Hi everyone!

This week I finally sat down and designed my project! I'm going to be looking into the biological carbon pump by looking for correlations between export efficiency, POC flux, quality and sediment community oxygen consumption. I also did a ton of work in R and finally got the hang of it (with some help from the internet and books)! I'm using very large data sets so R is going to be what I use to create all of the plots and graphs I need so it feels good to have a firm grasp on how to use it. I have started writing my introduction so I can put all my ideas and hypotheses in one place and start some analysis so I hope to have a completed draft by the end of the week!

With my mentor out of town this week, and given the fact that we don't have any fresh chaetognath or radiolarian samples for me to begin working on, my mentor advised me to practice running native PAGE gels on Frillagalma, Halitrephes, and Bathocyroe. So this week I have been preparing to run the gels (finding a protocol, making buffers, etc.). And today I get to actually run them!!! Whooooo! I have to wait until we go out to sea before I can collect the samples I need for my experiment, but this week is just getting some experience under my belt with how to run a non-denaturing gel.

Hello everyone!
I've spent most of this week continuing to measure octocorals and identify epibionts in VARSannotate. On Wednesday, I began comparing how a couple different measurement methods affect volume estimates in a sample of the data. I'm excited to begin looking at volume and epibiont-presence in relation to location, depth, DO, etc. Earlier this week, I was able to watch a few of the DOEST talks via BlueJeans. I found the talk about microplastics and AMI2 to be really interesting!

hello hello!

this past week has been almost exclusively computer work - searching through our new vampy transcriptome for my candidate genes, and checking to see if it has sequences that the old one didn't have that I could use as candidate genes. there has been a lot of speculation and brainstorming about why my genes didn't produce functional proteins, or why the genes weren't expressed in the bacteria, so I'm excited to get off the computer and start work in the lab again.

this next week will be a little hectic, though, because I will be working with some people from NatGeo, who will be filming some of our live specimens for bioluminescence in the seawater lab. so I'm not sure how much time I will get in the lab this next week, but will hopefully be able to get my sequences in some bacteria soon(:

good luck everyone!

Yo yo yo! Happy payday everyone!

MONDAY: Installed GitHub locally and cloned my BitBucket MCS repo (https://bitbucket.org/brian_ha/cpf-mcs/src/master/). Committed a working proof-of-concept Jupyter notebook for the CPF SBD-to-JSON conversion. Evaluated four different software libraries to automatically create CPF KML files, picked one (simplekml: http://simplekml.readthedocs.io/en/latest/).

TUESDAY: Started proof-of-concept Jupyter notebook for the CPF JSON-to-KML conversion. Discovered a lat./long. conversion software bug in my SBD-to-JSON code. Attended DOEST reception.

WEDNESDAY: Squashed (software) bug. Completed a working proof-of-concept Jupyter notebook for the CPF JSON-to-KML conversion. Conducted first technical demo/review of my work with and received feedback from Gene.

THURSDAY: Committed CPF proof-of-concept Jupyter notebooks to repo. Implementing Gene's feedback...

Hello Everyone!
This week for me has mostly included testing my current setup and determining how to match the movement of the larvacean by comparing various videos and looking at the kinematics of the movement. The next week will probably include a lot of tests with different materials. This week has been a very busy one! but I have to say I really enjoyed DOEST, there were some great talks and I enjoyed getting to talk to some of the board members and other MBARI staff.

Hi, I've had my first meeting with one of my mentors this week, and there's definitely a lot of things going on in CeNCOOS to get involved in. I've been trying to find audience research about what audiences across the US know about the ocean, and how they engage with and understand various data visualizations. I enjoyed listening to the DOEST talks on Tuesday and have since been researching more about phytoplankton and ocean acidification, as well as how we study these in the ocean.

Hi everyone!

This week I've been learning more about deep learning and getting familiar with some concepts. On Friday, I had a long meeting with my mentors setting down
the material needed for the project and pulling material from Github and Docker. Read few papers related to tracking systems. Also I enjoyed DOEST, and getting to talk with some MBARI staff.

Hello! At the beginning of the week, I began making a catalog of units from one of my humpback whale songs. I included the duration, low and high frequency, and total number of units in the song. After reviewing this with my mentor, I realized I didn't zoom in on the frequency enough to accurately record the low frequencies. I read some literature my mentor sent on other ways to identify units such as the self-organizing maps (unsupervised data) and methods to automatically analyze song units. Tom finished his finals! Yay! His first day was Wednesday and we made a brief plan, discussing next steps in regards to coming up with a set of features for the units, different clustering methods, and overall questions we hope to answer.

Good morning everyone!

This week, it consisted of reading more on the Deep Learning Book and becoming familiar with a software called Docker! By the end of this week, I'm going to be done with a small project that my mentors have assigned to me and my teammate in order to understand how to operate on the actual project.

It's been a little bit of a busy week, which has been nice. Thursday and part of Monday were spent nailing down the flow speed required to guarantee turbulence in our eddy covariance system. After that, I spent most of the rest of Monday and Tuesday testing different tube and motor systems to see which ones would meet our requirements. Part of that also involved going up to the EE tech lab and that was a really cool experience. It's a good group and they are super helpful if you need to learn a new skill or even a refresher. I've been soldering for nearly 20 years and Jose taught me something that just made a huge difference in my technique. Wednesday brought a new project that I'm super excited and a little nervous about. I'm going to try to create a model that describes the behavior of chemical density fluxes and how the response to disturbances like waves or tidal changes. I've been doing a lot of reading and researching. Most of my next week will be taken up with that as well.

Hello everyone!

Since I've had finals this week, I've spent most of my week studying and also packing up all my belongings in order to move out, so I have sadly not made much progress on my internship.

I did manage to continue familiarizing myself with the data a bit in my free time, however nothing too eventful.
I am very excited to finally start working and join everyone at MBARI next week, hopefully I won't be too far behind and can still make a valuable contribution.

Whats up!

Just finished up at UCSC and had my first day at MBARI yesterday. Spent the day yesterday working through some of the finer details of the project plan, building up an approach and schedule document, and reading relevant literature. Today I am at Hopkins to see a presentation by a grad student here studying blue and fin whale vocalizations. Also trying to get a dirt simple visualization of some of the humpback data done today (in jupyter notebook), just as a preliminary investigation.

Hoping to add some more descriptive features (frequency contours) to our feature set next week and start applying some unsupervised ML.

Hi all!

Overall been working on the release mechanism for the jellyfish tag. Knowing that I will have to solder in some wires to the iTAG, I have begun to learn how to solder and so far I have yet to burn myself. Although my mentor has been out this week, I have still been able to find help from others at MBARI which is great. Hoping to soon begin testing the release mechanism and brainstorming some designs.

Hi everyone!

Most of my week was spent setting up the wet lab for the abalone experiment. I have been calibrating water flows and oxygen sensors; today I believe we are going to start calibrating the pH sensors as well. Yesterday was really awesome because I got to feed the abalone for the first time! We went to the beach to collect ulva (green algae) and fed it to the juveniles and adults. I'm looking forward to finishing setting up the system so we can move forward with the experiment!

Hello MBARI,

I have finished the image analysis proportion of the project. Now, I am calibrating the upwelling system (O2 and pH concentration for now). Yesterday, we collected Ulva (green algae) from the beach and fed them to the red abalones in the wet lab. There's a lot of things going in the lab, but I will get the hang of it eventually. Excited to do experiments with the upwelling system next week!

Hello all,

This past week has been a blur. My work has consisted of developing queries, tools, and applications, all with the aim of organizing and combing through the frame grabs on the VARS database. Some of the tools that I've made so far: a program to remove black borders from images and crop them to size, a modified algorithm (from Brian Schlining) to add the MBARI watermark to images, and an application to query and summarize the data collected for each genus on the VARS database. Currently, I'm developing an application that will download and organize images by genus an species. What I've learned in the process are a few project-building tools (Maven, Gradle, sbt), a good deal on how poke through VARS with good queries, and some basic Scala.

Once I've finished building the download/organize application, I'm going to move onto some machine learning. With the images my tools will curate, I'll be looking into using class activation mapping to use the images in a few different transfer learning models. Currently, I'm looking into the models within Keras.

Hello!

This has been my first week at MBARI, and it has been a great, if hectic, start to the internship! My project is on environmental DNA, looking into Steelhead trout populations in the Carmel river and will be working in the ESP lab under Jim Birch. My project will also be comparing the effectiveness of traditional eDNA techniques against automated methodologies.

To sample for populations, water samples are needed to be collected from different sampling locations along the river, which are then filtered to concentrate any DNA that may be found in them. This is what the majority of this week has been focused on.

Monday was spent getting settled in, getting practice in the lab and preparing the equipment for our field sampling on Tuesday.

On Tuesday I was out in the field collecting water by 6:15am with the Carmel River Steelhead Association. We sampled three sites, going as far as Cachagua up the river, collecting 10L of water at each site. By 12:30 we were back in the lab to process the samples. Filtering had to begin as soon as possible after collection to prevent as much DNA degradation as possible. Once the water has been filtered, the filter can be placed in the freezer and analyzed at a later date. This meant I was in the lab until 9:30pm making sure all the samples had been filtered, bottled, labelled, and frozen.

Wednesday was spent dissembling cartridges from the automated ESP, cleaning up the mess from Tuesday, and prepping for more field sampling on Thursday.

Thursday was another early start, once again taking water samples from 3 sites along the river. These sites were further down the river, and so we were back in the lab by 10:30 and filtering before lunch. The rest of the day was very similar to Tuesday, getting out at a much more reasonable 7pm...

Today I will be practicing DNA extraction so we can get whatever Steelhead trout DNA we may have off of the filters, and having a go at qPCR so we can quantify how much we found.

Feel free to come bother me at my desk (208.22), and if you want to see what it looks like to filter water, let me know and I'm sure I can hook you up.

Hello everyone,

I know I am late, but I hope better late than never? The last week was crazier than I thought it would be with all nighters most of the week. But it is all over now, with and official graduation on Friday.

For my project I have set up my laptop and installed the software tools. I will be working with lidar scans, and trying to stitch them together into a comprehensive map of the ocean floor. I found some papers on similar topics and have started reading them. Next week I will be coming down to the office full time finally, and I hope to process data from previous outings to see the current pipeline for processing the data.