm not sure I'm totally settled on the style/tone of the writing. Too "cutesy" maybe? I've never written in a more conversational style for a blog before, so I'm still shaking out the style.

Profiles are starting to go up! Thanks to everyone who's sent one in so far and nice boat names. Send them to your parents/relatives.

Tuesday I met with Dr. Benoit-Bird to talk about her acoustic research as well as sat in on Dr. Birch's lab meeting for the ESP. Both projects are making progress, and I have a good outline of Dr. Benoit-Bird's webpage. This Wednesday I spent the day making a skeleton template of Dr. Birch's webpage for the ESP. Now that that's done, I'm going to start filling in information. In other words: I did all the fun stuff (ha) for these projects, and now it's time to actually write Dr. Benoit-Bird and Dr. Birch's webpages.

Meanwhile, the mobile cytometer and the wave glider hot spot pages have been updated. There's still a few more edits to make from Tom O'Reilly, but it's nearly finished!

Finally, the stray black cat by Phil's has accepted my friendship. I have named him KitKat and he is very soft.

Hi everyone!

So this week was a bit of a stressful one, but we're nearly to the end! Monday was amazing and I had a blast at the Aquarium with everyone. I have to say the jellies were probably the highlight of that for me. It absolutely love moon jellies, and having them in the touch tank was so much fun, especially watching everyone's reaction! The tuna were crazy interesting and getting to see the Mola in one of the tanks was so amazing! Trivia night with the majority of you on Tuesday was a lot of fun - and it was cool that some of y'all finally got to meet some of the other REU interns

In terms of the actual work I've been doing this week, the majority of the week has been spent working on VARS and collecting my enteropneust data. I've gone through a few "Pulse" trips so far, which are the trips the tripod have taken down, and have found quite a few enteropneust in each trip. As of right now, I'm measuring the distance of the fecal path traveled, the area of the enteropneust body, and annotating each one. One small issue is that I'm only able to measure the enteropneusts on the bottom half of the screen, as otherwise it's a bit too unclear/small to view, and since VARS doesn't have zoom capabilities there's not much I can do about it. But that's alright, I'll just be sure to mention it in my methods later on!

When not working on VARS this week, I was working on a project proposal for the REU. By the end of this week we've got to have a written proposal (by Friday evening) and an actual presentation for Friday morning! This includes an abstract, introduction, methods, anticipated results, and the broader impacts of the project. I've pretty much gotten my written proposal done with and today I'm finishing up the presentation. I was able to present what I had yesterday in a practice with fellow REU interns last night and got some great feedback from one of our coordinator's!

Later today I'll be on the panel for the WATCH Land Use Scenario and I'm super excited about that. But that's been my week! Hope everyone else's has been great and have an awesome weekend everyone! 

P.S. @EmmaBueren any chance you can help me gain that cat's friendship as well? 

Goodmorning!

This week has been really fun, starting with the visit to the aquarium and potentially ending with some progress on my new project. I ended last week with a kind of dead end on my mystery mollusc and pannychia, but I did get to poke a sea anemone and watch it light up. A couple minutes later Steve told me that I'm one of like 5 people in the world that's seen that in real life, which is kinda cool. I also poked a nudibranch (tritonia), and I'm ~90% sure I saw that one light up to, which would be extra cool because we weren't expecting that one to bioluminesce. So the slug is hanging out in our lab fridge until we decide what to do with it.

On Monday I got to start on the vampy project. I'll be making some cDNA from a transcriptome, amplifying it, and cloning it into a vector to confirm this gene as the one that expresses the luciferin in Vampyroteuthis. I started that process by finding some sequences in a database, aligning them, and comparing them to mass spec sequences from the person who started this project. This was all really new for me, because it requires using the terminal and R command line, which I've never done before. So it's taken a while to get going, but it is going. Today I'll be finding the gDNA for the transcriptomes that I was talking about, and then creating primers for them in geneious.

I would also like to take a moment of silence for our fallen comrade, the vamp that we caught on our cruise. This lil nugget survived longer than we all thought possible in the darkroom of the aquarium. He passed yesterday, and I picked him up from the aquarium this morning. So if anyone wants to come pay their respects (and see what a teeny vampire squid looks like in etoh) you're more than welcome to come pop by my cubicle today. R.I.P. Oh and I'll be dissecting him at some point to try and get some DNA/RNA to get a more accurate transcriptome sequenced.

My octopus kiss hickeys are slowly fading, and I'm sad to see them go.

Cheers friends,

Chloe

Hello everyone!

So things still aren't going as planned for my thesis... Last week I had decided to stick with just pelagic larvae for groundfish species and spent a few days collecting all of the available data. I was excited because there was a ton of data and I thought it was all going pretty smoothly. However, Monday I came across a fisheries report that stated that a large portion of the data collected from SWFSC was collected poorly and should not be used in analyses. Unfortunately 3/4 of the data I obtained was from the SWFSC time series survey, meaning the majority of my data was likely unusable. I emailed the man in charge of the surveys two days ago and I am still waiting to hear back from him as to whether I need to throw out all the data or if I can still make it work. Unfortunately, there are not very many long-term time series surveys out there that have the kind of data that I need for my particular research project... so I may end up having to completely change my thesis again depending on what the SWFSC person says. While I have been in limbo for the past two days I decided to reteach myself R. After speaking with some of the staff, I realized that most of the datasets that I will be working with throughout my thesis research are going to be way too large for Excel and that I was better off using RStudio for data analysis. I haven't used RStudio in a really long time so spending the last two days refamiliarzing myself with the program was necessary and will be useful in the future when I start working with large datasets. On a final note, I had a great time on the behind the scenes tour at the aquarium on Monday! I worked at the gift shop there a few years back and have been on the behind the scenes tour before, but I still saw/learned new things and had just as much fun! That place will never cease to amaze me.

Cheers!

• Danielle Fabian

Week 4:

I met Dannelle, an engineer/scientist who worked on SeeStar. She is recognized as the Raspberry Pi and Deep Learning expert among many other specialties. She clarified an overview of the SeeStar system and explained how my project contributes to the system as a whole. She is working on the Sleepy Pi to serve as the master, which will coordinate when the Feather M0 (slave) should sleep in order to conserve energy. I am working on the Feather M0, which then controls when to activate and deactivate peripherals (camera, light, temperature module).

The important factor here is to establish the protocol between the Sleepy Pi and Feather M0 and ensure that the Pi communicates for the Feather M0 to sleep only if it is not in the middle of retrieving sensor data. After testing and running a previous protocol designed by a past student on the Arduino ATMEGA 2560 I gained a bigger sense of how the protocol should work. I am in the process of adapting a similar protocol onto the Feather M0, but the translation from the ATMEGA to Feather is a little tricky because the Feather allows a specialization of serials, SPI, and I2C and requires pin muxing. Furthermore, this involves different libraries with different functions.

Additionally, Thom taught me to break down problems into smaller tasks. Instead of focusing on the communication between Pi to Arduino, he instructed that I focus on the Arduino. He also taught me how to use the oscilloscope to verify if signals were indeed being sent and received to discern where there were breaks in communication. I also made my own lil' UART serial.

Lastly, I've been working with Paul, Rachel, and Pierre in preparation for the DIY-ROV for the Open House. We stripped and crimped so many wires.  

Hello!
This week sort of flew by... Had a lovely time at the Aquarium on Monday. I've been helping Paul Coenen with the BYO ROV stuff - so far it has involved drilling, cutting wire, stripping wire (using the super fancy automatic stripper, what a luxury!!), and crimping wire. The soldering and wiring are next. I've really enjoyed getting to know some of the electrical engineers, and it has been nice to have breaks from my computer.

Speaking of my computer, I've spent this week learning about machine learning. I've watched some informative videos and worked through some useful examples in my Python Data Science Handbook. I am slowly getting a grip on it, and hope to get in some programming by tomorrow. I had a nice machine learning meeting with Nathan, Daniel, and our mentors yesterday where we got to learn about each other's projects and see where they overlap, and to chat about machine learning in general.

Outside of work, we had a successful trivia night on Tuesday. We won free drinks for guessing the number of goats in the Netherlands in 2013! Very useful information, I know. Emma, Beverly, and I also attended the Science on Tap talk last night in Santa Cruz. The next one is about marine mammals! And the t-shirt squad is working hard to get the ball rolling for our intern t-shirts.

Have a great 4-day weekend!

Hi Everyone!

This has been a great week! Monday's tour was really awesome..watching the tuna feed is by far the coolest thing I've got to see here thus far (Not including the trip to MARS ^-). As far as research goes, I've been working with my mentor on improving the DVM algorithm that we created last week, I'm pretty confident that its working as it should be, but will manually check its accuracy for detecting backscatter maxima and minima in the data. I've also worked on a function for automatically detecting sun rise/set time for the time-series, which is more convenient when comparing month to month and season to season data. Yesterday I began working with climatology data from CTD, and hoping to see a DVM pattern that compare to physical/biological characteristics.

During the time I'm not learning/working on Matlab, I've been putting together a research proposal and a presentation for the REU to be presented tomorrow, wish us luck!

Currently working on t-shirt design, stay posted!

That's all for this week,
Have a great 4th of July weekend!

Ash

Hi everyone!

Officially (almost) two weeks at MBARI for me. Crazy how quickly it goes by.

This week I spent a good amount of my energy fixing my broken body--it's now fully recovered, thankfully. Despite being in recovery mode, I managed to get a bunch of things done:

-I was given a similar timeseries for the M1 mooring out in Monterey Bay as those I had been working with so far, so I ran all the analyses I had done on the other two datasets for this one (PCA, cross-covariance).
-I made two different bandpass filters to measure diurnal and upwelling variation signal in our data.
-Read more background papers on upwelling dynamics in Monterey Bay and the greater Northern California region.
-Learned how to use CO2sys in matlab to project pH using pCO2 and alkalinity values available to fill gaps in pH in the timeseries.

I still haven't zeroed in on my project's question exactly, but I think I'm getting closer. My mentor is also coming
back next week, so I'll probably have a better idea by the next update.

Enjoy the long weekend!

Diego

Week 3 (I started a week later than most of you)

This week marks the start of a new project, the Benchtop simulator software is complete and behaves well when tested with previous mission logs. We have yet to test on an actual Coastal Profiling Float but as soon as we have one working in lab we will test the complete simulator system.

My new project is to implement a system for the CPF that logs accelerometer and magnetometer(compass) data at various depths. The goal is to measure underwater currents and hopefully use that data to correct for positional drift during missions. This week I got the sensors set up and tested them, the next step is to connect them to a microcontroller and get them talking. Eventually we want a self contained subsystem that is mounted in the CPF and logs data onto an SD card.

I've begun my project write-up for the Benchtop simulator in LaTeX at Overleaf.com. I'm sure many of you are already aware of it but if any interns are curious about LaTeX for typesetting their work I would be happy to show them the basics. Once you learn it you'll never write a report in Word again. LaTeX allows you to very easily change formatting to fit the standards of any academic journal, also handles figure placement, citations, and bibliography for you.

MBA behind the scenes tour was super cool, feeding the tuna is not an experience I will forget any time soon. Looking forward to more intern shenanigans and continuing the projects.

-Pierre

Success!

This week has been full of successes:

1. I went back out on the Carson on Tuesday and felt wonderful! We were also able to capture two Pseudothecosomata (we saw 6, but they are surprisingly agile).
2. I got the sequence results back for my CO1 samples and have 23 out of 37 that worked. I'm sorting thorough the data now and cleaning up the sequences.
3. I started the other two sequences today (H3 & 28S) and should have results by tomorrow.

Sorry that I missed you all on Monday- I got all the way to MBARI when I realized the Aquarium trip was that day... I heard you all got a great behind the scenes tour

On a non-research related note- I've been spending the evenings tearing my new house apart- hopefully it'll be livable by July 17 because we need to be out of our apartment...

Cheers!
Megan

Another week. More data processing!

• Finally have a working data processing pipeline that converts image data and MBARI style annotations to the format I need.
• Handpicked a training set for regular classification. This will allow me to explore how neural networks deal with interlaced video. It might also help me finetune a network on benthic imagery before I train the detection model.
• Had a first machine learning meeting with some other interns/mentors. Had a lot of fun. Lots to learn from everyone.
• Started experimenting with dealing with interlaced video.
• Rewrote pretty much all the code I've written to be more modifiable and scalable.
  Nathan

Hi all!

This week marked the end of the first phase of my experiment, which unfortunately looks like it might be less interesting than we'd hoped. The results from last Thursday's high resolution sampling were fairly similar to the results from the previous high resolution sampling - under the different light regime. Because of that, we did not do the high resolution sampling that had been planned for Monday, and I had a great time at the Aquarium instead!
The next phase of the experiment will involve changing the nitrate and carbon dioxide concentrations. I've spent a fair amount of time this week making new media for this phase. Gas with specific amounts of CO2 arrived today so we're going to start soon. We've been carefully monitoring the Chemostat that got too hot last week, and after adding some healthy algae it's starting to look better.
The cultures I'm growing in the incubator have had some wonky growth rates, but I'm hoping they stabilize within the next couple of days so I can increase the light to the next level. I'm also going to do a small salinity experiment to test how the algae do at different salinities.

I'm looking forward to the extra long weekend!

Hi all!

This week marked the end of the first phase of my experiment, which unfortunately looks like it might be less interesting than we'd hoped. The results from last Thursday's high resolution sampling were fairly similar to the results from the previous high resolution sampling - under the different light regime. Because of that, we did not do the high resolution sampling that had been planned for Monday, and I had a great time at the Aquarium instead!
The next phase of the experiment will involve changing the nitrate and carbon dioxide concentrations. I've spent a fair amount of time this week making new media for this phase. Gas with specific amounts of CO2 arrived today so we're going to start soon. We've been carefully monitoring the Chemostat that got too hot last week, and after adding some healthy algae it's starting to look better.
The cultures I'm growing in the incubator have had some wonky growth rates, but I'm hoping they stabilize within the next couple of days so I can increase the light to the next level. I'm also going to do a small salinity experiment to test how the algae do at different salinities.

I'm looking forward to the extra long weekend!

Hello everyone,

I have finally finished up the data mining (for now) and have started to pre-process my sound files. I am using Pycharm with python to turn my wav files into clear spectrogram jpeg files to begin throwing into my CNN. I had some issues with library requirements for the representing those graphs. The intern meeting Danelle set up for the ML folks was very helpful and it was nice talking to everyone about my ML approaches.

I also got to design an idea for a the shirt which was fun. I can't wait to see how they end up turning out. I really enjoyed the MBA behind the scenes tour and seeing the green sea turtle eat a fish.

Cheers,

Daniel