Hi All,

This week has seen quite a few kinks ironed out in terms of my OMF piece, which I'm hoping to have designed this weekend and have a color swatch to show Nancy by Monday. I'm also working on the piece for the aquarium and it's been great to discuss ideas and storyboard stuff with Alena. The OMZ piece is on hold while I wait for the Midwater team to get back from theri trip on the Flyer.

It's been really interesting and useful to answer questions about the process of illustrating posed to me by non-illustrators. It's really made me think about the way I work and what I do in a different way. Really loking forward to scuba class. Just have to make time to read the book!

Have a great weekend everyone!

p.s I have lost "the brick" (my cell phone) It looks pretty ancient and is large and silver. If anyone happens upon it would you let me know?

Thanks!

It was really great to meet Marcia. I appreciated the time she took to sit and chat with us; she's super cool.

After running around in circles this week and avoiding a near disaster (data loss) I've finally got a Java Virtual Machine up and running on my little ARM computer. SIAM is also up and running, albeit slowly, smoothly so far. Still need to talk with Tom and finalize what I need to do for the rest of my time here.

Next week will be lots of documentation, finshing the Ysi driver, and hopefully starting on my paper / presentation. That and the Point Lobos cruise next Wednesday!

I thought that using the YUV color space would be better than using RGB, because in the YUV luminance and chrominance are already separated. Feature extraction would be done in more meaningful images. But it turned out that RGB images can give better results. Why????

I am almost done with the presentation and wrote a little bit of the report.

It was cool to learn some secrets of Marcia's success: "I always think I am in the best possible job", "I am accepting this job because it's not possible to perform worse than my predecessor" (strong modesty, but it makes sense). Interesting opinion about some past intern who finished his project in the first 3 days: "He didn't learn as much as his colleagues because he didn't experiment the trial and error phase". I had a similar "problem": I got very good results in my first attempt (not in 3 days but in the first weeks), but I don't understand exactly why it worked. Now I am trying to explain the results.

 Have a nice long weekend everybody!!

This week I learned how to run a PAGE gel to analyze proteins. This was to see if I was even getting any protein from my protein preps, which i was. However, there is apparently no protein with the tyrosine in the chromophore. So, we ordered primers that would amplify just the tyrosine chromophore and I did PCR with those. After analyzing the gel, it turns out that the tyrosine chromophore FP is indeed present in the cDNA I'm using, which is exciting! Now I just need to figure out how to selectively amplify the tyrosine version, not the cysteine version. I tried a few different combinations of primers for PCR, but I dont think I amplified the tyr FP. I also learned a new cloning technique. I cloned part of the FP gene (from the start of the tyr chromophore to the stop codon; the 3' end sequence of this FP gene is not certain yet) into a vector which was then transformed into competent cells, which I can use for sequencing next week. Hopefully the sequence will illuminate the 3' end of the tyr FP. This would allow us to make more specific primers to select for that end as opposed to the 3' end of the cys FP. Its all getting a little confusing, but I'm doing my best to figure this little mystery out! I also really enjoyed the meeting with Marcia this week. I agree with Marco; I think Marcia's comment about always thinking she has the best job possible is a good way to look at life hope everyone has a wonderful weekend!

I also enjoyed Marcia's comments. I appreciate the fact that she took the time to meet with us.

 I volunteered to help the Young Women in Science group on Tuesday. The Monterey bay aqurium sponsors the camp and they do a good job. The young women are 10-12 years old and some students speak spainish so everything that is said is translated into to both spanish and english. Throughout the data we worked on projects that were both educational and fun. As we made observations, the students recorded everything in thier lab books and learned to graph and analyze the data. I enjoyed the students enthusiasim. Sailing on the bay is always fun too.  I think I will volunteer next year.

I found out this week that I will not be able to work on the ESP project. I am a bit disappointed but not surprised since we only have a few more weeks left and everyone is busy with project proposals till next week and then the ESP project manager goes on vacation. The good news is that my mentor says that I may be able to work on the ESP project after the intership is over. I am taking a genetics class in the fall so working with the ESP group as I am taking that class could be good timing.

 I have been talking with many people with experience with oxygen sensors and getting input on calibration methods,data post processing,  accuracy, biofouling prevention and instrument handling issues. It is extremely helpful to get input from people with years of experience in this area. I am also finding that the people I talk to are interested in what I have found out so far.

I am planning on doing another response time oxygen sensor test. Last time I did a test in the bay with the Ventana on Pt Lobos. This time I am going to do a more controlled experiment in the lab. I have been getting input from different people at MBARI, ACT( alliance for costal technologies) and O2 instrument manufacturers on how to do a good response time test. I hope to complete the test the week after next.

Next week I am going to go out on the Point Lobos with John Ryan. I am very excited because John knows a lot about remote sensing. He gave me a book on the subject a few weeks ago which I have been reading. I have lots of questions for him on the subject. Spending time with him will give me an opportunity to follow up and ask him questions. He has also asked me to help him get ready the day before so it should be a good opportunity to learn from him.  I also found out that Mary Silver will be on the boat with us! I am very excited about that because several people have told me I must meet her someday and next week I will !

I am also looking foreward to the tour at the monterey aquarium on Tuesday. Have a good weekend.

COOL... Taryn should meet Mary as well. Mary knows HABs.....

My plans for this week were big, unfortunately I could not get even a quarter of it done. My mentor had asked for a memory upgrade for the Laptop I was using as it was necessary for the visualizations softwares I was using. But since my computer could not be upgraded the IS gave me a new Mac on loan. That meant copying all my files and making necessary SW installations on the new Mac. To make matters worse, as I was trying to give a higher security clearance to an Applet I was writing, I made a mistake and modified system file security privileges. Because of this my OS was not running properly and I had to take it to the IS help desk and get it fixed. The work I did this week is pretty much on Wednesday afternoon and today. I managed to embed an applet in a browser that interacts with Google Earth's plug in. I also developed a dummy mini server application to simulate and stream the AUV's position. With these components my visualiser works well. My plan to get a low level understanding of TREX and put a component in there that would publish its internal status has become my high priority activity for next week.

I don't want to conclude my status update without appretiating Marcia for taking time to talk to us. I have found her talk to be very inspiring and motivating.

This week didn't quite go as planned but it worked out anyway. I was hoping to get my new prototypes in this week and begin testing, that didn't happen. The wheels shipped on Thursday so they should be here next week. There was an issue with one of my orifices though so I probably wouldn't have gotten to the new wheels this week even if they had arrived on time. I have been working more on my paper this week, writing the discussion and introduction. Unfortunately three are some issues that will most likely still be unresolved by the time I finish my paper for the 20^th. At least that gives me more things to talk about in the discussion. These issues can and will be resolved just not before the paper deadline. Hopefully I will be able to submit a revised paper when these problems are solved.

As usual there was also quite a bit of orifice testing last week. What was unusual though was that some of my data seemed to be backwards. My sapphire/ruby orifices were supposed to be the "best of the best", they should have given me the best results over all the other orifices, they didn't! I ran the several more times to see if I had missed something or set the test up incorrectly, it appears that I had not, the results were the same. Now, these sapphire/ruby orifices shouldbe the best, why they are giving me bad data I couldn't say for sure but I have some theories that I will explore next week.

The coming week is shaping up to be quite a busy one. I would like to get my orifices in line (make them do what they are supposed to do) and get testing started for the new pelton protos. I also need work in some time for the paper/presentation.

This week I've just been doing some DNA extractions on the MFB and matching them on the bench with Qiagen kit extractions. I've run multiple qPCRs of all the extractions and will hopefully be able to estimate the concentration of bacteria in them. Yesterday I set the MFB up to run 10 PCRs over the weekend and I really really really really really really hope they work so I don't have to go Office Space on the ESP...figuratively. As of yet, my paper is non-existent, but I'm hoping to change that this coming week. My presentation has been started, but has a LONG way to go. I specialize in procrastination though, so I'm not too worried about it. Besides all the project mumbo jumbo, I'm really enjoying myself! Everyone working in the labs are HILARIOUS...I don't know how we get any work done. As excited as I am to go home, I'll miss everyone I've met...almost everyone

Well, this is a bit late because the last two days have had me busy in two worlds - I run my own intern program at the aquarium and I've been over there interviewing teens for the positions and working with team mates on my project.  We've finally come up with a script to give Todd so he has something to work with when bringing together our introduction video for the Discovery Lab Ocean Acidification class.  I've completed my staff training outline and sent if off to the manager overseeing the lesson creation, she's adjusted it as need, and I've spent some time gathering images & information to use for the powerpoint I am creating for that... I am trying not to feel overwhelmed by the fact that I have to write a paper, put together a powerpoint for seminar, speak, build the staff training days & put together program packets AND make sure this lesson is accurately representing the topic of OA. Thank goodness for MBARI - it's great to have scientists at your finger tips!  I get to meet with Dr. Peltzer next week to talk chemistry and to ask for his feedback.  THREE WEEKS??? That's it?!  Have a great weekend friends! 

This week I generated an outline and site map of what teachers would like to see on a HAB page.  It's nice to have a little direction and something to refer back to, especially if you're scrambling for time like me!  The feedback has been really helpful...so now I'm researching the historical background of HABs in Monterey, writing a brief, easy-to-read introduction on what causes HABs and what organizations are doing to prevent/ mitigate the effects of it.  I'm also working with Raphe on coming up with a couple of case studies students and teachers can walk through --that way it gives them a chance to deal with the data and see what researchers go through to identify a bloom.  Furthermore, I'm getting real-time SST and chlorophyll data to have up on the site, so things are definitely getting exciting.  It's so bizarre that we only have 2 more weeks to work on this and then another week to write our reports and give our presentations!  This upcoming week will be spent trying to get some of this stuff up on the web and hopefully having the teachers evaluate it. I'm also really looking forward to the aquarium visit since I haven't been and going on the Lobos this Wednesday! 

Karen, that's a great suggestion!  I would love to meet with Mary at some point in time.  

This week I organized the best framegrabs of the eggcases to put into my presentation. I learned how to use more equipment in the videolab so that my video clips would work well with the projector in the Pacific Forum. I also did a lot of networking this week to gain anymore information about the eggcases. Even though I had some good specific questions to ask, there was not much anybody could tell me; however, I did get some good information I could possibly put into my paper.

Most of my time now will be making a good presentation and writing my paper. Even though there is little information about my topic, I still hope to spark interest in those who attend the symposium with some cool video clips and interesting observations I've noted about the Tomopterid eggcases.

Looked for changes with distance from shore and season on Line 67.  This may be meaningful.

Road trip down south to deliver two MBARIans to a research vessel (NOAA ship McArthur). 

Next week, find some defensable way to get rid of bad data points;  this should make things a bit clearer.

~

Last week I made serious progress on the autonomous control systems of the boat. Waypoint control has been written, though I've now found out it's a little overkill. I could've used a simpler, faster algorithm that should get the job done if the waypoint is within 500 miles (not a problem because I'd just rerun the algorithm if it got close to this). There're also a few bugs with it, but if I can figure it out I'll stick with my version unless I need to change because the dsPIC can't handle it.

I've also started developing code to use the ECAN on the dsPIC. The motor driver board doesn't seem to work when controlled serially by the dsPIC and we planned on using CAN to talk to it anyways, so we're going to develop the software needed for that now. Hopefully it won't take beyond today or tomorrow and we can start testing it with the hardware.

I also need to put up the mast and see how far it leans and affects the listing angle of the boat. It seems to not stick straight out the back but it's leaning to port.

This week I'm heading out on the Point Lobos, so that'll take up all of my Thursday, though I can hop back on it Friday. I'll be trying hard to finish ECAN early this week and then figure out how we can get battery charging working in the boat, so we don't need to take the hatch off to charge it onshore.

Last week I started looking through ocean needs documents for the west coast to start outlining my needs document. I am now flushing out my outline, filling in more information as I meet with more SF Bay managers/researchers/users. I had a meeting in Berkeley with the Invasive Spartina Project Director (Spartina is an invasive cordgrass that is invading SF Bay - it's also a problem in Oregon, Washington, BC, and Alaska). I also had phone interviews with the Director of the California Department of Boating and Waterways and a Fisheries BIologist who works in NOAA's Habitat Conservation Division in SF Bay.

I am collaborating with a fantastic programmer from NOAA, Lynn DeWitt, to create the real-time salinity map of SF Bay.  Last week she sent out a mock up of the product, which incorporated both of our ideas, and it's looking great.

This past week has been chaos to say the lease (which is why my update is so late!). In order to grow up the plasmid I've been working with, that closely resembles my mystery sequence, I had to transform it into E. coli and generate colonies. The first problem was that there were way to many colonies on my plate, so I had to just hope for the best and pick colonies anyway. Then, when I tried to visualize the plasmid after extracting it from the replicated E. coli cells, it ran really oddly on the gel, so I don't even know what kind of product I have. I still have not successfully isolated the plasmids yet. This weekend (yes, I was here ALOT over the weekend) I tested the QPCR primers I designed with Eunsoo Kim. This was way more complicated than I originally planned, but at 6pm last night (Sunday) I finally got some promising results. One primer set looks like it just might work, so I may be running a QPCR this week on some environmental samples. The rest of my week will be dedicated to trying to grow up my plasmid some more and work on my paper, which I've been trying to do (unsuccessfully) for about 5 weeks now.

My plan for the week was changed from working on security issues of ESB to working on XSLT transformations to make it work for SensorML. After doing a little research on the web, I realized that there are different tools available that can implement these transformations, and/or perform XML mapping. I got the evaluation versions of each of these and started testing. These tools are quite amazing!! For example, using Stylus studio instead of mapping every keyword on one XML to the other one, I can graphically map the keywords using lines that join them. Moreover I can define the meaning for each connection by choosing from the list of possible functions that it can do.

Finally I was able to get the basic version of the code transformation working, but there is a lot that can be done. For example, if the user name in the input XML document is "Kevin Gomes" and in the output xml it has to be written as "Kevin" for the first name and "Gomes" for the last name, then I have to use some kind of split function to perform this. I got the code, but somehow the xsl:import function is not working properly. Today I tried this on stylus and it looks happy with the code, but still not sure why it was not working with oxygen and servicemix-saxon

TO DO: There are lots of things for this week. I am going to meet Kevin tomorrow to talk more about editing the actual SIAM code to make it work with the ESB. Need to start writing my paper ASAP. SCUBA (book + video + exams).
Good luck to me