It's hard to believe we are nearly through Week 4.  My project is progressing, and after meeting with Jim and Yanwu last Thursday to discuss various optical devices for better understanding bloom dynamics, we came up with a team strategy for a larger project.  I feel better about how my work fits into the bigger picture now.  We had a productive meeting with Dorota on Monday, and I am looking forward to working with her on sleuthing out how to re-process the LISST data so that I can identify which combination of LISST channels can be used as a surrogate for chlorophyll fluorescence data, and how those combinations vary spatially in the bay.  I haven't spent as much time as I would have liked this week working with the Matlab scripts, but that is my plan for today and tomorrow.

My mentors were gone last week, and this week has been relatively quiet as well. I've spent a lot of time playing around with visualizing data with various methods (Matlab or Ocean Data View). Previously, I had generated some plots on Ocean Data View , and I wanted to try to recreate them in Matlab, which proved to be somewhat difficult but possible with a free mapping toolbox called m_map (which Dongsik told me about). It took me a weekend to learn how to use m_map, but I find it quite useful now. However, I went back to Ocean Data View for generating my plots, because the Matlab gridding functions (griddata and TriScatteredInterp) do not produce very smooth results compared to the DIVA gridding algorithm in Ocean Data View. Francisco pointed me to a gridding function available online that may help me, but I haven't experimented with that yet. If anyone knows of good Matlab gridding functions, do tell me. 

I have made surface plots of temperature, salinity, oxygen, pH, and sea pCO2 (collected by the wave glider), but this week, I merged wind data from the wave glider meteorological station as well as the M1 mooring station into my dataset and used these two different wind data products to calculate CO2 flux. The two wind data products give slightly different results. Part of this variation may be due to the height at which wind speed is measured--10 m above the surface in the M1 station (standard) and 1 m in the wave glider. I will need to look into the literature to see if I can standardize the wave glider wind speeds to the 10 m measurements.

 Late last week, Francisco expressed interest in collaborating with me on my project. Francisco had the exciting idea of comparing outputs from the ROMS-Cosine model to the observations collected by the wave glider. We talked about this Gernot, one of my mentors, and he thought it was an excellent idea. I hope this can move forward, as I would love to learn more about ocean models.

It was hard this week with Brian on vacation and having to delve into a whole new area - testing and monitoring memory use. I've been doing a lot of code clean up/annotating to prep the project to be made external. I've also been looking into how to do testing for the database connections and using Java VisualVM to observe what's using memory and how much memory the DSG as a whole uses over time. The purpose of all this is to find the "memory leak," which basically means the connection to the database isn't closing somewhere, so it causes the server to hang because it takes up too much memory. This has to be fixed before the DSG will work externally, but there are a lot of database methods and I'm not entirely sure what I'm looking for without Brian to explain things!

Well this week I completed the conversions of SST and chlorophyll into ARC GRID formats, which my mentor and I are very pleased about. Now I am on to the bear of HF radar. These data are in hourly observations of the u (east/west) and v (north/south) components of current. My first task is to create a Matlab code to implement a 3-day moving average over the observations and aggregate the 8784 hourly observations into 365 daily observations (of which are 3 day averages). So if anyone has a moving average code I can take a look at, I'd be very appreciative.

Here I am!!! The week of the 4 of July. I was very excited about it, and I enjoyed it a lot. Morning parade and BBQ & Firewoeks during the night.
I have written the code to make a query to the STOQS database from Matlab and get all the information of a database from Matlab too. Now, the next step its to move to the model output side, and try to combine both. During a talk with my mentor two weeks ago, I expressed him the wish to join my project with another intern project. In this way both project could be improve. He said that it was a good idea, so I talked with Michael, who like the idea too. This week I have had a meeting with Michael and his mentor, and he likes the idea too. So I hope that we will have a happy end. Michael and me are very excited about it.

Rough week for me so far.

Chad and I have spent most of the week trying to resolve the issues that I detailed in my last entry. We did a thorough inspection of the hardware with the oscilloscope and did find a few problems. One problem was what must have been a faulty logic gate; the chip select signal coming from the CPU board was inverted. Also, the buffer gate appeared to be malfunctioning. So, we bypassed the gate and found another work around to invert the chip select line. A new logic gate has been ordered. However, these hardware fixes did not resolve the communication issue – although they were a step in the right direction. At least the CPU can now recognize the other boards on the backplane even when the LVLS board is plugged in now. We started doing a more thorough inspection of my code and the signals on the SPI bus, which revealed a couple more problems, such as an error in the way I initialized the remappable pins. However, there remain more issues to resolve, because even though the oscilloscope shows bus traffic, the CPU still isn't able to communicate with the LVLS board. I'm starting to wonder if perhaps the PIC is bad, so as we speak, my mentor is replacing it with a new one. Worth a shot... fingers crossed.

Update: Replaced the PIC, didn't make a difference. Looking pretty hopeless without the help of a more experienced embedded programmer. Perhaps the one guy here experienced with PICs (Mike?) will be less busy in the coming weeks so he can help me. So, I've decided upon a new strategy: give up on the backplane communications for now, and focus purely on getting the peripherals on the LVLS board communicating with the controller. Instead of using the CPU as a debugging terminal, I can use the LVLS' own RS-232 port to communicate directly with my PC for debugging. That way, I can get every other component on the board working, before I decide to take a look at the backplane comm issues again.

Jason I have a 25-hr low-pass filter code you could take a look at if you're interested.  If you come across a 3-day moving average code, please do pass it along.  Have you tried Mathworks?

It has been a bit challenging this week to figure out all my lab procedures. I finished working with the new culture and am now adding background seawater samples collected last Friday to copepods in culture. There are many directions my project could go, so I'll have to narrow it down a bit.

This week, I met with one of my mentor's collaborators. He is working on predicting biological phenomena from AUV data to work towards an adaptive sampling plan. We also had our first lab meeting since I have been here, and it was great to talk to the others in the Vrijenhoek lab.

 I will be doing computer work while my mentor is away the rest of this week, and deciding what questions I'll have to ask him when he's back!

Sorry for the lateness, the holiday threw me off a bit - I got back from LA last night, it was a great little vacation but a long drive for just a few days.

Anyway, there's somewhat less to report about this past week than there has been for the others (three-day weekends and Fourth of Julys tend to get in the way of productivity), but I did manage to get some work done. I've been running a set of experiments to compare the sensitivities of the two laser Raman systems that my group uses - one that's permanently on the lab bench and another sea-going one. The idea is to figure out if the results we get in lab can be easily translated to predict what we'll find in the deep ocean and how accurate the two measurements are. Peter Walz and I wrapped up these experiments on Tuesday morning and I spent the rest of the day analyzing the data - it seems as though the sea-going system is significantly more sensitive than the benchtop one... good news.Today will be a bit of a catch-up day - I have a bit more analysis to do and there's always more to read, of course

 On another note, I took Geraldine's advice and downloaded Mendeley - I'm finding it to be a good tool and very easy to use so far, would recommend it to anyone who's curious.

Hello all! Sorry I'm a bit late...

This week has been interesting for me. It started out pretty well with my plankton identifications and was flowing smoothly but as the week went on, the project's end goal started to confuse me and interfered with where I could go from there. Needless to say, it all got figured out and everything's back on track. We ironed out the kinks and Danelle steered me back in the right direction So, now I have a better idea of the final direction of my project and more data to run through.
We've changed things up a little bit as well. We're actually going to be running 2 types of tests because the mediums are so different. So the LISST-HOLO images are going to be a self consistency test (more on that later, while the other two (holothurians and nanomias) are still going to be human vs. machine.

The 4th was fun, went to a fair and almost got sick on a few rides and rode a mechanical bull. Always fun!

This week I finished my project! The Pop-up Buoys have been altered to accommodate longer and thicker rope and are ready for the next deployment. Unfortunately, that won't be for a while, definitely not while I am still here. So for now they go into storage, and I begin my new project: increasing the drag coefficient of the submerged steel plate. This is require first some analysis of the motion of the Buoy (data taken from an onboard IMU)and the piston positioning (measured by a string pot). Analyzing the two motions coincidentally, I can find the difference and attribute it to plate movement (which is ideally zero). If the data analysis warrants plate modifications, I will first model them in Solidworks, calculate weight and buoyancy, and then apply structural analysis using Solidworks Simulation. Next will be materials ordering, building, and installation. Once the modification are complete, we can preform a drag test on the new plate in the test tank, and calculate its new drag coefficient.

Ok I guess I am the last one, sorry about that!
So this week, of course 4th of July and very interesting to see how many fireworks you can have in a city with huge signs with "NO FIREWORKS" and cops everywhere... Family here, enjoying every second of the Californian life style.

So but there was also work this week. First was the great news about me spending a week on the Western Flyer, I am sooo looking forward to it. Just hope I am not gonna spend my week vomiting I will let you know Never been on a cruise before so any advice is appreciated and Brandon already offered to help me. Thanks for that!

So now social media business: Have been working on FB and Twiter mainly. Interesting since the way to use those SM are completely different: twitter you need to tweet often during the day while on FB you need one good post a day.
The social media application hoot suite is finally becoming useful and saving us time to be more present on Twitter.
On Fb, I thing I start to see what works and what doesn't. I need to design a testing schedule to test my hypothesis. We have had some success with popular post reaching a fair amount of people and triggering engagement from the fans.
I also analyze the data from the survey I sent to the FB fans and it is interesting to see that they are as much interested in the MBARI science (new special, cool video) as they are about what is happening behind the scene here.

I also worked on the MBARI history that will be displayed on FB after the Open house.

All for this week... We are finishing week 5 (right?) this is soooo scary. In this place, time is acting weirdly... flying away faster than anywhere else...

Geraldine, we are finishing week 4.

Ok. Let's see who gets the last Confluence post between me,Justin, and Patti. :-p Sorry for the late post, by the way.

With a long weekend and a holiday in the middle of the week, my work progress is a bit disappointing, but is still slowly moving forward. With my HF Radar data for the ocean off the Georgia coast, I successfully generated empirical orthogonal functions (EOFs) out of the dataset and made plots to analyze. Today, my mentor said the plots look good and we are ready to move on......But, wait...I spent the whole week trying to generate those plots, but don't even understand what those plots mean/represent!!! So, this weekend I'm planning on spending some time looking into his code that generates all the plots as well as the process of how the EOFs are generated. Next week, I'll try to train a prediction model using the EOFs obtained out of the dataset and see how it comes out. Hope next week would be more productive.

Short week but I actually made some headway!
From the preliminary look at control systems, power requirements, and scientific instruments it looks like the primary technology driver for this project is the aero/hydrodynamic structure. Currently I'm trying to figure out a quantitative way to compare a tandem wing design and a reverse delta wing design. Over the past week I've worked mostly on getting a better handle on airfoil/hydrofoil design.  I've started learning XFLR5 (a 3D derivative of MIT's 2D XFOIL software).  Unfortunately the software dramatically limits the types of body shapes possible. However it seems to be effective in generating a ranking order between design efficiencies. To get a better Idea for more complex shapes I've also briefly looked at Autodesk's CFD package but it seems like it will be a little more tricky to set up for meaningful results from external flows. From what I've read so far it seems like getting truly accurate CFD values in the ground effect zone will not be possible. This means the propulsion system shouldn't be sized purely off these values. By the end of next week I hope to have finished the comparison between the aero and hydro dynamic efficiencies of the two air foil options and selected one so that we can begin physical validation of the lift and drag values.

It was a shorter week this week, but I still finished going through a good amount of dives. Some of the dives did not have complete annotations, so it took longer to go through the complete dive in real time. Also, a Davidson Seamount dive had a genus of primnoidae I had never seen before which was very interesting! I'm excited to have my mentor return (as he was on vacation) and work with him to figure out how to best organize and bin all the data that has been collected so far. As a side note, I look forward to moving in with the rest of the awesome interns this week!

Patty, where are you?
if anyone is interested.. You can follow along at our teacher workshop at http://www.mbari.org/earth/2012/schedule12.htm we update the webpage frequently during the day with photos, lectures, etc...
hoping that I don't melt out there.
George

Oh no! I am very sorry for my very late post...
I vow NOT to be the late this week! (:>)===<

It sounds like we all had a wonderful, but intense week with out projects!
I can't believe it was Week 4!
Time is going by soooo quickly!
I am realizing that I need to create a timeline, to make sure that all three components of my project are complete in time. It feels like time is already getting short, with the Open House, BBQ and all....

I feel as if the work on my project really kicked into gear this week...
I started digging into additional conceptual details pertaining to the textures of volcanic rocks, and did a bit more reading this week. There is an entire language dedicated to such things. I expected this, but it still caught me off guard! New vocabulary! Fantastic! Looking at rock samples through the microscope is just one component of my project, but I find myself immersed.

On Wednesday and Thursday, I switched tracks and started helping the lab prepare for the Open House. We are creating a video loop of recent research for the geology tent. I spent some time in the video lab, in order to select cool clips from the Log of the ROV Ed Ricketts during the study of the Alarcon Rise on the 2012 Expedition to the Gulf of California. It was so great to see the seafloor! There is so much going on down there!

That is it for now.
All of you are such incredible scientists/engineers!
I am so inspired by you!
Have a GREAT week!!!

-Patti