This week I started familiarizing myself with R using multiple data sets that my mentors provided. I was able to make scatter plots and line graphs. I can also run regressions. One of my mentors introduced me to VARS and I got to look at some images taken by our rover. I then read papers from my lab to get an idea of the research that they do here. On Wednesday I got to attend the seminar given by Isa Rosso. I attended a lab meeting and met with my mentors to discuss my project.

Morning everyone!

This week was mostly me re-familiarizing myself with my project from last year; where I left off, what worked, what didn't work, and what my next steps are. As a general overview of what my project is, I am trying to characterize and clone the luciferase (the catalyst of the bioluminescent reaction) from vampire squid. Last year, I was able to get to the last step of the project: expressing my cloned candidate genes into bacteria and assaying the expressed protein with coelenterazine (coelenterazine = a luciferin, i.e. light emitting molecule of the biolum rxn, used by vamps) to see if I could get it to produce light. It did not produce light. So now I will be trouble-shooting and trying some new methods to see if I can get some light out of these guys. I got to talk with a new member of our lab, who is a photoprotein expression wizard, and he gave me a bunch of ideas about ways to continue with my project. Because this project combines biochemistry with genetics with some bioinformatics, everyone in my lab was able to give me some excellent advice.

I'm so stoked to be working on this project again, and it's really nice to be able to come at it with some fresh perspectives. And I can't wait to hear about what you all will be working on! So best of luck to you all!(:

Hi! This first week I installed Raven, an interactive sound analysis software which produces both a waveform and a spectrogram and began reading through the manual. The spectrogram will be most useful for me as it depicts the frequency vs time of the humpback whale songs. One of my mentors introduced me to a PhD student, Will who has done research on song structures of blue and fin whales (lower frequencies than humpback whales) and he was very helpful in introducing me to bled software within Raven (band limited energy detector) which will be used to distinguish the whale songs given a set of parameters.

Hello everyone!

This week I was introduced to the abalone experiment we will be working on over the summer with my mentors and co-intern. We will be exploring how present and future conditions of ocean upwelling will affect juvenile abalone. Most of Monday was spent familiarizing myself with the experiment and past results related to the work we will be doing. Yesterday I learned how to use a software called ImageJ to analyze the size of abalone shells. We will be photographing and analyzing more shells for the rest of the week.

I'm very excited to move forward with this project and see the results of ocean acidification on this organism.

Hi all!

The list of accomplishments this week is extensive. Among other exciting developments, I found the closest printer to my office, the closest coffee and water supply, and successfully managed to navigate from my office on the second floor of the south side of building A to my lab on the first floor of the north side of the building B expansion and back. Having proven myself a master of my environment, I moved onto installing Reader and Matlab on my computer. These are indeed exciting times. I also met the other members of the Carbon Empire (as my lab styles itself) and started work on our eddy covariance project. I created a quick calculation that gives some theoretical flow rates for the pump we are planning on deploying with our setup. Today, I will be modifying one of the pumps that we have to create a proof of concept. To do this, I will have to get cleared to use some of the engineering spaces and that sounds pretty cool.

Hello everyone!

This week mostly consisted of deciding what I wanted to do this summer in the Bioinspiration lab. I was given two different options, one of them being the use of image processing, tracking, and control algorithms with 3D translational stages to track an animal in a tank for imaging measurements, and the other being the development of a soft robot of a larvacean tail, which by adjusting actuation and material properties hopefully will match the kinematics that has been determined for the tail movement, and if time permits, there might even be some opportunity to measure flow dynamics of the tail. After some thought into the decision, my mentor and I decided the best project for me currently would be the tail, since I have some background in biology and robotics. I am excited for the next couple weeks, and even though the project is not super straightforward, I look forward to a lot of testing for the next few weeks.

GOOD MORNING AND HAPPY THURSYAY

Wow this week has been really interesting, and I mean that in the BEST way. I feel like I'm constantly meeting new, friendly people around MBARI who are eager to have conversations beyond the typical, "Hey, how are you?" and "I'm good, you?". I have found that people are eager to teach if I show my eagerness to learn.

That being said, I started the week by doing the typical housekeeping things like setting up accounts for various things, downloading programs to my new computer, etc. As the week progressed, I began researching potential projects, I met with my mentor and had a fruitful conversation in which we narrowed down my project to two potential subjects. I then met with both of my lab techs who gave me two more ideas. And then my mentor emailed me three more project ideas. SOOOOO needless to say I will be spending a good portion of today and the long weekend reading previous papers in order to decide on a project. Speaking of an eagerness to learn new things, I spent most of the day yesterday in the lab with Darrin, a student from the Haddock lab getting his PhD. He taught me how to run a protein gel on bioluminescent particles from chaetognath (basically predatory marine worms that shoot glowy stuff out of their body to avoid predation). This is one of my potential projects to try and identify the gene that is responsible for bioluminescence in chaetognaths. Pretty cool things happening over here in B208.11

Hi everyone,

During the first few days, I've been getting myself acquainted with the people and tools I'll be working with over the summer for my work on FathomNet. Besides downloading countless software packages and libraries, I have begun working with VARS through SQL queries. From this, I am currently working on grouping all screen grabs from the VARS database by genus and formatting them for application. I'll most likely be writing most of my software in Java/Scala. I seem to have a good amount of work ahead of me, and I'm excited to get going!

Hi Kevin - thought I'd throw in my notes on SQL queries (from Steve Haddock). These have proved to be very useful - George (I can email this to you as well since some of the symbols apparently don't show up the highlighted lines below)
You can search in these ways:
?
-s : samples from a dive
-a : associations between groups
-c : get all annotations of concepts for all dives
WARNING: Genus along will not get the species.
Use -k option or put species in quotes
-k : species included within a higher taxon
-i : images from a dive (specify -p or -d)
-g : Retrieve PNG images, without overlay, instead of JPEG
-d : dive summary for dives or to specify dives
-f : print as formatted report mainly for associations and \-k option
-w : search on internal server of Western Flyer
-b : print debug output

For each of those, you can use in combination with
-p PI name or -d dive range and/or -c concept name.
?
-p : find dives for a PI
-d : provide a range of dives for a search
: d by itself without other flags above gets a dive summary
-a : get all associations between two or more groups, separated by +
secret option: put 1 at the end for full table (nothing is summary)
-k : get all species for a higher taxon (takes only one name)
secret option: put -f 1 at the end for quoted csv, -f 2 for full table
-p : get dive summaries by PI (or multiple PIs with commas)
to limit to the most recent X dives, put ,X at the end...
-s -p : get sample lists from listed PIs. Use ,X to limit to recent X dives
-s -k : get samples matching a broader KB concept
-d -k XXXX -d YYYY : get all annotations for KB group XXXS on a dive YYYY

Use grep, cut and sort to extract certain columns.

Usage examples:
vars_retrieve.py -s D422 R500 # can use either D or R for Doc Ricketts
vars_retrieve.py -d D422,v360
vars_retrieve.py -c Aulacoctena,"Bathyctena chuni"
vars_retrieve.py -i Paraphronima
vars_retrieve.py -i -c Bathyctena
vars_retrieve.py -i -d T412 # get all images from T412
vars_retrieve.py -i -g -d T412 -c Aegina # get all Aegina images in PNG format from T412
vars_retrieve.py -d v

Requires: pymssql module, freetds-dev, and unixODBC
Installation instructions are a comment in the source code directly below...

Hi,

Generally I've been working out the detail of what my project will be and what is best to produce over the next 9/10 weeks - it's looking likely to be around the in situ fluorescence cytobots that CeNCOOS are working with to try to monitor phytoplankton and harmful algal blooms along the coast of Central and Northern California.

I've spoken to Mary Miller from the Exploratorium about their approach to engaging visitors with oceans, ocean observation and specifically plankton. We had a great discussion about the challenges of communicating science, and specifically climate change in the current political climates.

I've also read a lot about CeNCOOS, the IOOS and ocean observation in general, including reading up on the methods that CeNCOOS use to measure the oceans and the ways they then analyze and communicate the data.

And most importantly, I've been working out the best way to make tea over here!

The first week at MBARI can be best summed up by the experience of getting lost in the buildings - its inevitable at the outset, but one find's their way eventually. In addition to all the typical on-boarding, my time has been focused on cleaning up NOAA/PMEL West Coast cruise data for total alkalinity calculation and assessment. I am primarily using Matlab, which I haven't used since 2014, so it feels similar to navigating MBARI. I can get the steps done, it just takes awhile! At this point I have calculated and mapped change in total alkalinity (change between measured and calculated, delta-alk) for three depth categories, over three cruise years (2011, 2013, 2016). Next steps involve running CO2SYS error functions to establish what delta-alk values are significant, and looking at delta-alk over salinity grades. I'm also looking forward to going into the field for local sampling in Elkhorn Slough next Wednesday.

Good morning,

I started doing image analysis on juvenile abalone shells. The image analysis program used was ImageJ and I have experience using the software. Currently, we will be observing the growth and calcification of the shells after being exposed by future upwelling conditions. I am really excited to work with live abalones and my mentor was talking about doing an additional project with the leftover abalone from the main project.

Greetings everyone!

This week has been really engaging with all the resources I have to read and practice with. I am currently reading a few papers and a book on Deep Learning to gain an understanding of where my team project is heading towards. I have met with my mentors for the past few days to discuss the prerequisites of the project and our plans as we move forward. If time permits, my partner and I may be able to create our own Deep Learning model later on to understand different results of the project.

Hello from the video lab!

Since orientation, I have spent most of my time familiarizing myself with the beautiful octocorals and holobionts of Sur Ridge. I've learned to measure and add annotations to VARS, and have since been reviewing videos taken by ROV Doc Ricketts. There's definitely a fascinating assemblage of life at 1000m, but the footage that has stuck out to me most so far was of a piece of man-made trash settled in between the corals and sponges! With that in mind, if anyone has any zero-waste tips or wants to talk about how we can reduce our footprint this summer, let me know! On Wednesday, I was able to attend Isabella Rosso's seminar on the physical-biogeochemical interactions of the Southern Indian Ocean. Meeting so many interesting people and learning about the wide variety of projects happening at MBARI has been exciting, and I can't wait to see what will unfold over the next nine weeks.

Hi all!

This week has been very interesting. I've been getting familiar with new concepts and tools that I'll be using this summer along with my co-intern. I downloaded Docker in my computer which will benefit our work flow. Also, I've been reading about deep learning and TensorFlow, and setting up my Github and other technologies. I talked with my mentors the past few days to get a deep concept and understanding of the project and the data that we're going to work with.

Hello everyone!

So far I have gotten myself a bit oriented with what my project will be over summer, and have familiarized myself with some of the profiler data in ODV and Matlab.
I have made some plots in order to better understand and visualize the data I will be working with, and I am very excited to work on this project!

Hi everyone!

Monday: Orientation. Spoke with Gene Massion about primary project (coastal profiling float (CPF) mission control software (MCS)) and two bonus projects (CPF Guidance & Navigation, CPF Control)
Tuesday: Reviewed Python fundamentals. Installed the SciPy stack via the Miniconda distribution. Prepared and demo'd a Python tutorial for Gene. Skimmed through "Clean Code" by Robert Martin. Read about UML.
Wednesday: Took a first stab at MCS architecture via flow chart. Evaluated using the Zimbra REST and SOAP APIs to automatically download CPF Iridium Short-Burst Data (SBD) telemetry. Gene discovered Mike. McCann has existing infrastructure to achieve this via Pismo. Will try to leverage this. Attended seminar on CPF data on the Southern ocean. Chose JSON as the file format to store CPF telemetry long-term. Began proof-of-concept of raw SBD to JSON conversion.
Thursday: Continued SBD to JSON proof-of-concept.

Visit me in the chemical sensor lab (Room 245)!

Hi everyone!

Unfortunately I am still finishing up classes and finals this week, so I not only have not been able to come down to MBARI since Monday, but I also have not slept! The good news is that I finish my design project today, and I did well enough on an exam yesterday to exempt myself from a final next week (one more day next week I can come down!)

 As far as my project, I discussed my options with my mentor Monday, and narrowed it down to two options. I am doing research this week in my "free time" and installing all the software needed to work with the seafloor data onto my laptop. One project involves processing LIDAR data, aligning different scans of the seafloor, and using the aligned data to get a good idea of how the ROV was moving across the bottom during a survey. I have found some papers on related topics and I hope to come in Monday with a good idea of where to go next, and how to process the data using the existing code base.

Hello! I like Ethan am still finishing up class, and will not be able to come in until Wednesday of next week. Therefore, my update will be brief (and late, sorry).

On Monday after orientation, I discussed a rough project plan/strategy with my mentors. In short, the plan involves first choosing features to represent humpback whale song units, finding the right encoding to discretize these song units, and performing analyses on the resulting encoded song. Since Monday, I have made progress by skimming through the manual for Raven that my research partner Miriam sent over (thanks Miriam!). Raven is the software that will be used to create spectrograms of humpback whale song for our analyses.

I am so stoked to be back at MBARI next week, see y'all then!

Hello, I am late! However, I was enjoying lunch on the beach with my mentor and lab group so hopefully that makes up for it! First week at MBARI has been good so far. Thankfully I am coming in to a project that isn't from scratch so I get to add on and improve upon it. Specifically my project involves this tagging device that we want to be able to place on jellyfish. Currently the task we face is the retrieval of the tag using a burn wire, which separates the tag from the jelly allowing us to retrieve the tag.
Hope all is well with your projects!
-Richard