This week has mostly been learning to use various methods for data visualization. I learned how to use Ocean Data View, a free program, for constructing contour maps of the wave glider data (sea pCO2, pH, O2, temp, salinity). The program is really useful for making all sorts of oceanographic plots and has a lot of good data sorting functions as well. However, I don't think the program is very well documented, and I spent many hours clicking various things before getting what I wanted. Besides that, I have also been playing a lot with MATLAB this week and making various plots. Next week, I will be working a bit in the lab helping with the development of a dual pH and dissolved inorganic carbon analyzer.

In the past few days, I've started setting up, calibrating, and running the laser Raman spectrometer by myself, which is great! I've taken data and have used the analysis program that goes with the laser to interpret the spectra I've gotten, so I feel like I'm making some good progress. I also have a better idea of the overall goal of my project (both from reading background papers and talking with the people in my group) which makes the work much more interesting!

The data I'm collecting right now are on the dissolution of CO2 in seawater - I'm determining what the detection limits are for the laser (what concentrations of CO2 it can measure) and, depending on what I find, we'll decide whether or not to go forward with plans for a new instrument that will make these measurements for pore water in the deep ocean. From there, I'll be doing some experiments to compare our laser Raman in the lab and the laser used on cruises when taking data directly in the ocean to see how well they match up with each other. I still don't understand all the steps I'll be taking to process the results, but I'm sure that will come in time... things are coming into better focus every day.

With all the intern activities and general MBARI activities, it seems like there will always plenty to do around here! And plenty to eat! Sidenote: I really enjoyed the speaker and all his photos yesterday, I'm sure most of you did too...

Successful week!! My first week of MATLAB has been fruitful. I've been in the process of downloading quarterly satellite observations from the CoastWatch website one at a time. I created a 'for' loop to download a whole year with one run of the script and it worked the first time! Victory! Yesterday, I hit it a major project milestone by successfully exporting a GeoTiff from MATLAB and having it work in ArcGIS. I thought it was going to take me another few days to figure that out! Victory! MATLAB is clicking. Now I'm creating scripts to convert hundreds of MATLAB images into GeoTiff format. I'm making progress.

This week I have continued familiarizing myself with the existing hardware on the SWFOCE's electronics chassis. For the first time, I powered up the CPU and environmental boards, and attempted to communicate with them serially using my PC. This presented a number of problems to be solved. The CPU board wasn't communicating serially, and the environmental board did not appear to be getting power. It turned out that the power supply board on the chassis had not had a known circuitry error repaired yet. I swapped that board with one that had been repaired and verified to be working properly. This fixed the power issue (it turned out that the CPU board wasn't receiving all of it's needed power either). However, the CPU board still wasn't communicating serially. It was discovered in the schematic for the board that the serial lines needed to be jumpered together. This was done because of my mentor, Chad, who often makes the mistake of swapping the Tx and Rx lines with each other (haha!). The installation of jumper allows him to correct that mistake if it is made. After properly jumpering the Tx and Rx lines, the board was finally able to communicate and display output on the HyperTerminal window. Next, I played around with some of the user commands that the previous intern had programmed in to the CPU board. I made sure that the CPU board was able to detect the type and slot number of any of the daughter boards plugged into the backplane. I added a few printf statements so that it would read out when detected (previous code only printed if the slot was open). Next, I began the daunting task of starting coding for the load switcher. This is what I am still working on today. So far, I have mapped the digital I/Os – a good place to start.

ETA: Also, a few neat things happened this week unrelated to my project directly. We had a chance to fly the ROV around in the test tank, which was a ton of fun. Easy to do when looking from a above, but a lot harder when using just the monitors! Also, we witnessed the christening of the Rachel Carson, which is MBARI's newest research vessel. Afterwards, we joined the rest of MBARI staff at the reception for the board of directors, which had great food, great beer, and great company. I also attended my first MBARI barbecue... absolutely delicious!

This week has gone by just as fast as week one, but I still have Friday! My work on the PowerBuoy project continues to revolve around preparation for deployment next Tuesday. Mostly I have been mounting necessary equipment (resistor housing and an antenna) and removing old equipment (extra batteries). Of course on Tuesday I spent the whole day following the Board of Directors around and learning about the Gulf of California expedition and all the other projects going on at MBARI. And of course I got to see the christening of the Rachel Carson. On Wednesday I took a trip with Francois to the storage facility in Castroville to retrieve some "pop-up buoys," which may serve very well in the steel plate recovery system I have been assigned to create. I will begin working with them to understand how they work, or if they even work at all. As I understand it, they have been in storage for something like 14 years...

Highlights of the week: The Joe Allen seminar, which was absolutely amazing and inspiring and just awesome. And flying the miniROV, which was a real treat.

This week has been extremely productive in developing my project!
I've established most of the guidelines of the experiment process, as well as identifying and then changing (for the better) the organisms that I'm going to be using for observation. I've planned out to use (1) moving ROV videos of Holothurians, (2) stationary video o Nanomias, and (3) STIL-HOLO images of phytoplankton as my three mediums and subjects for comparison of accuracy, strength, weaknesses and many other variables in human and computer capabilities to identify organisms. I've also been looking up a lot of background on the species for later use and a general idea of aspects that may effect identification.
This is a whole new way of looking at things for me since I usually don't look at the programing aspect. I'm really enjoying being exposed to this new way of thinking because, in the long run, it's really going to help me understand what I need and what can be done if I ever do research that involves this kind of thing.
Tuesday was especially exciting with all the seminars and meeting members of the Board. I really enjoyed al of the talks that I sat in on and learned a good amount. Also prompted me to talk to a few people like Charlie Paul and Steve Haddock. Broadening my horizons at MBARI!
And tomorrow I get to go out on the Zephyr... which should definitely be interesting. Going to have to take a few of those motion sickness pills...

Next week - Intern Cookie Break Competition..... Who's going to win? We'll just have to wait and see

This week I have made progress by becoming more familiar with the AUV datasets available to me, and by better defining the objectives of my project.  I spent a lot of time last week learning about the various AUVs' histories, mechanical engineering, instrument features, and operation.  I have been working with both Dr Bellingham and Thomas on using the existing scripts to present and visualize the data from Dorado.  I will look forward to working with some of the LRAUV data as well.  I am hoping to work more with the Dorado data, as that vehicle collects more biological data than the LRAUVs (Daphne and Tethys), because it includes bioluminescence and has gulpers that collect water for laboratory analysis.  An advantage of LRAUV data in studying phytoplankton bloom dynamics is the battery life is much longer, so the LRAUVs can be sent back and forth across a front, and continue to collect oceanographic and nutrient data for almost a month (~26 days).  I spent this spring collecting water samples for stable isotope analysis of the particulate organic matter from the MLML seawater intake and from a day cruise aboard the R/V Point Sur.  I think that project and my background in biology are drawing me towards favoring Dorado data for my project and potential thesis research, though I have not explored the potential for using the gulper water samples to run isotopic analyses.  I think that combining isotopic analysis with oceanographic and meteorological data is a fascinating way to study bloom dynamics, but it is also very tedious and laboratory intensive.  It seems it will be more reasonable and enjoyable to focus on assessing the relationship between variables such as optical backscatter, fluorescence, bioluminescence, etc. in order to determine what combination of variables is associated with blooms of certain phytoplankton species.  I have also talked with Dr Bellingham about potentially working with Microsoft Research for my thesis research, and I am looking forward to exploring that idea in greater depth.

Other cool things I did this week:

Monday: Drove the flyer ROV (which I am calling "Simba" until it is otherwise named) in the Test Tank.  That was most excellent, many thanks to Dale and George for giving us that opportunity.

Tuesday: Learned a great deal about research in the different lab groups at MBARI, and got a good feel for what a long expedition aboard the Flyer involves.  I was impressed by how all the presentations were well put together and communicated, especially since a lot of the data is still being processed.  I enjoyed the R/V Rachel Carson christening and the fancy reception afterwards.  I think one of my favorite things about talking with board members is developing a broader understanding of the history of MBARI, and seeing how highly everyone regards David Packard.

 Wednesday: Deployed Daphne with Thomas and Dongsik, and after work went sailing in Monterey.  Their yacht club is pretty cool, and a bit bigger and fancier than the Elkhorn Slough Yacht Club here in Moss Landing.  Dr Joseph Allen's talk on Wednesday afternoon was really great, I especially enjoyed how he communicated the experience of becoming a satellite of Earth (the trip there and back, and both riding in Columbia and operating an astronaut's jet pack).  So unbelievably cool.  I sure miss watching launches and feeling the shuttle return.  I appreciate how much he supports and recognizes the need for BOTH manned space travel and studying marine science.  Both of those fields of exploration are near and dear to my heart, and I find it annoying when people insist upon putting those at odds (mostly related to arguing which is more deserving of funding).  Dismounting from soapbox...

 I'm looking forward to going out on the Zephyr tomorrow!  Hopefully it will be operational again soon.

This week has flown by! A successful amount of work has been done, and the previous days have also been very fun. We've been able to tour the Moss Landing Marine Labs library and drive an ROV in the test tank. Also, on Tuesday I attended a couple presentations for the board of directors about the current projects at MBARI which was very interesting. Later there was a reception with amazing food and really interesting people! On Wendnesday, I saw former astronaut Joe Allen give a very inspirational talk about his adventures into space (which is almost as awesome as the deep sea). Also, a group of high school students came in for a tour and some of the interns shared their science experiences to inspire them and give advice.

Work-wise, I've gone through a good number of hours of video and have just started looking at my first dive from the Davidson Seamount, so I expect to see some really interesting organisms. I'm hoping to use my annotations in kml form and create a visual representation of the dives on Google Earth soon.

As a side note, I'm hoping to get scuba certified during my summer here, so I can continue to explore the ocean!

Cannot believe it is already the end of the second week. I will not report on the wonderful side activities that we have done this week, just want to say that it was all fun and super interesting.
About my project, this week on Wednesday we had our first big meeting with all the persons involved in social media. I presented the document I have been working on since I arrived. So we discuss what metrics we might want to follow in order to have an idea of the health of our social media presence. Then we discussed the goals for each outlet and finally I presented all the strategies that I would like to try.
At the end of the meeting my to do list was very long and I am working on it now.

All for this week!

I've spent much of this week familiarizing myself with the facilities and my project.  I ran into a couple of kinks getting my terminal setup and appropriate software installed (I think that is mostly resolved now). My project has been firmed up with my advisor into doing a brief Tradespace study on the proposed Shearwater UAV/AUV project.  From there the plan is then to design, fabricate and test a component of critical interest. This will likely be something to do with the water to air and air to water transitions. Over the past week I have created a skeleton of the Tradespace study I need to complete. I've started filling in information on wing design and propulsion systems. Currently I'm trying to get approximate lift drag characteristics from blended body craft without running a simulation. I'm also working on finding efficiency conversions for air propulsion systems (specifically propeller profiles) in water and vice versa. I'm fairly certain previous tests have been done on this so for the mean time I've got more reading to do.

Again in confluency, and another week has pass. I have the STOQS database installed in my computer and working, and now I have started to upload AUV data collected during the experiment AUV2011 done in Spain the past year. In this experiment participated Mike MCcann and now I am trying to recover all the data, process it and upload to the database.
On Wednesday I went to the sea with Tim Pennington and during half of the travel I had sea sickness and I did a feeding show to the pacific's fish as in the Aquarium. But finally it was a great experience and I could help to Tim and Margarite with the job aboard. But..... I lost the BBQ & Joe Allen seminar, there are too many things to do in MBARI.

Continuing from the last week, I've been working on data visualization to see if the HF radar data I have can be used to apply Sergey's surface currents prediction algorithm. In his algorithm, we train the prediction model with the historic data, and this data quality analysis step is very important because we do not want to use bad quality data to train the model, which will result in bad predictions. Sometimes we have bad HF radar returns due to bad weather conditions, etc., which causes missing data, and in order to fill in this missing data, interpolation is often used. I have both the original data with gaps, or missing data, and the interpolated data. Sergey and I looked into the plots and movies of both original and interpolated data, and came up with an idea of what portion of the data we are going to use to train the model. Beside the data quality analysis, I started trying to get myself familiarized with Sergey's MATLAB code he used before. Also, he visited MBARI yesterday and gave me an instruction on what in his code needs to be changed for my data. I'll be running into a lot of problems and code errors while working on the code, but I am hoping that I can get something done with his code by next week.

Other than my project, I've experienced fabulous things I didn't expect: playing with the flyer ROV, christening of the R/V Rachel Carson, deployment of Tethys - a LRAUV, and boat sailing. Now, I can't imagine what would happen next week and can't wait! Below is a picture of me (taken by Diane Wyse, thanks! ) trying to catch Tethys, hoping it comes back into my arms...

I went out on the Zephyr this morning, but we hit a fishing rope and it got tangled in the propellors, so we had to limp home. I was back by 9am, so I didn't get to sleep on the boat to make up for getting ur early like I wanted to. I got a few pictures anyway, which I'll probably put up on the blog (you should all be making posts too! ).

This week has been more on the Quality Control stuff but Brian and I had a discussion (just now, actually!) about re-focusing to tidying up the web side of things so it can be pretty enough to make external soon! Then there will be all the testing of the page once it goes external (errors...errors everywhere I bet...). The web design side of things is more my strength than the database side anyway, so I will get more done if that's my focus and won't have to rely on Brian so much. I'm excited to finally be able to show my friends and family the DSG!

This week seems to have been a timed puzzle of getting lab work done and participating in the intern/MBARI activities! I am working more on my own now in the lab on the time-intensive part of individually picking out, filtering, taking pictures of, and freezing copepods for later analysis. I enjoyed the seminars I was able to attend between running back to finish experiments in the lab. The Paul Allen talk was a definite highlight, as well as driving the ROV...and I think by now, most of the interns have decided not to bring lunches when the board is in town! I'm looking forward to a full day of lab work on Friday. Hopefully, I'll be able to finish preparing copepods from culture 1 so I can start on a newer batch of copepods as a comparison.
Side note: the lights in the lab apparently turn off automatically, at least after 6pm or so! Not so good for transferring tiny critters on filters...

I'm sorry for the late post!

Week 2 of the internship was amazing!

The week has been a flurry of activity, and I must confess that my project is barely launched! I did finally have an opportunity to sit down and talk about my project goals and parameters this week, and that is a good thing.

The multitude of awesome non-project activities included, but were not limited to, the following:

• Monday we had our tour of the library at Moss Landing Marine Labs. Another beautiful marine facility! Afterward, we had the incredible opportunity to drive the MiniROV! I was super-paranoid about crashing it into the walls or floor of the tank, so I was timid with my movements! This was a really awesome, unexpected treat, for sure! Thanks Dale!

• Tuesday was a huge highlight of the week: the Day of Engineering, Science, and Technology. It was an incredible seminar that summarized much of MBARI's recent project work. The presentations and synopses were outstanding and inspiring! The day was complete when we were able to watch Julie Packard christen of the R/V Rachel Carson, and then feast wildly with all-MBARI in the atrium!

• On Wednesday, we were treated to a seminar by board member, Dr. Joe Allen, who gave an incredible presentation of his experiences in space! He was a funny, engaging speaker, and gave an inspiring talk! All of this...after the fantastic BBQ put on by the LRAUV team and the Czars! Yum! No shortage of great food opportunities here at MBARI! Thanks so much!

• On Thursday, while many of the interns were involved with CSUMB, I was in a Submarine Volcanism Lab meeting with Dr. Clague's crew, and visiting professors and graduate students from UCSC and the University of New Mexico. I was a, "fly-on-the-wall", for the meeting, but they gave me a full set of maps and spreadsheets so that I could follow along. I took notes, etc., while they discussed their major collaborative publication of data for the Endeavor Ridge study. The meeting lasted all day, and I learned a lot!

• Today, I learned how to process the plunge cores of sediment, and look for Foraminifera that may be sent to a lab for C-14 analysis. This information will help Dr. Clague's team determine the ages of the various volcanic flows of a given ridge system. The cores we processed today are from the Alarcon Ridge in the Gulf of California. These are the cores they collected only ~6 weeks ago via Western Flyer and ROV!
  

Everyone was so right about the time going by fast this summer! It certainly is! We must make the most of it!

We miss you George! We hope that you had a great vacation!

-Patricia Lieberg Clark