Hi,

I'm crashing the exhibition development meetings for Deep 2020 tomorrow, so am writing this early. I've been developing a brief for my phytoplankton exhibit this week, as well as writing a short news story for the CeNCOOS website about the white shark cafe. I got to sit in on a global phytoplankton workshop on Monday, which was interesting to hear what the issues are in the science community and how they are making decisions about the focus of ocean observations over the next decade.

It's been fascinating to talk to Helen Scales and hear from her and Aaron John Gregory about their work communicating fish - we've got a surprising number of connections in common so hopefully that will help me once I'm back in the UK.

I've also been planning (and baking) for the CeNCOOS breakfast tomorrow - hope you'll all come along!

I'm stealing Alisa's idea and posting tonight.

It's been more reading and coding this week. Monday I spent most of the day learning to code diffusion simulations and animate them to get a feel for how they work. Tuesday was more of the same. Today, I spent some time with my mentor going over some assumptions that will affect how the model we are creating works. We had an interesting discussion of boundary conditions and the physical meaning of constants of integration.

I'm adding some data analysis to my activities next week, so I should have some more to write about in my next entry.

Goodmorning!

I can't believe next we will be halfway through the internship!! It's flown by. But I finally got back into the lab this week!! It was awesome. This week I grew up some of my old cultures from glycerol stocks so that today I could do a transformation into RosettaGami cells, which contain a plasmid that provides rare tRNA that E. coli don't usually contain. They also have a broken proton pump, which creates a reducing environment in the cytoplasm to help form disulphide bonds between cysteines in my protein. Hopefully, this is what was missing from my expression systems last year, and I can get an expressed protein this time!

Additionally, our bioluminescence protein expression wizard Manabu re-assambled our newest vamp transcriptome so that the gene transcripts that were assembled were more realistic (fewer longer transcripts instead of a bunch of shorter ones). We also were able to conclude that one of my candidate genes isn't actually a gene, so now I only have to work with two candidate genes instead of three. This is good news. On the flip side, the reassembled transcriptome also means that I can re-BLAST my seqs, to see if there are other transcripts that can be considered as candidates for the luciferase gene. So I may be back to three by the end of the day!

All in all, I'm stoked about this week and incredibly excited to continue working in the lab and getting these proteins expressed and glowing. Best of luck to you all, and happy (early) 4th!

This week I've been on the water! Paragon captain Brian has had to do some last-minute recoveries in the Bay so I've been able to get out twice already to recover a coastal profiling float and a Liquid Robotics wave glider. I am also headed out on the Paragon again today to help Chris Wahl recover the WG Tiny after a CANON experiment. The instrument's supposed to be a pretty fouled with algae, so apologies in advance to my roommates for the impending smell. Yesterday I boarded the Rachel Carson for Amanda Kahn's cruise to sample and collect from deep sea sponges. It was incredibly exciting to watch the ROV pilots master a new probe (measuring sponge respiration flow rates and O2 levels) as well as see Amanda get genuinely excited herself over the success of the dive. It was a small cruise - just Amanda, her collaborator Phil, the crew, and the interns - so we all got a lot of time in the control room and even got to "fly" Ventana! In addition to all the boat time I've been starting up on a new phase of my project focused on assessing the success of algorithms developed to predict total alkalinity from non-carbon system parameters (Temp, Salinity, and O2) in Monterey Bay. The algorithms are either meant for global applicability or regions just north/south of MB so it will be interesting to see how the predictions compare to actual measured data in this area.

Today is an exciting day, I am at sea! This is my first trip out on the RV Rachel Carson, we are headed into the bay to do some mapping with the AUV. My mentor is running tests on the ability to localize in real time using past bathymetry data and the mapping data being collected.

 I brought my work with me, but since this is my first trip out I will probably spend most of my time on the deck seeing all the operations. This week I have successfully imported the mutibeam data into my program and transformed it into a local coordinate system. Origionally All the data is in latitude and longitude, which can be hard to deal with algorithmically since it is not a cartesian coordinate system. By transforming all the data into a local cartesian coordinate system I can more easily view and manipulate the 3D data. My next step is to put the new localized data into a standard point cloud format so that I can try out some algorithms on it.

This week I got to go on the Paragon on Tuesday and recover a wave glider which was really cool to see in person. We even got to see dolphins swim by on our way out! On Wednesday I got to return to sea on the Rachel Carson! Luckily, I was not seasick and at one point the boat even rocked me to sleep. It was so much fun and we got to see a ton of whales and sponges and an octopus. The interns even got to drive the ROV! Getting back to my research, I've moved on to analyzing my data and will be calculating my p-values today(finger crossed they're significant!!). With the introduction for my paper done I have moved onto outlining and writing up my methods. I have started to think about how I am going to format my poster for open house since it will be here before we know it!

Hello!

Monday this week was spent practicing PCR from which we got our first bit of data from the project! I am pleased to confirm that the MBA Steelhead trout tank water has Steelhead DNA in it, which is reassuring...

Tuesday was more DNA extractions which went smoothly.

Wednesday I was on the Rachel Carson - very exciting, loved every second of being on the boat and watching the sample collections happen in the control room. I even got to live out a dream of mine by flying an ROV, even if it was for a very short amount of time.

Today and tomorrow is continuing my extractions - if everything goes smoothly I'll have all my samples extracted by end of Monday next week, ready for qPCR after the July 4th break.

Hope everyone's had a quite good week!

Hello everyone!

So this week was really awesome! I am making good progress on my autonomous change-point detection function, and now starting to stress-test it on different profiling floats in order to find any problems there might still be.

We got to go on a surprise paragon trip on Monday, since an iridium sensor attached to a CPF which was deployed that day failed, and it needed to be recovered. It was really cool seeing how the process works here at MBARI, which was very different (and I'd say much more efficient) than the ones I have experienced in the past.

Also, we got to go on the Rachel Carson all day Wednesday. We got to see the ROV live in action, and first gathered oxygen samples inside deep-sea sponges, then also gathering actual samples of different organisms to study later on. We even accidentally collected the cutest shrimp, which should be swimming around in the sea-water lab at this moment, while collecting a fully-intact sponge.

Although I got extremely sea sick, it was a really enjoyable trip. And we even got to operate the ROV a bit as it came up to the surface! This week has been really amazing, and I'm excited to experience much more here at MBARI. Also, I'm very excited about the project I am working on, especially after gaining more insight on how my project ties into international analysis of the oceans biogeochemistry in todays lab meeting.

I hope everyone had an awesome week as well!

Hi everyone,
I spent Monday and Wednesday of this week helping Yuuki and Larissa set up the Abalone experiments. My favorite part of the day was feeding the adults and learning that they can see similar wavelengths to humans. (Thanks for the fun-fact, Yuuki!) On Tuesday I read through a few papers from people at MBARI related to benthic community ecology, double-checked some of my notes from previous clips, and began annotating videos of site markers at Sur Ridge from different months and years. I'm excited to begin assessing whether/how these communities have shifted over time in the next few days.

Monday: Fleshed out the SBD Command Builder: added a CPF dropdown menu, radio buttons, submit button. Went out on the Paragon with Brian Kieft to recover a broken CPF!
Tuesday: Added a LOT of CSS to make the Command page look good. Met with Gene to identify the seven CPF commands. Began adding input validation, error messages, and submission confirmation.
Wednesday: Went out on the Rachel Carson for the first time and spent 90% of the cruise seasick. I mustered just enough strength at the end to clamber into the pilot seat and fly the ROV though! Special thanks to Dr. Nina Buzby for taking care of me!
Thursday: Had another lab meeting. Working on making the command builder bullet-proof.

Hello hello!

I was sick for the first two days of this week but have recovered and am back at MBARI working on implementing the first stage our humpback whale song processing pipeline. The pipeline as a whole aims to analyze the hierarchical structure of humpback song. The stage that I am working on currently aims to "pre-process" the audio signal (put it into a format that is ingestible by the sequence analysis techniques we would like to try). Good to be back!

After reading through a few more papers on classifying social vocalizations, I have now updated my catalog on song units for the 12/07 song. I found 17 distinct unit types within a 6 minute song. There is even a violin call! I might just have to make a trip out to sea one day and serenade or accompany the whales!

In order to confidently label the units with these new descriptions (ex: wop, grunt, moan etc), I compared the frequencies and spectrograms of the papers to those in the song I'm analyzing. It was extremely helpful to hear the different vocalizations in order to more accurately label a unit.

I also compared a few more clusters from the 2D plot on jupyter with my updated catalog and while there was still not ideal clusters, it looks a little more hopeful. One paper mentions classifying the units by 4 different classes- low frequency harmonic calls, tonal, pulsed, and noisy/complex- so we may end up finding it easier to cluster based on classes.

Wednesday I went out to sea on the Rachel Carson and I loved Amanda's excitement about testing her oxygen sensor on deep sea sponges. Besides getting nauseous (which I've never seemed to have a problem with), I had such a fun time getting to drive an ROV, see humpback whales super close, and see the fascinating deep sea creatures.

Hi everyone,

This week was very busy for everyone in the wet sea lab. We finally got the experiment running yesterday, so that was exciting! We spent Monday calibrating the water flow on all of the tanks for the last time, and on Tuesday my mentors and lab techs were making sure the system was up and running correctly. Then yesterday, we basically had a science assembly line going on which included a buoyant weight, wet weight, and picture station. We weighed and took pictures of almost 500 abalone of different sizes. After collecting the data, the animals were successfully placed in their experimental jars and hooked up to the system. It's been a lot of work for everyone but we got it all done and its a relief.

Greetings and salutations everyone,

This week required a lot of setting up to get started on writing code for my team's project. On Monday, Mayra and I met up with our mentors to speak about the upcoming steps for our project and understanding what is happening within the code of our mentor's work. On Tuesday, I had a meeting with my mentor, Danelle Cline, to get into detail on our plan and set up my Eclipse IDE and Docker image to use the Xerces XML Parsing API. We weren't able to make our project run the API that day, but on Wednesday, we managed to have my Eclipse IDE run the Xerces API correctly and I managed to get started on writing code for the small project I was assigned. Today, I will be finishing my part of that small project and try to work with Mayra to put our code together.

Hello,

As Larissa explained above, it was a busy week in the seawater lab. To prepare for the abalone upwelling experiment, I came to the lab on last week Friday, this week's Monday and Tuesday. Me, Larissa, and my mentor built 60 chambers and made the materials we needed to conduct the experiment. On Monday, Erin helped in our lab to calibrate the seawater flow.

Yesterday, we started to work around 8:30 and ended around 19:30. Laurissa, Erin, and I were measuring and taking pictures of all the tagged abalones (around 500) and by the time we finished putting the abalones in their experimental chambers, we were all exhausted. The cool part of yesterday was that we got to feed kelp to the abalones.

From today, we are starting to mostly focus our work on husbandry and image analysis.

Hi all,

 In the last week or so, I've been focused almost entirely on the Mesobot project. Stereo calibration has proved a worthy opponent, and I've spent most of my time understanding the intrinsic and extrinsic parameters that define the accuracy of calibrating a pair of cameras in a stereo pair. I've completed programming a basic application to run stereo calibration on a pair of Grasshopper3 cameras, and I've captured around 50 calibration image pairs. Right now, I'm focusing my efforts on understanding the optimal conditions for calibration in order to get sub-pixel accuracy in the calibration (so that 3D points can be triangulated and reconstructed with great accuracy).

Other than that, I've been curating the frame grabs that I've gathered from VARS. I have more or less perfected the border removal algorithm and am currently processing and watermarking the images. From here, I'm going to be gathering a range of summary statistics from the data as well as creating some visualizations of that data for some external collaborators working on the FathomNet project.

I've also been working on some machine learning on the side. I've built a framework for using a few different machine learning models (from Keras) for transfer learning. Specifically, I'm working with ResNet50 right now. Eventually, however, I want to get a small deployment onto a Google Cloud TPU (Tensor Processing Unit) to see what kind of results I can get at this early stage with the data that I've collected.

The last bit I've been working on is some basic image processing to see if I can segment a giant larvacean (Bathochordaeus) from its housing. Right now, I'm applying my own video stabilization algorithm to generate a stable background, then running the video through a couple different background subtraction models (MOG and MOG2) to detect only the moving animal relative to its housing. I'm going to generate a mapping between the stabilized coordinate system and the world frame with the stereo camera setup, so that (eventually) the larvacean can be tracked and followed separate from its housing by an AUV/ROV.

Hi all,

Recently I have been finishing up testing the last parameters that affect the burn wire corrosion time for the release mechanism on the iTAG (lots of excel spreadsheets). At the same time, I have begun sketching out some possible ideas for our overall design package and how we want the electronics package to be hooked up to the base that will be attached to the jellyfish. Once I can agree on a design with my mentor, so then can the testing and actual creation of the overall package be done. Hoping to have that done by next week!

Hi everyone!

This week has been busy. Monday, we had a meeting with our mentors in which we talked about the upcoming steps for our project. We went over from some pieces of code in our mentor's work that will play an important role in our project. On Tuesday, I met up with my mentor to have more references in some structures and classes included in their code. I started working on parsing the paths of the images to XML files in which I have direct access to the file by an existing command. Today, I'll trying different test cases and possible assertions in non-existing paths, so I will be able to put my code together with Raymond's

Hello! I am very late, no excuses except that I was doing so many things today I totally forgot to.
This week was a productive week. I have some molds for larvacean tails, and I have been physically modifying them to make it easier to pour material into them and change the stiffness of different parts of the tail. Today I grabbed the mold I had modified and turned it into a solidmodel on solidworks to 3D print a couple of them so when I make adjustments to the tail I can do it quickly and do many tails at a time (I also learned how to submit a work order to get the molds printed).

Besides playing with the molds, next steps include being able to analyze my videos using matlab, which I have never done and hope to pick up quickly, and I have been pondering about including artificial muscles in my model (coiled nylon which "contracts" when you apply voltage (or heat) to it). My mentor told me there may be someone here that has worked on artificial muscles before, so I might be looking for that person next week to get some guidance on how to include that in my model.

glad to hear a lot of you had nice productive weeks!

hello all, thank you for your updates! great reading what you have been up to and I'll see you on Monday! Tom has volunteered to help me on Monday with the shopping/cooking - that might be enough, but if anyone else wants to help, let me know. I have also have a tour group of NASA interns this Saturday if anyone wants to help out - we may see them again at lunch when we go to NASA in July.
I'm up in Newport, Oregon enjoying some unusually pleasant weather (blue skies) as MBARI and the NSF RCRV (regional coastal research vessel) and the Oregon STEM Hub are co-hosting an educator professional development workshop (www.mbari.org/EARTH) helping educators figure out how to integrate data into their classroom. We've done a necropsy on a Guadalupe fur seal, gone zombie shrimp hunting on the mudflats, toured a NOAA ship, toured all the gear that they are putting out for the Endeavor array as part of the Ocean Observing Network and eaten way too much good food (including a dinner at the Rogue Brewery). Presentations tomorrow and then I'm heading home.

WOW I'M SORRY I'M SO LATE!!!!!!! I guess I'm the new Ed haha.
This week has been a really exciting week. I finally ran my first protein gel SUCCESSFULLY!!!! WHOOOO! And on top of that, we tested Eukronia fowleri, one of the bioluminescent arrow worm species I'm working on, for luminescence and it GLOWED!! So since we used the same sample to test for luminescence as we did for the protein gel, we now know that one of the bands on the gel is responsible for the luminescence, but we just don't know exactly which one yet. So! We cut out the bands from the gel and are going to send them in for mass spectrometry, which will HOPEFULLY take no more than two weeks. In the meantime, I'm going to run a time sequence on the chaetognaths to determine how long and at what conditions their ability to produce light decreases Happy FriYAY