I just read the other Confluences from last week. Sorry for not getting to them earlier. Usually I read after posting, but as I was one of the earlier posts, I did not go back to check later. I will try to be better about it. Jason and Diane, you are welcome to stop by sometime if you want to see my plots.

Diane, I am interested in what you will be doing at CeNCOOS. Do tell me more!

At the end of last week, I met with my mentor to show him what I have done so far--mainly the analysis of the TS plots from the wave glider and the Fulmar CTD data. My next steps are to look at the effects of biological productivity versus gas exchange on CO2 and O2. I have made some plots of O2 and sea pCO2 versus salinity (the conservative tracer) with the z-variable as chlorophyll a or CO2/O2 flux. I have particularly interesting plot (CO2 or O2 versus salinity, the fluxes shown vertically as vectors) that shows that the waters are a strong CO2 source to the atmosphere during upwelling events and a strong O2 sink.

Last week, I attended another one of Steve Haddock's Python workshops. I'm really thankful that he takes time out of the week to provide us this valuable service. Although I may not have time to really learn Python this summer, it is good to be introduced to it.

This week I am working more with the Fulmar CTD data. I need to generate CTD profiles, then process the chlorophyll a data from bottle samples to compare with the fluorescence-derived chlorophyll a. Then hopefully by next week, I can get to comparing the Fulmar underway pCO2 data with the wave glider pCO2 data and also look at the pCO2 time series from the M1. This May/June upwelling event had the highest pCO2 seen thus far (1200 ppm).

One problem I had this week was generating the CTD profiles. It should a simple enough task, but somehow there were no station labels in the data file I got. I had mistakened another field for the station label and generated a bunch of plots that were wrong. I spent a lot of time writing Matlab code to find all the unique lat/long, label them with a station ID, and then find how many repeated casts were done at each station. Then I wanted to plot the variables at each station for all the casts done at that station. Oh yea, and for upcast only. Some of the casts had both upcast/downcast, some only had one cast (not sure which direction). It was a challenge for me to sort through this mess. I didn't want to write sloppy code, but I ended up just doing what I knew would work. I ended up with a hideous code with too many for loops, but it got me what I wanted. Perhaps I need a lesson on Matlab style. Diane, if the references you are using are good, please direct me to them!

Anyway, I did enjoy the BBQ this week, and welcome back to Geraldine! I saw the Western Flyer return from my office.

Going out on the Fulmar to grab more water samples was such a great experience. We even saw some humpback flukes and a Mola mola! Evelyn seems to have a good eye for spotting these kinds of things. I came back from the cruise, found that the fridge I was using had to be defrosted, and had to move all my samples into a fridge on the other side of the building on a different floor. I also spent the next morning mopping up water from the lab floor...oh well, these things happen...

As such, I have experienced some delays processing the water I've collected, but I'm hoping to freeze most/all of it today in preparation for later analysis. I am starting a sample log because with the number I am dealing with, I will probably forget details about the processing later...

Looking forward to outreach today.

I was handed my first defeat this week... and it came at the hands of ArcMap, which is a program I am very good at. Batch processing files through a model is easy when you only have one input; however when you have two inputs it tricky. I spent a day spinning my wheels on this and then decided to just revert back to Matlab to run the process. If there is time toward the end of this internship I am going to try and resolve this issue. I may be able to ask for help at the Monterey Region GIS User Group Meeting today, where I get to meet a well-known spatial ecologist and python programmer, Jason Roberts, from Duke University. He's designed the Marine Geospatial Ecology Tools that I became familiar with during my time in grad school. Some of those tools may be capable of assisting with my CeNCOOS project.

 In spite of the defeat I managed to finish the HF radar dataset. Tomorrow I begin with COAMPS wind.

 The BBQ was delicious and a ton of fun! Thanks to everyone for chipping in with all the work!

It's been a busy week, though I haven't spent too much time in lab. My mentors and I have started talking about how I should be wrapping up my project (eeeeeek!), which I was a bit concerned about before the week began. We've come up with what seems like a doable plan, though, so I think everything should come together just fine. I have a few more lab experiments to run, but other than that I'll be shifting towards more data analysis and planning for my paper/presentation in the coming weeks.

I think the highlight of this week so far has been the Fulmar trip. It was awesome! Good weather + no seasickness + water sampling + gumby suits + many whales = successful day. Marguerite, our leader for the day, was really nice, energetic, and happy to answer all our questions. She was an MBARI intern in 2003, so it was interesting to hear how her career has evolved since then.

I also had a good time planning for (and eating at) the BBQ yesterday and I'm excited to do YWS volunteering just a little later today! Should be fun. Can't wait to hear all about the Flyer trip, Geraldine!

This week I was very busy making the BBQ budget work and I think it paid off - we did awesome! Everyone tells me they loved it and I've heard everyone is giving rave reviews. And with good reason - I couldn't believe how amazing it all tasted together! All the flavors meshed perfectly and the meat and veggies were perfectly done - hats off to George and Jason, our grillmasters! And thanks to everyone coming in in the morning to chop and prep everything.

Now it's back to programming but there's not too much to do until Brian gets back. I'm working on a page I was doing for the video lab before the focus shifted to pushing it external and adding in some stylistic code that can be used in the future when the nice formatting tools become available with CSS3.

I'm excited for Open House, the Aquarium tour, and our mentor BBQ - George always knows how to keep us busy in fun ways!

Hi everyone, I am back! I had one of the best weeks of my life. As you know it was my very first cruise and I pretty much didn't know what to expect. Everyone on board was just super nice with me, very adorable people!! The pilots are the best dudes ever! I received a Doc Ricketts T-shirt from one of the pilot himself!! They told me lots about MBARI, the boats, the ROVs and they even taught me how to play Call of Duty ?.

On a more professional side, the cruise was a midwater expedition and in a nutshell our main missions were:

• Hunting for deep-sea squids in general and vampire squid in particular. One of the aquarist from MBA was on board because the aquarium will open a cephalopod exhibit in 2014 and they would like to display some deep-sea species. So while we never saw a single Vampyrototeuthis we did caught some Taonius, chirotheutis, Gonatus. They will stay at MBARI for now and hopefully survived... I will stay in touch with the aquarist to be updated about them. Hope they will be fine...

• We run 2 batches of Midwater Respirometre Sytem (MRS). So basically you have 8 chambers where you can measure gas concentration. You put a shrimp Sergestes similis in 6 of the 8 chambers (the 2 other are controls) and you hang the whole MRS on a mooring at about 200 meters depth for 24 hours and then the ROV comes back and picks up the MRS and analyzed the respirometry data. So you get some in situ data about respiration instead of running the experiment in the lab.

• Hunting for amphipods, sinkers and other species that scientistS will bring back in the lab for different kinds of experiments.

If you want to know what we did on a daily basis, just follow the link: http://www.mbari.org/expeditions/Midwater2012/index.htm

I was in charge of writing the logs and that was the best way for me to get to understand what they were doing, why, the timing of the day and everything! I really enjoy taking care of this part of the expedition. I also learnt how to annotate during the dive, which is very interesting, best way to remember species name!

Today I have so much to catch up with, it is scary and my main task seems to try to keep my brain awake and fight my dock rock. But this hard day is totally worth it!! I am sooo thankful for this amazing experience!!

This week has been a kind of test for me to see how much I can handle with this project. I came to the realization on Tuesday that, with the tasks that I took on, I wouldn't be done with this experiment before the internship ended. So, we have officially dropped nanomia processing and identification from the project and am now doing only holothurian and plankton identification. Phew!
So with that change in the project, I will be ready for my actual experiment by tomorrow and will probably be starting it then, depending upon my testers. Brandon and Jason are going to be participating in it and we'e looking to see if John Ryan (who the LISST-HOLO images of the plankton belong to) would be willing to participate or someone in his lab because we need at least 3 experimenters to get a rounded data outcome.
Thank you to all of you that volunteered too! We're trying to use people that have had some kind of experience in identification to get a novice perspective so please don't be offended that I didn't choose you
So now I'm on track and ready to go and not feeling a huge amount of stress either. I've started writing my final paper (or at least thinking about it....) and my presentation (at least the outline....) so things are going well.

The BBQ yesterday was great. Good job Erica for pulling it all together at the end! And thank you George and Jason for your awesome grilling skills! Yummy

I'm really excited and looking forward to the Open House this weekend. It's going to be so much fun! Can't wait

(p.s.: stinks that we only have 2 more confluences scheduled.... )

First off: what a great BBQ. Hats off to Erica for taking the reins on this operation and to Jason for being an awesome Grill Master.

As for work, I've made a lot of progress this week. All the SolidWorks Simulations have been completed, and I now know the optimal plate thickness and material, while still being as light as possible. I spent this morning getting quotes from different metal vendors, and will place an order today or tomorrow. I never would have guessed that metal plate would be so expensive... Once I have received the materials, I will be ready to assemble and test the new submerged plate, and be able to calculate its new drag coefficient. On the side, I did some work on the high load power converters, which also failed last deployment.

Can't wait for the Open House this weekend. I'm brining my family and girlfriend. Should be fun!

First of all, thanks Audrey for the compliment on my observational skills. The Fulmar cruise on Tuesday was really amazing. Great weather, no sea-sickness, tons of whales, dolphins, clusters of jellies, and some mola mola. Everyone on the boat was really nice and very interesting.

On Wednesday, the intern BBQ was a huge success. Thanks to Erica for organizing it so well!

Thursday I volunteered for Young Women in Science which is an educational outreach program run by the Monterey Bay Aquarium. I got to hang out with some awesome girls, monitor sand crabs, and boogie board on a beautiful beach. It was great to see that a lot of the girls were really excited about being there. One told me "I LOOOVE THIS! THE OCEAN IS AWESOME!"

Project wise, its crunch time. Next week is (sadly) my last week, so I'm trying to wrap things up and start on my presentation which will be next Thursday at 9am. The time has really flown by! I'm looking forward to the open house tomorrow.

Seems like I'm not the only one who didn't update yesterday... phew!

Anyways, this hasn't been the best week to make tons of progress, since I was sick on Monday, and much of my time on Tuesday and Wednesday was occupied with preparing for the BBQ... which was fantastic, btw. Kudos to Erica for a great job spearheading the effort! I only wish I had made more rice so that there would be leftovers...

I have managed to make some decent progress this week, however. Since making the digital I/O expander chips functional last Friday, I've been busy writing various functions/routines to service them. I created a new source file entitled "expander.c", which handles all operations to the expanders. I wrote functions for initialization, device reset, clearing the GPIO registers, simple reads, simple writes, setting individual bits high or low without changing the other bits, and an initialization routine which sets the I/Os to their default state (high or low) at the beginning of the program. This is the "fun stuff" involved in embedded programming, when you can focus on developing the overall structure of the software instead of spending hours just trying to make the damn device work.

I've also begun coding for the next set of devices on the board that I want to program: the digital potentiometers. They are important to the board's operation, because their settings affect when the circuitry triggers certain conditions (over current, over voltage, under voltage) on the scientific instruments. So far, I've written a simple function that resets them. Next, I am going to focus on making simple writes (again, via the SPI bus) to set the potentiometer to it's desired settings. Overall, good stuff.

Now, I have lesser time to stay at MBARI than the time I spent here. Feel like I should speed up my work progress!!! But, things don't always go my way. I've trained my prediction model using EOFs generated from a historic HF Radar data. Then, from the model I generated predicted sea surface currents. Everything looked good by then. To verify the outputs of the model, I simulated some drifters and virtual moorings, but the errors seem too big (we have some error metrics for the simulations). I haven't figured out what went wrong. My guess is either 1) the data over the training period are bad, or 2) I made some mistakes in the code. Or, it is also a possibility that this result I have might be the best I can get from my data. Ugh... I'm stuck now. I'll try to figure this out, and hopefully it won't take long.

By the way, Happy 25th Anniversary, MBARI!

The BBQ was awesome and I enjoyed it a lot, preparing all the things for it and eating all the very good meal. This week has been special, cause tomorrow my family comes, and I have been preparing the house, getting the car, buying groceries... the sad part is that I will not be here for the Open House, but sure that I will enjoyed a lot the pictures and the stories that you explain me on Monday.
At the beginning of the week my project wasn't working good, cause I have to do some changes in the STOQS code and it's quite difficult for someone new on python. But on Wednesday I figured out the way to do it and now all it's ok. The next week my mentor come back to MBARI and I am really excited to show him my progress. Yesterday I sent to a national congress in Spain the work that I am doing here, it's a small congress but I hope that they accepted the abstract. Thanks to Anna for the english correction.
I am really jealous of the people who has gone to the sea, they have a nice weather and watch a lot of animals, and I only watched waves,waves and waves...
Enjoy a lot tomorrow on the Open House.

Yikes, busy week!  First I want to echo the previous statements, going to sea was a lot of fun, and the BBQ was really tasty, good job team!
Unfortunately the automation for my CFD studies didn't go as smoothly as I hoped.  Setting up the design study always takes longer than expected. I was able to get through a couple simulations of a preliminary blended body and finished up the CAD work on another wing morph design for the tandem profile. Unfortunately the CFD program crashed near the end of the simulation I ran over night so still no results on the tandem wing design.  I presented what I've worked on so far at Santa Clara with Bill Kirkwood to Dr. Kitts lab group. They all seemed pretty interested which made that fun.

See you all tomorrow at the open house!

Hi! Sorry for the late post! I must be the last one...

Can you even believe this is Week 6 of our Confluence entries?
Time is flying by at an ever-increasing rate!
Yikes!

...and what a week it was:

I was sad not to go out on the Fulmar, but my back has been so whacked, that I think it was a wise decision.
Maybe there'll be another chance? There is always hope!
I am so glad that you all had such a great cruise! Mola mola, too! Wow!!!

Welcome back, Geraldine! I read your Confluence entry, so I can say that the trip sounded really wonderful! Yay! I will have to go to the blog for more, and then perhaps, meet up with you soon!

Thanks to incredible team work and Erica's leadership, the Intern BBQ on Wednesday was a fantastic success!
The food was so amazing. Congratulations, everyone!

Wednesday was topped off with a great lecture given by Dr. Mary Silver. I adore her! She is such an inspiration, as are those of you who participated in the YWS program, to those younger women that you met.

I'm happy to say that my project was finally gaining some momentum last week, although I have not worked on it at all this week, with all of the Open House and BBQ preparations. I look forward to the project work next week, but need to figure out a time budget. I need to split blocks of time between the microscope and computer. Eventually I need to use ArcMap to illustrate the boundaries of a set of distinctive lava flows in the Gulf of California that were sampled on the 2012 cruise. I am starting to become nervous about running out of time!

We need to be creating a PowerPoint in the first week of August or so, right?
George and Linda: Are we going to have an Intern meeting that focuses on the presentation?
It is fine, if we don't...I am just curious!

So, Evelyn, you are to give her presentation next Thursday, and must leave in the days afterward?
I am so sad to see you go!
You rock!

I look forward to the Open House tomorrow!
The geology group is short-handed, so I will be in their tent all day. Drop by, if you have time!

Have fun, everybody!
It will be so great!!!

-Patti

Do I really get to Confluence last this week? Such a privilege! 

My week has been not as productive as I would have liked for my project.  I did have some really great intern experiences, helping with sampling and deployments on the Fulmar, trying on an immersion suit for the first time, and mentoring girls in sand crab monitoring and boogie boarding.  I thought Mary Silver's talk on Wednesday was really cool too.  The topics she covered are exactly why I think studying HABs is cool, because of the human and environmental health implications.  I enjoyed hearing the historical perspective she added, and hearing about her experiences in Zanzibar.

In terms of my project, I put together a blog post for the MBARI and MLML student blog, and put some work into the background and outline of my paper.  I have spent the times I've been in this week working with different LISST data sets on Jim's scripts, and I had a couple productive meetings with Jim in the latter half of this week.  He has some big project ideas to refocus my project to include LISST-HOLO image data, wherein I would make a time series of data about species (most likely class, possibly genus) abundances and distributions and compare that to the LISST-100X data from the Dorado mission(s).  It sounds like a really neat and ambitious idea, and I am looking forward to meeting with Sam's mentor Danelle on Monday or Tuesday to get a feel for how practical it would be to do.

Open House today!!