The end of the program approaches... I am feeling it as I imagine everyone else is at this point. This week was filled to say the least. My new pelton wheels arrived early in the week. I had to spend a few days modifying my testing bench to accommodate the new wheels then I got to test them. The first tests were disheartening, the numbers I were getting were under what I had been getting with the "inferior" wheels. Fortunately my sadness was short-lived. The data that I had been comparing my new wheel numbers to was from rounded inlet tests, the orifice that I was using with the new wheels was square, as soon as I switched the orifices the problem was corrected and I saw some good numbers. Now my task is to determine the optimal impact position for the water jet on the new wheels. I will finish out the week playing with the stream adjustment until I find the spot that produces the most power. Once I get the orifice placement dialed in I can collect some good data and then have some numbers to compare to the curves that I already have.

In other news the paper and presentation are coming along. I am going to try and go over the presentation some time towards the end of next week. I want to run through it several times because I have a feeling that, as it stands, I will exceed the 15 minute time limit. The paper is going to take some time to organize and "stitch" together, I have the pieces but I will need to assemble them into something that flows. Some sections also need some work and maybe a little more substance. All the paper/presentation organizational stuff is on schedule for next week.

After an incredibly long weekend testing out the primers I designed, I was finally able to pick out a good set. By using a gradient PCR I found the best annealing temperatures for those primers and was finally able to run a QPCR on Monday afternoon (after the microwave incident). I pipetted my first 96-well plate...by hand...individually. It's surprisingly had to keep track of the little wells, but I was able to get through it. Tuesday morning I got my QPCR results. They weren't terrible, but they could definitely be improved. I had some slight water contamination and one of the dilutions wasn't actually a dilution, but nevertheless I think it was a pretty good first QPCR.
I also ran a quick PCR to make sure that the negative DNA I was using to test my primers was not degraded and still capable of amplification. It was supposed to be the simplest PCR ever, but of course something had to go wrong, and there was water contamination. At least I know that the DNA is alright, but I may have to re-run the PCR.
Wednesday was pretty much devoted to the BBQ for me. I hope you all enjoyed it, and I know I had a lot of fun doing it (even though I was here until 2am on Tuesday night). Roman, thanks for being a champ and stepping up to the grill. And to the other people who helped with prep (Katherine, Harriet, Durga, and anybody else I might have forgotten), you all were real life savers.
Today and next week I will be running another QPCR, and I will re-transform E.coli with my plasmid again to see if I can get some better results. I'll also be working on my paper. I have so many different protocols to write up that it's definitely going to take awhile. Hopefully I'll have time to write amidst all my lab work.

I spent this week finishing the report and presentation. I sent them to my mentors and they said that I'm done with the proposed project. It's hard to believe.

Now I'm starting with a new project: adjust a Java interface to call the classifier functions. This way someone with no experience at all with Matlab programming will be able to use the classifier without much effort. That is the task for next week.

I spent most of the week gathering, configuring and testing equipment for my O2 sensor reponse time experiment. It is a simple experiment but it has taken longer then I expected to gather and test the componets.

Next week I still need to find an A/D converter to interface to the SBE43. I am hoping that the test will be done by Wednesday. I will spend the rest of the week doing the post processing of the data. I then want to meet with 3-4 people to review the data results.

Unfortunately, I could not go out on the pt Lobos with Mary Silver this week. I was going to go out on the Pt Lobos on Tuesday of next week to do more tests but I am behind schedule on the responce time experiment so I am going to focus on that and get it done.

I enjoyed the behind the scenes tour of the aquarium. Thanks for setting that up George.

This week I was exceedingly productive. With some help from Mariano in my lab, I have written a basic autonomous control system for the boat! Given a pair of GPS coordinates, my boat successfully navigates between the points, slowing to stop on top of the end point.

 I also shipped off the motor board to be repaired. It'll get there Monday, so hopefully they can repair it and turn it around quickly.

I have planned out the rest of the things needed for basic autonomy for the boat. I need to verify that these will work and go ahead and order them.

I've been continuing developing a CAN-bus driver for the microcontroller we're using. It should be finished early next week and then when the driver board comes back, we should be able to finish testing it. I did find out that it would cost us a pretty penny just to upgrade our hardware to use a CAN bus. This is unfortunate, but given how useful and robust it is, it needs to be done.

Next week I have a Point Lobos trip that eats away my Monday and no Friday. Gotta finish boat integration next week as the software should now be set for remote control! I have to write a driver for the GPS, but then everything should be set for waypoint autonomy.

This week was awesome. I did major development. First, I got to install and run TREX with the simulator on my computer. I got to run different missions and observed the generated log files. Next I started modifying one of the reactors to publish the status of the vehicle via a socket. With this my html page,which I developed last week, with an embedded Java applet was able to read the streaming data and show the status on Google Earth's plug-in. Step by step I included publication of active vehicle behaviors and showed a visual representation of it. Thus far I am really happy by how it is working.

Next week I will start writing my report and preparing my presentations. Also I will be working on the possibility of depicting the plan generated by TREX (The autonomous agent or the controlling SW).

This week started rather distracted and I feel I've lost some important time.  As my project starts to wrap up there are still a few pending items which I did manage to address though.  I worked closely with Todd Walsh, putting together the introduction slide show/video for the OA Discovery Lab class - we are about 1/4 of the way to completion.  Stitching together images and video so they flow well and make sense is more challenging than I anticipated, especially when the images have been pulled from different sources!  I can't wait to see Laura's graphics placed into the whole thing!  I spent a couple of hours with Ed Peltzer asking those nagging chemstry questions that just hadn't been clarified by any reading I had done - he's also been given the program description and materials for review.  I also took a nice chunk of time to work on my paper.  Next week, I work with Todd again and  hopefully get the "okay" from Ed so we (my colleague, Rachael and I) can finally get the entire program description and training materials put together so they can be handed to Monterey Bay Aquarium school program staff during our training week of Aug. 31st - Sept 4. 

I can't believe the summer has gone by so quickly...

This week was alright. Has some good talks with my mentor and the folks over at NOAA and hashed out what the outcome of my project provides for them.

In the midst of getting the ARM processor and instrumentation ready for a demo, more work has surfaced and hopefully I can get this all out of the way on Monday.

Still need to do the paper, but working on the presentation.

Good boat trip on Wednesday.

Things have finally started to work this week! Hooray I knew that attaching Lucky the frog to the MFB would work. We were able to put new reagents on the MFB and run PCRs that actually amplified...imagine that. With the PCRs going well, I was able to go through the whole process from extraction to amplification on the ESP for the first time this weekend. Each extraction and series of PCRs takes 12 hours, so I'm glad I was able to get things going.

I've been working on organizing my paper and presentation as well. I'm going to go over my paper with a few people in my lab this week and will hopefully get a draft written soon. I'm more concerned about my presentation at this moment in time since I can revise the paper post-program. I'll be working on it a lot this week. (yay)

work with this tyrosine chromophore has become more convoluted and confusing than ever! I thought using these primers would work, but it appears that PCR with the tyr chromophore primers and the old cysteine primers creates a chimeric protein with the tyrosine chromophore, but the ending of the cysteine gene. Upon further review of the 454 contigs (done before i got here), it seems that the tyrosine protein has a different ending, so we made primers specific to that ending. there may even be a different beginning (3'end), so we ordered primers for that as well. once they finally arrived on friday, i did PCR and got two products, which is really strange. This weekend I worked on transforming the PCR ligation into cloning cells for sequencing. Unfortunately, when i arrived on saturday i found lawns on my plates, and then noticed that I used plates without ampicillin (booooo), so after another transformation, i come in to find only 6 colonies for sequencing... i'm not sure if the transformation worked because so few colonies grew. i may have to go back and start again from PCR, but the problem there is that i dont have any more cDNA! so i'll have to wait for meghan to make some more... but hopefully these 6 colonies will have the full tyrosine gene once i sequence them! I think i'll have to try a good luck charm like monika did... any ideas?

This week was a continuation of writing the content for the website, so that I can get it running this coming week.  I still have to get it approved by Raphe and Heather, my mentor.

 I can't believe this program is going to end in two weeks!  Definitely a little nervous for the paper and presentation.  I have a feeling I'm going to be working on trying to get this webpage up until the very last minute...and get teacher feedback so that I can make some last minute adjustments before it goes up on the big screen. 

 Since this coming week is so short, I'm worried about getting enough time with the technicians to put up all the links, images, and whatnot but we'll see.

Hey everyone!!

This week I have been working on my paper and trying to gather as much information as I can. I have also made a few connections with fellow researchers which has taught me a lot about networking. I really enjoyed the tour of the aquarium!! That was the hightlight of my week of course and I learned so much there as well.
and so that's it. =)

Hi All,

This week has been a week battling with OMF design ideas, which have now finally been resolved. I think these two illustrations I'm doing for MBARI have turned out to be the most challenging projects I've ever tackled as an illustrator! I don't think much will worry me after this in terms of complex projects

It's amazing how long designs take to come together when you're trying to include so many elements and processes. I'm now running behind schedule, so this week will be pretty manic as two pieces need to be completed by the end of the week (won't have time at the weekend as that's filled with scuba class). Next week is presentation time....wish me luck with powerpoint!
Good luck everyone!
L

In a meeting with my mentor, we tried to visualize how the actual integration works with ESB. It looks like there is a lot more work to do. Especially with the routing.

When talking about integration at the organization level, static routing is not very efficient. I tried to figure out if  dynamic routing is provided by the Service Mix. Eventhough EIP and Camel can be used to achive the routing for OMF, but both of them are static routing algorithms.

This week is my presentation week. I started with my presentation. Will start with my paper today.

I have created an outline for my final CeNCOOS Needs Statement for SF Bay.  I'm still scheduling meetings and adding information, since there are still many more groups to talk to. 

I met with Linda this week to talk a little more about our presentations and figure out how to tell the story of my summer and project. 

There is good progress creating the salinity map of SF Bay. I have instigated some discussion among the higher-ups to get SF National Estuarine Research Reserves data into our database, and useable in real-time!

This coming week I'm meeting in Oakland with a woman from the Coastal Conservancy on Monday, and working on writing my needs document and starting my powerpoint presentation.

I'm so looking forward to Devin and Durga's presentations!

Began putting plots into Powerpoint and now feel much better about my project.  Its good to get oranized and try to define what has actually been acomplished this summer. 

On the other hand I tried a multiple linear regression of the data and got very poor results. 

Chavez has left town for the rest of the summer, so I'm down to one advisor.