Yesterday and today have mostly consisted of background research (reading more literature and wikipedia tangents) and grasping the bigger picture of my project. Today my mentor and I identified the main issue that I will be handling which concerns machine adaptation around geophony and anthrophony noise sources. I am just about to install Raven to begin looking at data that has been collected in the past couple years. Raven is a program that draws a spectral map of a given sound file. It also has band limited energy detection software that will help pick up all instances where blue and fin whale calls may exist (given an average frequency, bandwidth frequency and dt).

Daniel

Dear Diary... just kidding. Haha.

I wrote my update and then the connection timed out so I lost it. This is my rewrite.

After ~5 tries, I got STOQS (the software my mentor created which I will be working on) up and running on my work laptop. Now I can start working through some examples and familiarizing myself with Python things.

I'm leaving this evening with the Haddock Lab on their cruise. Might take a brief hiatus from STOQS to work on a small programming project for Steve, and also to read his book and the Python data science handbook my mentor left for me...

That is all. Hope this wasn't too vague.

Have a great week!

Rachel

My project has been tentatively set; I will be working with the vampire squid (Vampyroteuthis infernalis - not actually a squid, it's a weird relict from the evolution and separation of octopods and decapods into two separate phylogenetic groups) and trying to identify the molecular sequence for its luciferase enzyme in its bioluminescence pathway. The luciferase enzyme is the enzyme that activates the luciferin compound, which is the light producing molecule. Most of these compounds will be located in the arm tips of the squid If we are able to sequence the luciferase transcriptome, we will then make clones and test them to try and produce bioluminescent activity.

 This is all still kind of up in the air - it will depend on what we get during the cruise, and if we find an abundance of something very very exciting, or if we don't find any vampire squid, or if we find a bunch of other glowing things.

The week so far has mainly consisted of figuring out how I will go about my project. After viewing some time lapse videos and images through VARS that the tripod picked up from Station M at a depth of ~4,000 m I've decided to work on behavioral patters of the Enteropneusta, or acorn worm. These worms are known for creating a fecal spiral or sometimes switchbacks. I will be working through images on VARS and identifying the Enteropneusta wherever they may appear, as they come and go from in the water column to the sea floor. After identifying I am measuring the worm's size, and the diameter of the spirals or switchbacks. Once all collected I will be going on to try and identify a correlation between amount of food available and whichever pattern it creates. But right now I'm mainly sifting through the years of images available to me on VARS.

Dusting off the cobwebs...

I had to stretch way back to my undergrad molecular bio class (~10 YEARS... I now feel old... ) this week as I started my research project. One component of my summer will be helping my mentor Dr. Stephanie Bush describe a new species of Pseudothecosomata (a pteropod). Aside from describing a new species, this project may aid in reviving Pseudothecosomata, which was broken out into three families. I've already extracted the DNA (hopefully) from some samples Steph already had in the freezer and we should run PCR today to see if it worked.

I'm missing Monday's meeting- I'll be on the MBA collecting cruise. I've been out on a couple of these before and they are really fun! I believe we are looking for corals, anemones, and flapjack ocotpuses! Wish us luck!

Megan

Hi all,

this week I was introduced to the data set that I will be working with as well as some ideas as to which direction I would like my research to proceed in. I am working with a data set of backscatter, temperature/salinity, currents and surface fluorescence from a Monterey Bay mooring (M1 ADCP) taken from 1992 to 2016 and will be using the data to either look at zooplankton diel vertical migration patterns from backscatter profiles or using recorded current patterns from the mooring to observe zooplankton dispersion and retention. Another idea is to use the data set along with a model to observe particle migration from the Monterey bay coast and see how it is being affected by Ekman transport and upwelling and compare that to what is actually observed in the data from 1992-2016 backscatter profiles. I've also been getting myself familiarized with the data set using MATLAB and reading primary research on the topics on interest.

I'm going out on a cruise today with Chris Wahl to retrieve a wave glider near the Santa Cruz area and test atmospheric equipment while we're out there.

That is all for this week, have a great weekend everyone!

Ash

The week so far has consisted of me mostly getting my sea legs (ha ha) with Wordpress and installing photoshop, and a lot of reading about MBARI (annual reports, technology roadmap and the 2011 strategic plan for 2011-2020). I'm also starting a mini-quick project of editing some information sent to us by Tom O'Reilly who works on the mobile cytometer (which measures cells) and the wave glider (an autonomous vehicle that keeps the shore in contact with underwater devices). That's been really interesting, and I'm excited to eventually put it into Wordpress and design that page presentation as well. Major project is still pending, but I'm hoping to finish the O'Reilly project by the start of next week/end of Monday, so Nancy and I were going to start brainstorming that after. I'm also scheduled to go out on the Rachel Carson the 19th/20th to take pictures and I'm really excited!

Emma

Hello!

This week I've been solidifying my project and started to set up some initial testing. I'm working with a strain of eukaryotic algae from the Arctic, Micromonas CCMP 2099. The main part of my project will be looking at physiological changes, as shown by chlorophyll fluorescence, to the algae when they're grown under different light regimes. That experiment will take about 2.5 weeks to run, so I'm going to continue with a longer term project comparing how the algae do under different levels of nitrate and carbon dioxide. This week I began growing cultures of the algae and testing to get initial growth rates. I'm also working on learning how to use R so I can more effectively analyze the data later in the summer. I'll be with Megan on the Rachel Carson collecting animals for MBA, so I won't be at the intern meeting on Monday.

This week in the life of an MBARI intern:
I did some important things this week like finding the maps to the different MBARI buildings, uploading a picture to my confluence profile, getting my computer setup, organizing my mailbox and calendar. I was also granted access to the CeNCOOS google analytics resources and have been analyzing some of the data to gain insight into the website user base to set goals on increasing visitors to the website and a target demographic. I met with Dr. James after the seminar yesterday and had a very wonderful and interesting conversation and I think I made a friend! Additionally I have been reading CeNCOOS strategic plan, getting familiar with the website and doing the background reading on how to use google analytics to inform educational resource design, augmented learning/augmented reality and trends/ issues in informal science outreach. My mentor set up a meeting for me next week with Mary Miller from the San Francisco Exploratorium and I am beginning to prepare for that. I think it will probably take me a few more days to finish the reading the literature to finally work out the details of my project. Overall a great first week, I am grateful for the opportunity and excited to get to work with some many amazing and talented people.

Alia (My nickname is Lili though!)

Hey guys!

It has been a great week so far! I have enjoyed getting to know everyone and hearing about all of the interesting projects that will be worked on this summer. As for my own project, this week I have started to gather data related to my thesis. I first did some background reading on the relationship between groundfish with pelagic larvae in the Pacific and climate change. My thesis involves assessing how larvae and adult groundfish are potentially affected by climate change. I am attempting to focus on species that are important to fisheries. So far, I have been mining all of the Pacific hake data that I can find from various databases, including outside of MBARI. I have separately collected data for larvae, juveniles, and adults, and will be analyzing the data to see if there are any patterns occurring among the different age classes and larvae, as well as between the fish and climate indices. I am excited about my project and can't wait to see how it turns out! It is going to be a fun summer! Please don't hesitate to contact me if you need anything!

Firstly, I downloaded and installed basic software onto my work environment, such as my mentors' SeeStar source code and its dependencies. I also dual-booted Ubuntu and fiddled around with the Arduino IDE.

My task has been to catch up with the SeeStar project and understand the overall picture and of course, compile, and run the code onto the hardware.

Thom introduced me to several engineers and technicians, gave a tour of the labs, and reviewed how to use an oscilloscope and voltmeter, as well as the safety protocols. I have been provided with copious resources!

Right now I am focusing on the serial communication with the SeeStar Module and observing the power consumption of the system in order to study ways to reduce it.

 Next week will consist of setting up a system in Raspberry Pi based on the work of one of the mentees.

Hello!

This first week has been very busy. Here are some of the things I've done:

• Talked extensively with my mentors as to what my project should be given what data we have.
• Read 5-7 state of the art deep learning papers related to object detection and classification.
• Made a 8 slide presentation justifying my proposed deep learning network designs for my project and introduces my project.
• Setup and customized my computer to support the research I need to do: package managers, python packages, preferred terminals, github ssh keys, desk layout, printers, and learning how to use a MAC for the first time in 8 years.
• Started reading through various open source implementations of the algorithm, Fast R-CNN.
• Started learning Google's deep learning library Tensorflow.
• Researched the standard data format for object detection and classification.
• Started coding a data processing pipeline that will convert previous work to the format we require. Involves extremely precise extraction of video frames and conversion of MBARI style XML files to VOC style XML files.
• Refactored document structure and content of our shared Google Drive to accommodate a 10 week scale.
• Learned to make salsa chicken in an instant pot.

Nathan

Hi everyone,

Most of this week was used to learn background information about previous works done by my mentors and the upcoming sea expedition.  I read multiple papers written by Peter Brewer and Ed Peltzer that ranged from learning the best type of Gaussian distribution to fit Raman peaks of sea water, to what type of water was present in jellyfish mesoglea.  I then learned how to work the lab's Raman spectrometer by calibrating it and looking at the chemical composition of a couple liquids and some plastic samples from a fish's gut (they were pretty large pieces, which makes me nervous how big the fish was...).