I had a great and productive time this week while being out to sea. On Monday, my lab gave me control over the ROV for most of the day and I was able to guide the pilot to several Chiroteuthisand observe some great behaviors and conduct in situ experiments by removing the tail of the juveniles and observing subsequent behavior. On Tuesday, the aquarium linked up with us while giving a deep sea presentation and my lab gave me the radio and let me do the talking to the audience in the auditorium. I was so excited that I really forgot to say a lot of things, but hopefully I made some sense and was entertaining in some way. Also, on the motor back to Moss Landing, I saw my first large, mesopelagic shark while I was talking on the phone with someone from the deck. It was probably just a blue shark, but exciting nevertheless. Back in the lab I am still working on my ethogram, but I am almost done and would like to finish today so enough with this! Bye!  

This week was nice (kayaking was very good, thanks again)! So I now have my data set and I am starting playing with them. Paradiopatra tube worm patch are not very abundant and it is challenging to give inetrpretation. I will now study more the associations of animal within the pacth over time. I am also back reading to discuss more my results. I hope to have more conclusions next week.

This has been a busy week, but then aren't they all busy weeks! Monday's kayaking adventure left us all buzzing and tired. It was so nice to get out on the water though and see some otters rafting together. I stopped data collection on Monday which left me with approximately 6,000 observations to use which is awesome. I have already converted the pixel measurements taken in VARS to the actual length measurements. I still need to look at the differences between time periods and species...lots of work there. I am starting analysis on these data today so hopefully I can have some results early next week. Crissy, Linda, Claire and I have been going back and forth on how to handle the Canadian Grid aspect of using the ROV video...more to come on that later.

This week we got the STOQS application installed on Kraken and begin to produce some long queries with the application and view the logs of those queries using pgfouine. Although we are seeing increases in responsiveness, we are not see as much of an increase as expected. Which means either some configuration is not working as expected or that the application responses main factor is not the database but some other part of the application. The later is probably the issues since there is a lot more going on inside the STOQS application then just retrieving the data from the database.

Currently we have been running these test on the spinning disk part of Kraken and thought we would see more of an increase in performance once we switched from using the spinning disk to using the FuisonIO card, this card is a solid state drive that connects directly to the PCI slot. However, when we switched over to the FusionIO card yesterday and ran the same load as we first ran on the spinning disk, there was little difference. The load was working faster but only around a second or two faster compared to the spinning disk. Now we are starting to look into why this is, since we thought we would an increase of at least a few seconds.

I have also been working on my paper this week, which I haven't made the most progress on but feel I'm at a good point for where I am in my project.

On a none project related note. Kayaking was awesome, thank you for giving us the opportunity to do that it was a ton of fun.

I've been running trial batches of copepods through the LISST-HOLO this week, and encountering some frustrating road blocks from the tubing not fitting to lack of detection to the pesky things crawling off my filter! Next try is a horizontal system that will hopefully slow things down enough for the particles to register with the HOLO. I'm looking forward to having John Ryan back around next week to help me with understanding how it samples in situ, as I can get really good results using a static sample chamber. I'm starting to feel a bit worried about the lack of time and how much I have left to do, but hopefully once the system is working my actual experiments won't take too long.
I've also been digging around in the LOPC data, but there are so many files that appear not to have been processed, it's hard to get a feel for specific experiments. I'm talking with Mike McCann about making those available.

Kayaking on Monday was great, thanks for organizing that!
I've also been sailing with Thomas Hoover in the Wednesday Night Races out of the Monterey Yacht Club, which has been great. There's often room on spectator boats if anyone just wants to get out on the water!

I started out this week meeting with my mentor about whats left for me to do for my project; honestly it seems never ending, but I'll get it finished- -We discussed my presentation and created a layout for it that seems informative enough and that he or I could use for future presentations. It's just a matter of filling in the missing pieces now. As far as choosing motors, we've looked at few that included (I believe I mentioned this last week) the PRD Fireball go Kart engine and the Kawasaki KLR650 engine and am researching a potential diesel engine. I'm creating a trade study to look at these potentials to determine which will work better for this system. For propulsion through the water we are looking at already existing motors that are being used by the existing AUVs. Bill and I decided that these would be a great option because MBARI has already done so much testing and design for these and have proven to work great for AUVs. I've received some useful information from people who worked on the previous AUV designs and now am just trying to determine what all the values mean and matching a motor for my system.  These include looking at efficiencies and power output and shaft size and optimum rpm. Not going to lie: this is continuously a learning experience. Today has been pretty rough with trying to remember where I am; whether I'm looking at sea or air operations and staring at spreadsheets of number doesn't help

Kayaking was a great way to start the week with having a shortened weekend and all, but the open house was really fun! Looking forward to relaxing this weekend and cranking out some of my paper and enjoying some beach time. 

This week I officially started my experiment with "true" trials! The process for each trial has been somewhat challenging.  For the most part, the urchins travel down the mazes towards the kelp sensed flow, as expected. However, select urchins don't respond and hence stay still where initially inserted (outflow area) of the treatment. 

Chris Lovera has been helping immensely with figuring out WHY the urchins may be responding this way. We found there has been some glitches with inconsistent water flow between the treatments and the three tanks we are using (Tank #1, #2 and #3).  We observed air bubbles forming within the tubing. Thus, we think we are having issues with not having enough water available within the whole water system. Because there is a lack of water available for the treatments, oxygen concentration may vary, causing a different response from the urchins.  

Nevertheless, I am learning a variety of behavioral responses from the urchins.  No direct correlation between the treatments and the acclimated urchins assigned to pH levels (7.2, 7.5 and 7.8) can be determined yet. More trials are in line!  Workin this weekend! Whooo!

Heyo! This week has felt a lot more productive than last week, mainly because I'm getting to know MATLAB (thanks Alba!). I've nearly completed my script (non-MATLAB users read a string of commands for analyzing and plotting data) and exported all my spectral data so that it's ready for processing in MATLAB. I've also finished up the introduction and materials & methods sections of my final paper and will be sending the draft to my mentor, Peter Brewer, for review because he will be out of the office for a good part of August. I've also been working with Peter Walz to get a pressure cell functioning so that we can use the laser Raman to get a spectral sample of some reference decane oil (without methane saturated in it) at the same pressure/temperature conditions during the ROV cruise. This reference spectra will allow us to compare samples taken in situ to the reference to quantify the rate of degassing of methane from the decane oil.

Outside of my research project: Open House was wonderful! My mom and one of my brothers came up to the area for the weekend. It was great to have them see firsthand the amazing internship I'm a part of! Kayaking in the Elkhorn Slough on Monday was the bomb dot com! Really enjoyed the intern bonding aspect and learning the natural history of the slough from our two kayaking guides. Thanks Linda for organizing!

Open house was a lot of fun, being across from the squid provided lots of amusement/horror when things got slow at our booth. We had some really good questions from the attendees, the best of them coming from a kid who couldn't have been much older than 10. I'm convinced if we gave him a parts bin and schematics he could have built Patrick's ammonium float by himself.

This week has been more method development. We added a gas diffusion block to the system  and changed a couple reagents to allow us to look at water from the slough without having to worry about background fluorescence from dissolved organic carbon or plankton. This isn't necessary  for open ocean water, though in high plankton concentrations it could be helpful. I had to re-plumb a lot of the instrument in order to get the diffusion block and 4th reagent line to work, this wasn't terribly difficult but hunting for the correct fittings takes forever. The longer lines and characteristics of the diffusion block required adjustment to the data acquisition and processing methodologies; it took me longer than it should have to figure out why my scripts weren't finding accurate peak heights on the new data. 

Last Friday we had planned on sampling off the dock today while the tide came in and peaked but we haven't been able to get things co-ordinated with the small boats dock so it looks like we will have to sample next week. The only reason for today was the wider tide swing, but the tides next week are decent too.  Still collecting data has kind of gotten me worried about writing this paper. I know  I have enough material to discuss and go into painful detail for my method protocol, but the time frame has got me concerned. I forsee long nights  in my future but I imagine I won't be alone.

Oh my, I was so caught up in work... so I'm late.

At Open House I was a part of the Information booth and I had the opportunity to greet guests and have some interesting conversations with several. Most were so thankful that MBARI opens its doors like that. One woman told me it was her favorite thing to do out of the whole year and she must have said thank you about 12 times.

I also wandered around and took pictures for the website. That was fun and gave me an excuse to really get in there at all the booths to see what was going on. I loved the dock and the machine shop! And the fish and squid printing was priceless. This one little girl ran off leaving her mother holding her painted dead fish. I wanted so badly to take her picture as she called after her daughter with a look of concern and disgust on her face all at once, but I figured she would rather not be memorialized that way. 

Kayaking on Monday. Super fun and so hard to get back to work in the afternoon.

This week I am focusing on my methane mounds illustration. Last Friday I met with Victoria Orphan. She explained the geobiology of the mounds to me and offered a solution to visually explain the chemistry by way of the microbes in the sediment. Today I met with Ed Peltzer to combine his thoughts with hers and now everyone wins. Victoria will also be able to use my illustration and most importantly she said she will contact me in the future now that she knows an illustrator who "understands this stuff".

Many thanks to Alba and Diane for the T shirt coordination. Alba collected 112 orders and we emailed that info off to the printer today. Success!

I finished all the work proposed by my mentor for the internship by this week, so next Monday I will have a meeting with him in order to demonstrate how is it working. He has suggested me to include my program to the program that they did for the serial communication, this way the end user can select if it's a serial or a IP connection and the PUCK test tool should be completely compliant with both versions.
I haven't thought on the possibility of unify both programs, but probably it won't be so much time to put them together and I will be able to finish it on time. So it's a good idea to try to make a test tool completely compliant with all PUCK versions, what I think will be useful for PUCK instrument manufacturers.

On Monday I had a meeting with Kent and Tom in order to talk how do they want the final paper structure. After discussing which kind of paper is the best for this work (tutorial, step by step set-up etc...) I started writing as they suggested me to do it, this way we will have enough time to revise the final paper presentation.

In other terms last week we had the MBARI Open house, I stayed almost the whole day on the MOD ticket table, with Miguel, Wilson and Dylan. It was a really good time, because everybody was really grateful about our job and on the same time we were enjoying what we were doing. So what else could we ask for?

On Monday, I went on a cruise of the Midwater lab. It was awesome! I had a really really really good time! First we collected Nanomia for the MRS (which I learned was the Midwater Respirometer System) and we left it out on the mooring; they picked it up the next day. Then we went hunting for Ben's squid, which was fun! He was trying to describe behaviors and change of colors in the body or tail once he detached the tail from the body. We saw baby Humboldt squids, a baby red octopus, some jellyfishes, fishes, a comb jelly, and I asked Bruce a hundred thousand questions, which he seemed happy to answer.

I also have spent the rest of the week collecting money for t-shirts! We finally made the order this morning for a total of 112 t-shirts! So that's that.

And then I also started to learn how to use Sigma Plot, a very useful tool for plotting data. I got a little tutorial from Reiko on Tuesday, and did some plots for my presentation/paper. I've also had to go back to my equations because I didn't remember some calculations and was, again, getting mixed up. But that's solved too. So hopefully I'll be able to finish figures today, and start describing results tomorrow. We'll see how that goes.

Yikes, sorry I'm late!
For starters, Open House was a great time!! I am so grateful for everyone who took part in making everything such a success! It was nice to see everyone's faces floating around and engaging with our visitors. Special shout-out to all those who helped with the children's and social media booths! I'm pretty sure I was running on pure adrenaline and you all got me through!

It has been yet another busy week!  Kayaking on Monday was amazing (a nice arm workout as well!).  I finally got access to the Spartan software which allowed me to show the crystallization of the hydrate. That made my morning I spoke with Ed Peltzer who gave me maps of expedition.  I was able to make rollover images on the map to show the specific sampling locations. Now I'm figuring out how to edit the .mov files and post them directly into Dreamweaver.  I'm keeping in mind ways to tie in the MBARI resources as well as connect this page to our social media pages. All the pieces look like they are coming together which I am thrilled about!  I'll be here this weekend to make sure the train keeps rolling.  I participated to the WATCH panel today which was, again, a great experience, and we laughed at how the kids drilled each other after their presentations.

Another great week here at MBARI. I've preoccupied myself this week with visualization of our CTD data, which is recorded alongside every VARS annotation in the database. This can be useful for explaining trends in biological data over longer periods of time - ie, el nino or the like. I'm currently working with my mentor to get that into a state suitable for analysis. Meanwhile, I've been spending some time generating figures for the presentation in R, which can be a lot of complicated syntax. However, I'm happy with the stuff we have and hope to finalize that next week. Still more analyses and other work to be done, but I can see it all coming together!

This was a really good week at MBARI. The electronics of my final module are done, it is fully operational. What I am doing right now is trying to build the housing for the whole module (with a lot of help). I am still trying to figure out how to make it super lowe power consumption, which I cannot still accomplish. After putting the module in the housing, all what I have to do is making the sensor more user friendly, and I will  be done .

This week has been productive albeit short. We went kayaking on Monday and saw an otter hauled out with a baby in the pickleweed, that was really cool. The end of the day Mon through Thurs I ran more tests using the ECO puck, and have begun analyzing data from my filtered ASW. I also have dark counts values, so I can convert all the count values to useful information (concentration). My plan next is to run some samples in the fASW and compare the background from the filtered vs unfiltered samples.

I can't believe the summer is coming to a close soon, next week I'm getting the LISST-100 together and hopefully getting some particle size distribution values. Then it's data analysis, writing, and presentation time!

Met with mentor to go over my updates and things to focus on( there are so many interesting things, yet time is a factor). Matlab has not been cooperative with me, in terms of having dimension mismatches. I think I'm getting there to produce my supporting figures (clue...it has to do with upwelling). I will be off the Buffalo for a friend's wedding, and I have been stocking up on the data sets so I could work on them while I'm there (no choice, I've gotta pull this through), and the weekend is not going to look pretty. Have a good weekend guys!

I finally got my benchtop engine simulator running! The stainless steel clips that I am going to use to secure the pressure vessel are not quite done, but I've been able to do some basic testing safely by removing the springs from the piston I use to simulate pressure. I have all of the sensors that I need up and running, and I am almost done implementing a PID controller that should regulate the position of the bellows. This may come in handy next week when I will need the bellows position to be constant for my added mass testing of the test tank prototype. Things that I have left on my agenda include finishing up my PID control, evaluating pump efficiency as a function of pressure and bus current, and estimating the added mass and drag coefficients of the test tank prototype. If I have time after that (haha) I will work on the coulter counter that Gene and Ginger have started on.