Hello everyone!

I hope everyone was able to enjoy their 4th of July weekend!
I realize it's only Wednesday but I figured I'd post now since I have the time...
this intern-week was fairly short because of the holiday and as will my post:

Proposals presentations for the REU on Friday went great! I was impressed with everyone's on-going research project and how well we all did!

Right now, I'm still refining the DVM algorithm from last week. I'm hoping to have that done by the end of this week and continue working on CTD data from shipboard. Francisco Chavez stopped by earlier today to get an update on my progress and suggested some literature for me to read on carbon export by vertically migrating zooplankton. Very interesting paper if you like to learn about carbon export or plankton, email me and ill forward you the link. I'll be meeting with my mentor tomorrow either morning or afternoon to discuss the next step in the process and talk about the SACNAS deadline that is coming up soon (July 14th). I'll be working on my abstract and scholarship application for their October conference, I'm hoping that'll make it to Salt Lake City this fall, I'll keep you all posted that's all for now.
have a great weekend!
Ash

Week 4:

Only 2 work days this week. There is now the guts of a Coastal Profiling Float up and running on the bench in my lab. I've now been spending my time polishing the interface for the testing system and gathering data to compare results of the different methods used to calculate required pressure. This was a step away from the secondary project I started last week but I hope to have this finished and finalized in the next few days so i can spend the rest of the time focusing on the new project.

I'm enjoying seeing my system in action and looking forward to the aquarium sleepover on Saturday

Pierre

Aloha everyone!
Short but busy week. This week I misread days and scheduled things stupidly. Currently trying not to be annoyed with myself. Finished my HABs survey draft which I will be asking all of you to share with your people on Facebook. PRETTY PLEASE. I got to speak with John Ryan about the updates to the HABs timeline for the CeNCOOS educational resource section and we have scheduled an interview time for next week. I also put together some pdfs of the top 20 pages from the CeNCOOS website for specific time periods. I am looking forward to the BBQ today and the sleepover this weekend. I hope the aquarium isn't haunted! I hope everyone has a good productive week, see you all soon.
Mahalo for reading,
Alia

The summer is going by way too quickly...

Had a blast over the holiday weekend adventuring with David, Emma, and Ellie (and Beverly at the end!). We went to a vegan festival, hiked in Big Basin State Park (the oldest state park in CA, fun fact), and swam in the creek at Pfeiffer Big Sur State Park. If you notice me having any difficulties opening doors, holding heavy things, etc., it's because I skipped one too many rocks... We ended the weekend with a grill-fest on my mentor's sailboat (10/10 recommend grilled pineapple) and a lovely firework display at the Watsonville Municipal Airport. I will happily offer my new-found vegan grilling skills for our upcoming intern BBQ.

As for work, I have been a bit frustrated lately realizing how fast the program is flying by as I slowly progress in my programming endeavors... 10 weeks is not long enough - I still have so much to learn!! I am currently working on a script that will implement unsupervised machine learning. In English, that means I'm writing a program that will make my computer detect patterns in the data all by itself - like magic!

Happy Thursday!

Morning!

Hope everyone had a wonderful long weekend adventuring and celebrating and eating etc. I drove down to LA to see my closest friend's song that she wrote/sang performed by Illenium at the bougiest night club I've ever been to. It was SO COOL I feel like a proud mom. It will be officially released at the end of the summer but if anyone wants to listen to it... Crawl Outta Love it starts at 6:30 but it gets better at like 7:30(: So that was pretty incredible.

Yesterday I created some cDNA from RNA that we had from the vampire squid. The reverse transcriptase strand switching cDNA protocol is pretty complicated and it takes ~6 hours, but it was successful and now I can work on trying to express the symplectin-like protein (the luciferin) by cloning it into a vector. I'll be finishing up making and ordering my primers this afternoon. We ended yesterday by running a gel of our cDNA to see if we actually made anything, and it was really satisfying to be able to see the results of the days work. I can't believe we're already this far into the summer. I never want to leave and I feel like I'm just getting started on my project.

Oh and also I'm house sitting for someone at MBARI so I won't be in the apartments for a few days. See y'all at the bbq!

Hey guys!

Short week but things are going better for me in terms of my project! Still haven't heard back from the fisheries person concerning whether or not I can use all the data I collected last week so I have moved on to a separate part of my project. I am going through the time series images taken at Station M and doing a count of all individuals that I find for the grenadier species that are found there over the entire time series. After I finish the counts, I plan on assessing any trends in the data and comparing the data with climate indices. Until I hear back from the fisheries person, I won't know for certain which direction my project will take. I will keep you guys posted! Hope everyone had a great 4th of July weekend!

• Danielle F.

Hello,

Hope all is well. Not a whole lot to report this week other than I've been making progress on the spectrograms that represent my sound files. I'm dedicating my day to debugging and communicating with Danelle (who is out for 2 weeks) through Git. Hopefully I can get a nice looking spectrogram by the end of the day.

I'll see you guys at the BBQ!

Daniel

Hi Everyone!

I hope everyone had an amazing long weekend! I had an absolute blast, finished the REU proposal presentation on Friday (Ash and Daniel y'all did amazing!) and I got to take a few REUers down to LA. It was a lot of fun having an excuse for my local self to be a tourist! P.S. if any of y'all wanna take a trip down there lemme know - maybe I'll go with and y'all can have a place to crash at! 

Other than that, it's been a super short week! Yesterday I spent some time trying to extract information from VARs but since my mentor Crissy isn't here it's been a little difficult, can't seem to crack the last step but I'll be going over that on Monday (thanks Linda for all your time trying to figure this out with me!). I'll be spending the rest of the day just collecting more information form VARs. 

The t-shirt people have all been busy solidifying the design (thank you so much Rachel for all the graphic design work!), Danielle and I will go tomorrow to talk to the company that will be printing them and hopefully we'll have a more solid idea on that.

Have an amazing weekend and see y'all at the BBQ! 

Victoria

Week 5:

I've gotten two out of the three serials working and learned a lot about the Feather M0. I've been picking up debugging techniques with the oscilloscope and FTDI cable. I got all three serials working. What was frustrating is that the pinout-muxing from the libraries were too generic and did necessarily match with the pinout of the board. I've been trying to search for other files, but worse comes to worst I suppose I can customize the files I have to match the board. I am apprehensive to do that because I do not want to damage the board by providing incorrect voltages.

Even if I only have two serials, I think I will work on the sleep protocol soon. There are lots to learn do and learn, but I am not complaining.

Hey everyone! Hope you all had an awesome long weekend. Short week this time.

About a third of the time was spent working on experimenting with interlaced video and convolutional neural networks. I used a technique known as transfer learning with Google's network known as Inception V3 on three types of images (interlaced, de-interlaced, and my "smart" de-interlaced). The results showed that convolutional neural networks have a much easier time working with de-interlaced images.

Another third was setting up some more scripts to move a lot of my data pipeline onto atlas shares (yay backups). I would have processed the data this week except the VPN didn't work out exactly as I expected. Not a huge deal as the code is the primary bottleneck for this sort of data processing and all I have to do is press run when I'm at MBARI.

The last third was spent away from coding (which I've been sucked into for about 3.5 weeks) looking at the higher level details of my project and learning more about the tools I am working with. I re-read through some of the previous intern papers to get ideas how to write mine. I re-read through the Faster RCNN paper. A paper called "Unsupervised Underwater Fish Detection Fusing Flow and Objectiveness". I also watched some videos that explain how Resnet50 works. Basic forms of object detection in images. How to incorporate multiple data sources into a neural network. Fully convolutional neural networks and how to visualize how they work. Basic understanding as to how Inception blocks work.

Nathan

Whistle while I work...

I've been spending my time cleaning sequences since my last update. CO1 and H3 are a bit wonky and not completely aligning with the sequences Stephanie already had done- we're trying to figure out why the same "species" is falling out into two groups on the phylogenetic tree... the plot keeps thickening Hopefully, the next round of sequences will shed some light on the situation- hopefully.

I've also started to compile the literature and figure out how to write a species description. In this exercise, I've learned:

Many pteropods were described by Germans, pre-1900. This has left my pool of references small, but I think I have enough to compare our new species to.

Stephanie gave me a bunch of images to use for the line drawings I'm going to do. I'm going to spend my afternoon going through them and starting sketches.

Cheers,
Megan

On a side note, if anyone needs hardwood floors refinished- come talk to me- I'm now an expert with a drum sander

I have spent this shorter week writing up my work and refining figures. I also had my first meeting with my mentor (he's back!) to talk about what I've been up to and where to go from here.

By writing up my work, I noticed large differences between Año Nuevo, Hopkins and the M1 moorings and it is apparent that the closer you are to an upwelling source the greater variability you will see. There are many other things that play into it at Hopkins and M1, but it's been interesting to try to make sense out of all these signals.

The future of my project still seems uncertain. I will finish looking at the small window of the timeseries I've been working on and come up with a few conclusions that can be tested against the entire timeseries (or a larger portion of it), particularly because data from recent months seems to show greater variability.

I also met with Charlie Boch who is working on ocean acidification experiments in the lab by reproducing pH, dissolved oxygen and temperature variability observed during upwelling events. We might be working together as the Hopkins and Año datasets are shallow enough to accurately measure the effects that biological organisms see during these events.He is interested in knowing the duration of increased pH, lower temperature and lower O2, as well as their amplitudes and rates of change. His project is trying to tie this to climate change, especially since the natural ranges of an upwelling environment are similar or greater than the global-scale changes being predicted in ocean pH on a global scale.

Biggest take away from this week: writing things up makes you remember the big picture. It's so easy to get carried away by the small details of one figure or one bug in your code and forget what it all means and what the objective is. Anyways, it was a good learning week despite being extra short.

Looking forward to the bbq, thanks George!

Diego

Hey y'all!

Right off the bat, if you have any fun Fourth of July photos, you'd like to share with the blog that would be great! Email me at ebueren@mbari.org, and it doesn't have to be a lot of information (one pic and then literally just an email of "I went to X place to do Y thing") to include. It'll be fun! Get your internet fame! Your family will love it!

Also, if you haven't done the mystery picture yet, do it! http://www.mbari.org/animal-plant-mineral-or-man-made-2/
Same goes for if you haven't sent me your profiles (you know who you are, we're down to the final three!) (EDIT: and then there were two...)

As for what I've been up to, this 2 day week was not as productive as I was hoping, but I did get some good research time in. I watched Jim Birch's DOEST lecture on the ESP to get a better background of info, transcribed Kelly Benoit-Bird and Larry Bird's interviews, and am now getting ready to start writing (ha, I said that last week). Susan (social media) also posted the first mystery picture on instagram and it got like 200 likes, so that was really cool! I've also worked on getting some new intern profiles up thanks to some proof-reading from Alia (thank you!!) so be ready for those.

On a fun note, this weekend was great. Ellie, Rachel, David and I went hiking and racked up some mileage (and some sore but happy muscles for me!) plus took a bunch of great pictures. Lots of good food and cool trees, plus I think we all accidentally got new LinkedIn profile photos because the lighting was great at Big Sur.

Emma

Hi everyone!

I got back from the BBQ and realized I'd forgotten to submit my update today! I had a great weekend (after quickly checking on my algae on Saturday morning) exploring the area!

The short week has actually been quite productive. The algae have been taking longer to acclimate to the different light levels than we anticipated so we changed the structure of my experiment. I am now growing cultures under seven different light levels at the same time - it's quite a setup in the incubator. This has meant that I've been spending more time sampling and less at my desk this week which has been fun! I also made new graphs to track the progress of these new cultures, and I'm working on writing an R-script to analyze the results from the sampling measurements.
One of the chemostats was acting up this week - its lid kept popping off. It was open for a while on Wednesday, and we're concerned the culture is no longer axenic. I'm going to do a bacteria test in the next couple of days to check if it has been contaminated, really hoping it's not.
I'm really looking forward to the whale watch and sleeping at the aquarium this weekend. Hope everyone has a good time!

Ellie

Hi everyone,

Sorry for the delay on the Confluence.  I have finished collecting Raman spectra for 0,10,20,30 and 40 degrees C with varying pressures between 0-1500psi for fresh water.  From that, I was able to run the Matlab software and see the 5-Gaussian distributions on it and plug those numbers into Excel.  It's a pretty tedious process to keep converting and renaming files, so I'm glad that's finished!  Now I've just been making a variety of plots to see if any of these variables we are testing have a noticeable trend.  It's not looking extremely clear right now, but I am going to talk to my mentor this morning to look into it more.  I know that the data I collected at least fell within the expected range of activation energies (previously determined by my mentors) based on  Arrhenius plots; they had fresh water activation energies between 1.5-2.9 kcal/mol and my data fell between 2.54-2.61 kcal/mol.

Other than that, the 4th of July weekend was a blast.  We went hiking at two different state parks, saw fireworks in Watsonville, and had some other fun adventures.  On top of that, we went whale watching this past Saturday and saw 2 BLUE WHALES.  That was easily the highlight of the weekend, followed closely by an unforgettable night at the aquarium and making a copious amount of peanut butter cookies for the cookie break this afternoon.

-David