This week I finally finished watching thousands upon millions of videos about Tomopteridae eggcases and larvaceans that can be easily mistaken for the eggcases. The next process is choosing which videos produced the best framegrabs to transform into a presentation and constructing graphs using SIGMA plot to show distrubition in the water column. In addition to video footage and graphs, I have been researching papers and articles about polychaete worms and their reproductive mechanisms since so little is known about Tomopteridae worms.

Hopefully next week I'll do the DNA analysis test and also KAYAKING so my update will be more exciting.  

Webpage is up...that is exciting tho.  

I have 3 classes of animals: R, L and other. Other is any kind of event that cannot be placed in R or L: other animals, marine snow etc. We are trying to distinguish among these 3 classes. The new algorithm, using color, gave better results than the original version, which uses only grayscale information. However, we still have weird results: lot of R's are being considered as other. I am trying to figure out why this is happening. It has been difficult because I have a bunch of numbers in 8-D space and they don't have any physical significance. I'll probably spend next week debugging these errors, analyzing images and testing new parameters for the algorithms.

Hi everyone,

So ths week has been a bit of a dud work-wise! T-shirt design plus BBQ kept me pretty occupied. But the BBQ was fun (though I was definitely in recovery mode yesterday

Hopefully I'll manage to meet my deadline for this week in the 1 day I've managed to dedicate to my actual illustrations! Hoping to get 3 rough compositional sketches ready on the OMF to send to Kevin and Nancy. I must say this OMF piece is proving pretty hard to get going on. It's conceptually tricky and it's hard to see how I can improve on what they've got already in any meaningful way. Hey ho, hopefully working on the compositions will help me figure out which way to take things. It'll be nice to do some fun field-sketching this weekend though as a bit of a break from all the brain/design work!

Managed to update my webpage, and Nancy (my mentor) has been wonderful, helping me to get to grips with dreamweaver. She's editing my personal website for me so that hopefully I can see how she does web design and come away with a working online gallery etc.

Don't forget to order your t-shirt if you haven't already!

Cheers

Laura

As I mentioned in my last week status update, my plan for this week was to communicate with Keith Grochow and start integrating some stuff with Google Earth. I emailed Keith a couple of emails on Monday but I got the response just today, so my plan with COVE is gonna be taking most of my time next week. On Tuesday I wrote a couple of scripts to generate a surface plot of temperature data collected on July 1st AUV run. I got disappointed because the interpolated data in Matlab became very sparse in Google Earth (because of the actual physical separation)  and showed many ''bars''  here and there. I tried to interpolate the data to cover all the spaces but the size of the 'kml' file was too big that it crashed Google Earth many times. I changed my strategy and showed the data on a line trajectory and now it looks cool.  Yesterday I had lunch with my Mentor and all members of the Autonomy team. We discussed their next year plan and they enlightened me where my final work for the summer should be headed. It is gonna be tough to achieve that but I will do my best. More or less this is what I did last week...and oh ya did my part with cleaning in Wednesday's BBQ.

Next week, I will be working on the COVE using the approaches Keith suggested today. Also I will start working on extending the script that I have to include other sensor data and vehicle status.

Project update July 10, 2009, Roman Marin IV

This week was a very busy one. My shipment of sapphire orifices arrived Thursday, a little late but at least they got here. Most of my time this week was spent in the ME lab working on parts for the new orifices. The sapphire orifices are very small and as such are a little more difficult to work with than my steel orifices (but not too much thankfully.) In addition to working in the lab I have also been working with Solidworks, drawing up parts and creating assemblies. Now I have some really nice drawings to go with my physical models.  I also got some tips on how to put text up on my external web page (thank you Bryant.) I will hopefully be able to add more stuff to my page soon.

Overall, I would say this was another successful week. I am a little behind on my machining which will delay my sapphire testing a bit but not too much. My other main problem this week was with the website, it was hard (for me.) Next week should be another busy one, I hope to catch up my machining and add some more content to my webpage. I should also be able to get some more tests in towards the end of next week. I'm looking forward to Monday's trip to the slough and also catching up on some sleep this weekend.

At the beginning of this week I heard back from a few marine managers I contacted last week. I've scheduled 3 meetings to propose potential CeNCOOS data products for their projects. Now I'm thinking about how to prepare for those meetings, and make them productive despite my newness to the CeNCOOS system! Wednesday was largely shot for work b/c of the bbq, but it was really fun to hang out in the sun with all of you! Good work everyone! But, I did get some reading done on the West Coast Governor's Agreement on protecting our oceans (Washington, Cali and Oregon governors unite!) and some of what I learned from their Action Plan came up on Thursday at the SF Harbor Safety meeting that I attended in Richmond (the pertinent info was about new regulations for low sulfur fuel in near-shore shipping). After the Harbor Safety meeting I got to have lunch with a woman from NOAA NERR (National Estuarine Research Reserves) and talk about NERR's ocean obs needs in the SF Bay. Thursday evening, my mentor (Heather Kerkering) and I met with two men from Exploratorium Outdoor Exhibits program, and they showed us around their exhibits at Fort Mason. It was so awesome. They do beautiful, insightful work. CeNCOOS is going to help provide real-time ocean obs data for their new exhibits at Piers 15 and 17. I hope that I can help get that collaboration started this summer, however, the timeframe for the project might not line up well with my time at MBARI.

Next week I want to start to solidify what my project will be. I want to make sure I have a completed product by the end of the summer. All of the projects I've been working on are collaborations and my progress depends some on the needs and response times of other agencies. So I think I need to plan carefully to make sure I can get something done in time!

How could I forget the BBQ? I couldn't, it was the best. Thanks to everyone who made it happen. I cannot even begin to express how much I appreciate being given the opportunity to BBQ all day, so fun.

The BBQ was awesome.

The rest of the week consisted of configuring the PC-104 Arm processor with Debian Linux. After compiling the MOOS code (SIAM) and transferring it to the board I found an error with the current Java Virtual Machine (JVM) installed. I'm hoping to rectify that error today but if not it leads to a very important question that the MOOS team has been discussing; does the Linux kernel need to be upgraded?

If the kernel does indeed need upgrading this solves the problem of finding another compatible JVM, as Sun Microsystems provides an ARM based JVM with a much higher compliance than what is currently on MOOS hardware. It's exciting for me because what I discover has a high possibility of changing the development path for MOOS software and hardware, which gives my work more of an impact that originally thought.

Also, GLERL (NOAA) has finally sent me a Ysi-6600 - a CTD with far more sensing parameters than the Ysi-600 currently connected to my system. I'm happy with my Ysi driver code so far and hope to add more robust control methods soon. The driver is usable now; just far from complete.

Next week will consist of more development on the PC-104 board. I've never compiled a kernel from source before so this should be a learning experience. I'll also [hopefully] edit my webpage...

On a side note, I met someone in the AUV lab who went to my alma mater (Hope College, MI). It's a small private liberal arts school so I was definitely geeked to meet another EE/CS guy, especially after finding similar ties with people and local microbreweries. Go Dutchmen!

What a great week!  It was productive both socially (BBQ) and "professionally".  After three weeks of being distracted from my project by the NMEA conference and the EARTH workshop, I am finally settling into a nice pace. Tuesday, was awesome and scary all at the same time - I was asked to speak for half an hour each to two student groups in the Pacific Forum.  I warned Todd not to laugh at anything I said since I really didn't feel like I had enough authority to speak about MBARI.  It went great though and of course, working with kids is what I do, so I felt right at home!  Yesterday was spent at the Monterey Bay Aquarium discussing the high school lesson our team is creating on the topic of ocean acidification.  There have been some areas that have needed clarification - we sat down and chatted with our resident chemist who discussed the carbonate buffering system with us and put us through a test of sorts. This project is a bit of a challenge - just how does one even begin to talk about ocean acidification in a 45 minute time period that has a 1/2 hour live animal component, and must cover California high school science standards!!  We have run into a snag with a video piece we are hoping to have by September. We had asked Sea Studios for permission to use clips from "One Degree Factor" but alas, they are not their own clips.  We are thrilled that Laura Volsett, illustrator extraordinaire has agreed to make clips for us - phew!!   I contacted Todd in AV who has agreed to work with me to find video and photos of scientists at work for this class and finally, I have gotten in touch with Dr. Jim Barry who has also agreed to chat with me next week to go over the lesson description we have created and to give us some advice on what to place on a table we've named "Future Oceans"?   No...microbes won't do!  Great week!  Have a fabulous weekend folks, it was fun working with such a stellar group of BBQers!

Completed AUV 2010 engineering project report . Worked on Oxygen sensor evaluations this week. Got cables and software together on Monday. Went out on Pt Lobos on Tuesday. 3 oxygen sensors on Ventana ROV. Took water samples  at multiple depths and processed with reagents. Watched Benthic Rover deployment to MARS. Very exciting. Nice day on the bay. Processed data the rest of the week.

More Oxygen Sensor data processing next week. Also need to complete winkler tritrations on water samples taken. Did not get to meet with my mentor this week. Hope to meet with him on Wed of next week.

I'm just going to echo everyone and say that the BBQ was great!  All my CeNCOOS co-workers absolutely loved it.  So cheers to everyone for organizing, cooking, and to the random dude who finally locked the upstairs fridge!

This week got a little busier.  I finally finished writing emails to all my contacts; however, no one has really written me back yet --except for one middle school teacher all the way out in North Carolina.  It would be great to get in touch with some educators here in California, especially since I'm trying to create an educational HAB website specifically for the central/ northern region. 

Steve (my mentor) is trying to get a hold of his daughter's middle school teacher, but that's still proving to be difficult.  I guess it is summertime so it's challenging to reach people, especially teachers.  If any of you know middle school teachers in the area that wouldn't mind emailing or chatting with me on the phone real briefly, please let me know!  I need to get a better idea of what type of HAB information middle school teachers would find most appealing and beneficial to their students.  It also would be good to get a general sense of what level/ language should be used to present the material.

Anyway, the rest of the week was spent investigating real-time data websites (specifically those that showed chlorophyll a concentrations and SST).  CeNCOOS's web-tech guy, Fred, showed me this awesome graph on ERDDAP today, and he is currently helping me to develop a graph that superimposes chlorophyll a concentrations onto SST images.  So, that will be great because it's real-time data and a sweet tool educators can use in their classrooms.  The ultimate goal of this project is to provide all this HAB information on one site and make it accessible AND understandable to both the general public and students. 

So the project is finally shaping up and I'm glad to at least have a focus.  My current limiting reagent is the teachers' responses, but hopefully they'll get back to me next week.  So I'll work on filtering through more websites, interpreting/ translating scientific jargon, and hunting down some enthusiastic educators.  

Oh, and I'm super excited for Monday's kayaking trip. YEAH!

This week I was very productive. I worked hard on integrating the remote control hardware into the control software I was already building. As of right now the throttle control should work remotely for the boat. I'm finishing the software for the rudder, though I'm running into a couple of problems there, but it should be sorted before the kayak trip!

I've been talking with John Ryan and the harbormaster in finding a place to test the boat. For the initial test, now that the Western Flier is gone, its dock should be enough area for us to keep the boat on a leash and remotely drive it around. We're planning on a Tuesday test. This should be enough time for me to finish the software and that means my adviser from UCSC can come and watch.

I got some more parts besides the remote control: I spent a while making some connectors and picked up a motor driver board for the ballast motor. This means that we should be able to remotely control all the boat's actuators with this remote control without ordering more hardware.

I've also started recording all observations about the boat state as I'm working at it online in a wiki to keep track of things. Many things aren't documented and when I figure them out it needs to be written down somewhere so that's never a problem again.

I've also been trying to get my desktop computer here running all the software I need for it to work. It's a slow process as everything I want to do doesn't seem to work, which is definitely a theme with me...

I also spent ~3 hours in the sun grilling on Wednesday, which seemed to be an amazing success (even though the BBQ chicken took a little longer). Unfortunately, though, I'm pretty burned from that day as I didn't realize I was in the sun the whole time until the very end!

Next week I'm planning to have the boat under remote control and perform our first live test. I would like to integrate the motor driver board into the system also and add the ballast motor to be under my control. So after next week we should be starting on the autonomous part of the project!

I also need to do some more mapping of the systems on the boat and some of the finer details: how much current do the PV panels produce and at what voltage? Is there a solar charge controller onboard? Do the PV panels work? What is the max current we can push the propeller at? What is the motor used for driving the rudder? What's the gear ratio for the rudder? How does the bilge pump work?

This week I've mostly been troubleshooting PCRs on the MFB. I've had to replace some reagents and am running a few PCRs over the weekend to see if it all worked. I've also run a few PCRs with our primer sets (primers that allow us to replicate DNA of certain bacteria) to see if they cross-react with bacteria that are readily found in the environment. The results showed a lot of cross-reactions with one primer set, so we might have to make new primers or use other published ones if we want to use them as indicators of water contamination in the field.

Next week I'll be able to run DNA extraction and PCRs with environmental samples if the MFB works over the weekend. Yay!

This week was like testing my patience. I had been waiting to work with my mentor on my project, and by the time he came to my office, my computer was crashed. One of the suspected reasons for the crash was virus. Mr. Bill, from IS department, took my hard drive for virus scan. If the virus scan results true, I had to be prepared to lose all my data and setup(which took me 2 days to install). By the end of the day he came up with one good news that the s/w he was using didn't detect any virus. Thereby, the next suspect was the hardware, so they replaced my processor. The next obvious idea was to recover the data from the hard drive of previous processor. Here comes the worst part, the drive didn't respond. So finally I had to reinstall all my s/w; however, since I already did this work before it took me only one day .  

Finally, I got chance to work with Kevin on Thursday. He went through the project structure, which took 3hrs and asked me to work through the simple object messaging using NMR(Normalized Message Router). Even though the concept looked simple when demonstrated, it is taking time to embed my code to the existing project. Sometimes my brain crashes with all the unsynchronized threads running inside.

Barbeque was awesome!! Thanks for each and every one in the team for active participation.

Note: Many computers are very old. From my experience, I suggest all the interns to save their files in their respective Temp boxes (check for your temp box in Mycomputer).

I'd have to say that this past week was pretty busy and slightly stressful.  My main task was to re-run the PCR of my environmental samples using my "mystery bug" primers.  I really had to get it just right since the environmental samples that I'm working with are extremely precious.  After running several unpromising gels, my mentor and I decided that, because there were so many bands in my gels, I needed to excise the bands and run a gel purification.  The DNA extraction protocol was pretty tedious, and I didn't even get any product from two of my samples.  Not good.  Luckily, one sample did work out rather nicely so the PCR product has been ligated for transformation into E. coli cells to create a clone library.

On a positive note, I got the chance to sit down and talk more with my mentor about my project.  I'm really enjoying working with her since she's incredibly smart and really cool.  Although some of the phylogeny and ecology stuff may go a little over my head, I'm proud of myself for understanding the majority of the genetics-related stuff that we talk about.  (I knew I wasn't much of an ecology person coming into this program, but c'est la vie and I'll have to get over it.)

I really enjoyed helping with all the preparations for the BBQ.  I especially liked telling the check out guy at Costco that we were buying 60 pounds of chicken just because I was really hungry.  I'm sorry I couldn't help out more the day-of, but an intern's gotta do what an intern's gotta do.

This coming week, I think I'm most excited for kayaking.  Even though I have no upper body strength whatsoever, it will be a great chance to take a break and hang out with everyone, as well as do a little exploring.  For work, I found a couple more articles that I want to make my way through to help me write a better introduction to my paper.  I will continue to use programs such as BioEdit and ClustalW to align sequences on the computer to design primers for a quantitative-PCR that I will be running in the near future.

For two days this week I was set to another project.  My lab group's proposal for next year needed some supporting evidence so I was set to try to show which, if any, of the historical CTD stations were redundant (to stop visiting them and reduce costs).  We had a lab group meeting, and my advisor was not convinced by my arguments.  Oh well.

Obtained six hour upwelling data for the past few decades and incorporated them into my data set. 

Began principal component analysis (haven't really done this before) of the nutrients in the data set and think I have come to some useful simplifications.  I'll be meeting with advisor #1 next week to discuss progress. 

This week I experienced what its like to truly be a scientist--four weeks of lab work down the drain! The vector I've been using doesnt seem to be adequately taking up my gene. The colonies that I suspected were glowing were probably not. When I did a protein purification, the elute didn't glow at all, although it seemed as if the sample that was originally applied to the column did glow. This made me think that the protein wasn't properly sticking to the beads, however, after doing a negative control protien prep, I saw that the applied sample was glowing just as much as my protein sample, leading me to conclude that the fluroescence was due to cell debris that remained in the sample. SO after many failed attempts to express and purify the fluorescent protein, and much brainstorming with my labmates, I decided to use another vector system completely, which means starting from square one. But hey, thats what science is all about!

This week started with a day of acting as "fly on the wall" in a meeting of Monterey Bay Aquarium managers and MBARI staff who went over next year's proposals - as always, my exposure to such meetings is a great way for me to learn the ins and outs of the relationship between the two institutions.  There are great ideas for next year!   Our ever important intern meeting took place on Slough waters in kayaks - who doesn't enjoy that!? We had some encounters with sea nettles which were just gorgeous in the water and of course, plenty of marine mammals.  I am trucking along, making progress in the creation of the aquarium's new high school lab called "Carbonated Seas: an Investigation of Ocean Acidification".  I met with Dr. Jim Barry and handed him our program "packet" in the hopes that he will offer some valuable feedback - next week I meet with him for a longer period of time to get the scoop on ocean acidification research at MBARI (I hope I can find mini tapes for my recorder!).  My program script is almost complete - I found that it took me longer than I planned because there are a few areas of this topic that I am unsure of, so of course, I had research papers and text books strewn across George's desk (he was out!) which I had to stop and refer to.    I had a very exciting meeting with Todd Walsh who will work with me to create a movie for the introduction of the lab!  What an incredible resource he is!  I am spending Thursday and Friday at the aquarium with a fellow educator who is also working on the ocean acidification lab.  It's always good to see my colleagues  and of course my animals!