Hi All,
Hope everyone's week has been amazing!
This week I set up a timeline with my mentor as to when each step should be done (approximately) and hopefully I'll be able to stick to it! I've been doing mainly research this week, reading up on the deep-sea enteropneust, or Tergivelum baldwinae, which is the enteropneust I will be looking at. I've also read a few other papers on carbon flux in the deep sea and how that may have affected other organisms, such as holothurians (Linda I read a few of your papers!). After taking extensive notes I've started writing my introduction for my paper which I intend to have a rough draft done by the end of this week. I also had the opportunity to go on the walking tour with the board earlier this week during DOEST and it was awesome getting to see all the other work that has been done here at MBARI!
Victoria

This week I solidified my plan for my project, and got everything started. The algae cultures are growing in the Chemostats (a system that lets us control the nutrients available to the algae) and in vessels in an incubator. Yesterday, we started the Chemostat experiment. We're growing the algae under different light regimes (sine wave, square wave, and always on) to study how this impacts their physiology. I'm going to sample from the Chemostats once every day and multiple times a day when we do periods of high resolution sampling to check how they change their behavior throughout the diel cycle. When this phase of the experiment is done, we are going to change the levels of nitrate and carbon dioxide to study how they respond to different environmental conditions.
I'm using the cultures growing in the incubator for a growth-light experiment to look at how their photophysiology changes under different light intensities. We're starting them at a low light level (10 micromols) and they are already showing some changes! The cell size seems to be shrinking and the chlorophyll increasing. These responses allow them to harvest more light from the low light condition.
On Monday I went out on the Rachel Carson and had a great time! We collected deep sea corals, anemones, sea stars, and a flapjack octopus.

Pipetting is not like riding a bike...

Last week I touched on how I had to dig deep to remember the concepts and techniques I am using for my summer's research. It looks like I didn't dig deep enough because I've been pipetting wrong for a week and a half! I knew something was up because my volumes were off, but couldn't figure out what it was until I watched my mentor pipetting something. The mystery has been solved- I was doing it wrong.

In spite of my wonky pipetting, I have been getting results! Today I'm working on PCR for the rest of the samples we have and will hopefully be sequencing tomorrow.

I also went out on the Rachel Carson on Monday and was sicker than I've been in LONG time... Dramamine "Naturals" is a bottle full of lies- I'll be going back to my scopolamine patches.

Onward and upward.
Megan

After hours of playing with the sound analysis tool Raven, I have finally been able to start data mining. I'm hoping today I can collect at least 20,000 blue whale b calls using Raven's band limited energy detector. This week I have also decided to use a convolutional neural network as my machine learning classifier (more to come on this decision later).

I went on the Carson tuesday and I did a good job of not getting sick. I wasn't able to stay in the cabin for too long to avoid nausea, and as result of that, I couldn't get any work done on my project unfortunately. It was an amazing experience and I was able to see the installation of the new hydrophone that collects the audio I am using for my project. I also saw dolphins and humpback whales really close to the vessel.

Oh, and the Warriors won!

Week 2!

This week I was able to meet my mentors, Monique Messie and Francisco Chavez, yay! we discussed our research project of characterizing Zooplankton Diel Vertical Migration in Monterey Bay and how we're going to use the given dataset of acoustic backscatter profiles to do that. This week, We began writing a Matlab program that traces DVM for a random day within the time-series, this looks at the data manually as single days and the purpose to get a 'feel' of the data before automating DVM tracing overnight. Currently, I'm working on my research question for the REU as well as the research planning guide and project timeline.
I've also been reading up on Diet Vertical Migration Behavior, Current Biology, and programming too!

Ash

I can hardly believe that it's been almost two weeks already... yikes.

We returned from sea yesterday. The cruise was awesome, stop by my cubicle if you want to see cool pictures!

Since I was at sea, I didn't accomplish much of my actual work. The combination of sleep deprivation and drowsiness from the rocking of the ship was not conducive to productivity. When I tried to run STOQS from the ship, it didn't work. It took me almost the whole cruise to figure out how to get it up and running again, and then I was able to load some data sets into it. I'd consider that an accomplishment, since that was what I had hoped to achieve before leaving for the cruise.

I am counting the days until my mentor arrives... we're down to 4 now. If I seem extra happy on Monday, you'll know why.

Cheers.

Rachel

Well, I'm officially back on land and the number of potential projects I have collected over the past week has increased. We did catch a vamp, but he was just a wee thing and we wouldn't have enough arm tip tissue to get a reliable sample, so we sent him over to the Aquarium. They're working on a tank that's just right for the vamp so he won't die. My fingers are crossed.

 So, for the rest of the summer, I will likely be trying to identify and clone the luciferase enzyme in:

a) the mystery mollusc

b) ostracods

c) vampire tissue we have frozen 

d) a sea cucumber

 and who knows what else. I'll be busy and excited. 

Today I'll be packing up the ship with the Haddock lab, and maybe do some bioluminescence assays this afternoon. I'll also be daydreaming about octopus. Whee!

Cheers,

Chloe

Hi everyone!

This week we started to solidify my project. I'm going to be working with James Birch to update the website for the Environmental Sample Processor (ESP) as my larger project, because there's a lot of older content from before the website changed. It all needs to be looked at, edited, and updated. I'm also working on updating the profile page of Kelly Benoit-Bird, who is doing acoustical ecology in the bay (which is REALLY COOL). I had a chance to see her present to the BOD during DOEST and took a bunch of pictures. I'm also going out with her Monday/Tuesday of next week to take more pictures and see what the Rachel Carson is like!

I've also been working on writing/editing new descriptions of the Wave Glider Hot Spot and an autonomous cytometer. Both are on their way to completion and I'm hoping they'll be done soon!

The other thing I've been working on is co-running an updated interns blog with Alia. I spent way too much time trying to figure out the aesthetics of the blog (which I learned is not easy on a free Wordpress account) but I think it's officially ready for content, so Alia and I will be connecting with people next week to start getting some intern profiles up and running, as well as a few other fun ideas we have!

Emma

Week 2:

The communication between the current SeeStar modular setup is functional. I can upload code onto the Arduino using the FTDI cable and can communicate and receive the Help Display and Functions through a regular serial cable. Chad taught me how to read a schematic diagram and I gained a greater appreciation towards their design.

I set up the Raspberry Pi in order to recreate a student mentee's design of SeeStar. I am having a problem with connecting to networks and re-installing the operating system. I may have also shorted a card reader?

As cumbersome as my trivial problem is, it has motivated me to reach out to a handful of staff around me. They are teaching me how to connect to networks, ensure that addresses are assigned correctly, and navigate through the terminals. Eric, one of the software engineers lent me his card reader. Perhaps later today, I will receive soldering lessons from Jose, an electrical engineer. My biggest accomplishment for this week was getting to meet and learn from many of the bright minds and professionals at MBARI.

Hello everyone,
I will not be in the interns meeting on Monday because I will be meeting with Mary Miller at the San Francisco Exploratorium to see what they are doing and have done with CeNCOOS data/ monitoring information as well as their augmented reality exhibits. I am very excited to visit the Exploratorium, it will be my first time there. At the same time I feel it might be intimidating to see all that they are able to do with augmented reality given the money, time, resources and expertise they have to spend on development. Regardless it is important to see what has been done in order to imagine what can and should be done. That is what I spent a good bit of time doing this week, was looking at what has already been done to not step on anyone else's toes and at the same time see what is feasible to do in 8 weeks (whatttttt!!!!) My mentor and I came up with some short term projects I can work on in the mean time like updating the HAB timeline and perhaps making it a bit more interactive/ engaging. A side project I am doing for my mentor that I thought would also be helpful is to create a template for reporting on the google analytics from the CeNCOOS website. I got to speak with the seminar speaker Heidi Cullen for a short bit of time and I gained some insight on the informal side of science communication and education which I am not as experienced. I worked with Emma on blog design and ideas for content. We will be doing a sort of game each week with microscope pictures we take of things we have collected in and around MBARI that you can guess what it is in the comments section so be on the look out for that. We havent decided if we have the resources to do any prizes. So winning the game (not the lure of a prize) might just be the gratification and motivation to play. I also spent a fair amount of time this week networking and eating free food.
Mahalo
Alia

I spent most of this week familiarizing myself with MATLAB, as it is the software that I will be using to analyze data.  I then practiced fitting 5-Gaussian peaks to previously collected water spectra (both sea water and pure water) at different temperatures to see how the peak areas changed.  These were compared with the values my mentor obtained to see if our peak-fitting methods were the same.  They worked the same for the pure water but not the sea water (I was using an older MATLAB code that had different starting points, so I have to re-do those). Now I'm looking at how the 5 peaks change for pure water at different pressures (from 0-1500psi) at a constant temp.  I also graduated Sunday, so if you know any chem lab jobs that don't require 3+ years of experience and a Masters degree, let me know!

Hello fellow interns!

I hope everyone is having a great week! This week I have been working on collecting as much Pacific hake data as possible from multiple sources so that I can attempt to find a pattern occurring between climate change and the different life stages of Pacific hake. It has proven to be a challenge so far, due to different datasets undergoing different methods, as well as different spatial and temporal scales. I had a meeting this morning with Linda, my mentor Ken Smith, and a few other people from the Smith lab to discuss my thesis and how to go about determining which datasets I should keep and throw out, as well as what steps I should take next for analyzing the data. It is going to be a lengthy process but I am very excited to finally begin working on my thesis and am confident that I will yield some interesting results! For the rest of the day I will be doing a lot of background reading and cleaning up the data that I have collected so far. It has been a productive two weeks!

• Danielle Fabian

Hello everyone!

Here are some of the things I've been working on:

• Read through a few papers related to object detection, classification, and image segmentation in images.
• Made a program to process previous work into a new data format. It involves video frame extraction and some text processing.
• Configured my remote connection to one of MBARI's powerful computers. Also set up the user account to do the machine learning workloads.
• Set up my desktop computer to also run heavy workloads.
• Started looking through and thinking about how to annotate/fix up my dataset.
• Learned some more basic Tensorflow.
• Networked with a lot of people.
• Started thinking about my final paper. I made a google doc so I can just start writing things down. I'm not the best or fastest writer so starting early is necessary for me.

Nathan

Hi All,

So this was the first week of work for my project and things are going well. I'm tasked with creating a benchtop depth simulator for use in testing the Coastal Profiling Floats. These floats go to set depths in the ocean and take all kinds of measurements before resurfacing. They measure depth using pressure sensors. My job is to trick the pressure sensors with compressed air controlled by a regulator that I, in turn, control with the computer. I've finished a simple simulator already and so far it's looking very possible that I may finish the entire proposed project by the end of next week. Hopefully I wont be eating my words next Thursday but we'll see. If I do in fact finish the complete simulator next week, that will leave me 8 weeks to try out some other interesting things on the float. I've talked with my mentor about several possibilities including implementing an acceleration sensor to determine drift from undersea currents.

Also went out on the Paragon this morning to help deploy and retrieve a float. Motion sickness is a thing.

Overall things are going very well.

-Pierre