Wow! The last update...

This week I did a demo presentation to my mentors. I spent too much time (22 minutes) on that, because I have difficulties on picking the correct words and also because I have too many slides and they are too fancy (lots of appear and disappear effects).

I sent the classifier results to Marc'Aurelio Ranzato, the guy who built the original version. He was happy to see that we've made some progress and improvements to that.

I started to work on other layers. There is a Java interface that runs on top of the classifier. We use the Matlab compiler to create a shared library and then the GUI calls the functions on the library. We have to make sure that all layers properly communicate with each other in order to create a package easy to use for scientists at MBARI and at partner groups.

Next week I will continue to work on the Java GUI.

The last update indeed! The summer past very quickly.

Most of the work I did this week was organizing all the unorganized scripts I was writing now and then into one generalized application. Then I rapped the Google Earth based dynamic visualizer in a near html page. I found a bug just a while ago which I am going to fix today or on the coming days. I also started working on my report, and if all goes as my plan, I will finish it before my presentation. Next week, I will be working on my report and presentation.

Title : "Dynamic AUV Mission and Data Visualization with Google Earth"

I had such a wonderful summer.

The summer has gone by quickly. Working at MBARI has been a wonderful learnnig experience.

This week I put together all the componets for testing O2 sensor response time. I made the measurements at room temperature and in a cold room where the temperature was 4 C.  It was really cold in the cold room. I should have brought a warmer coat. I have started to analyze the data.

I enjoyed Devin and Durga's presentations. I am looking forward to seeing everyone elses presentation next week.

Next week I will be busy summarizing the data, finishing the presentation and the paper.

Thank you George for all that you did this summer to support the intern program. The program exceeded my  expectations.

Sniff... it's the last week?!  Wow, that zoomed by pretty quick!  This was a great week which began with a trip on the Point Lobos to collect urchins and brachiopods - it was my first time out and it was pretty amazing!  No sea sickness, just pure adventure!!  I was determined to soak in every second and I did - even got to help with the collection!  Tuesday was the Monterey County geology tour with Gary Greene; I will never look at a cracked side walk the same way again!  Wednesday morning, a few interns, George and I spent time with a Camp Sea Lab summer camp filled with girls - what a bright group of young women with great questions!  I've been working with Todd Walsh trying to finish up the introduction video to the lesson I've been helping to create, so far so good.  It won't be done by the end of the internship but it's well under way. I am hoping to get more hours with Todd today.  I visited the aquarium's exhibits department who are helping us by creating some fun props for the lesson - they're looking great!  I spent yesterday photograhing the props and a mock set up of what the classroom will look like when we teach "Carbonated Seas".  Next week will be all about finishing up my paper, presentation and completing the preparation for the two days of training I will be giving my department. 

Title:  "Carbonated Seas": Communicating the Science of Ocean Acidification to a High School Audience at the Monterey Bay Aquarium

The final days of the program are upon us. I have managed to find a good stopping place for my project which is lucky for me because there aren't many good spots to stop. Today I'll be getting the last portion of data I need leaving next week free for my paper and presentation. I also budgeted a little time for anything unforeseen that may be a problem next week. This weekend and next week will be spent cleaning up my paper and refining my presentation. I'm going to have to put in some serious practice time for the presentation too.

The geology tour on Tuesday was excellent. I had no idea that the area we live in as crazy as the fault map makes it look. I feel like a volcano could erupt in Hollister at any minute. I really did learn a lot more than I expected to though and the fact that we had the chance to see what Gary was talking about while he was giving the tour was wonderful, it really was cool.

Devin and Durga's presentations were great and I really appreciated the fact that they stepped up and showed us how to bust it out even on a short schedule. 

This has been a great summer, I couldn't have asked for more. I learned so much in ten weeks it was crazy. I got the chance to do things that I've never done in all my years living here. I want to thank everyone here at MBARI, my mentors Andrew Hamilton and Larry Bird and especially George and Linda for making it all happen.  

 As it stands, the title for my paper/talk: "Wave Energy For Vertical Profiling"

Things are moving really fast now.  I'm working hard to squeeze in a few more meetings, and get everything integrated for my paper and presentation.  This weekend and next week will be all about getting the paper and presentation done.

I've met so many people doing interesting work in SF Bay this summer, which is very valuable to me, as this is my home turf and my area of interest.

Now it's time to distill out some big picture take home points from all of the information I've gathered over the summer, and package up all the information and beginnings of projects into a tidy packet that I can hand off to my mentors so they can carry it forward.

I have really enjoyed my work this summer. The program is fantastic. Thank you all and Linda and George.

Title is likely going to change...but for now: "CeNCOOS in SF Bay: beginning partnerships, pinpointing data needs, hunting down data"

wow, saturday already. amazing how fast 9 weeks can go. Don't forget about the BBQ on Sunday at Connors - and if you can, also add your update/title if you haven't already. One more week to go

and if you're bored and want something to do tonight - my boys are in Oliver at the outdoor forest theater starting at 730 pm. seats are $12 for students and seating opens at 6 pm, you can bring food and drink.

Working title: "An Autonomous Surface Vessel: The Missing Piece of MBARI's Robotic Fleet".

Last week was very good. I received the new motor driver board I'll be using in the boat and have been working hard on the software so that I'll be able to use it this week. I've finished the software portion such that I can write what I need for remote control to work, though it will need a little more work before it's  integrated nicely with the rest of the software I've written.

 I talked to some people around MBARI about how best to set up on-shore charging for the boat. I think I have a setup that should work. It's time to order it and get it all installed.

This week will be all about working continuously on the paper/presentation in line with getting remote control for the boat working. I think all of that is possible by Thursday, so here we go!

 Also, congrats to Durga and Devin for being done and it was fun working with you this summer!

THEE TITLE: Real-Time Water Quality Monitoring

This week I've just been trying to fill the holes in my data. I was able to run PCRs with standardized concentrations of bacterial DNA. This is great because now I can compare that data to the data I got from my environmental samples to estimate the concentration of bacteria in them! YAY (I know you're all secretly excited too...on the inside (That's what she said)).

It's kind of depressing to think that I only have four more days of work at MBARI. I think I might be the only person in the history of time to be bummed about going to Hawai'i...I'm sure it'll pass MBARIans, you will be missed.

Last update, wow. Still can't believe how fast the summer has gone.

Nice to have finished the presentation and I'm done with the 1st draft of my paper...still needs a bit more work. Just wishing I had more time here to stay and further my project.

My last day is tomorrow so if I don't see you good luck with your presentations and it was great meeting you all.

Le title: Expressing a Novel Fluorescent Protein from a Mid-water Siphonophore

 So, the last update, eh? i wish i had better news, but unfortunately, no glowing bacteria. i thought this was going to be the week, but alas, science foils my plans! I finally got an adequate amount of colonies that supposedly had my insert in them (they were white in the x-gal screening). I even did a digest and there was a band the size of my insert. so, i started on an epic sequencing binge: i grew 48 overnight cultures, digested all 48, and then sequenced all 48 (sequences pending... i should have them tomorrow). i also ligated my insert into 6 competent cell batches, plated them out. For some reason i got a lawn--the plates have carbenicillin in them, so perhaps the concentraion was just too high... so I'm not quite sure what this means, but i'm hoping my sequences tomorrow will illuminate something about this tyrosine chromophore!

guys, its been so much fun! seems shorter than i thought it would be (thats what she said), but i'll always treasure these past ten weeks i've learned a lot from everyone and i couldnt have asked for a more diverse, fun, engaging group to spend my summer with!

Gosh, can't believe it's already the last week!  There's still so much to do and tweak.  I've completed most of the content for the website, but I still feel like there's a ton of information I didn't even touch upon.  Hopefully this will be enough to provide the basic framework for an educational HAB page.  I'm working with Tom tomorrow to get all of it up, but I still have to get everything approved by Raphe and the other researchers...and not to mention the teachers!  I should have something decent by Thursday, but I know I'll definitely be working on it during the weekend.  Also have to work on the presentation and paper!  I'm not too sure how I'm going to present this, but I have to have something solid by tomorrow.  This week is going to be crazy!  Hmm, and title?  Well, how about "CeNCOOS's Educational Harmful Algal Bloom Webpage: Making Real-time Data Accessible and Understandable to Intermediate Students"  Might change it later...

This past week (and weekend) was spent running a bunch of different QPCRs to try to get a good standard curve out of my plasmid dilutions. Unfortunately, it's been really hard to get good results. I've struggled with bad dilutions and tons of water contamination. My goal was to run a QPCR using environmental samples. That way, we could tell in what locations and depths my mystery bug appears. However, all my lab work has left be absolutely no time to work on my paper and presentation, so I'm really going to have to struggle to get stuff in. I still don't have a title for my presentation, but hopefully I can crank that out soon enough.

SCUBA finished this weekend, it was pretty epic (that's what she said.) I also met a cool navy diver there, he goes deep (also what she said.)

I have  been engulfed by the world of phylogenies for the past two weeks-- which has been a nice breather from lab work.  I have a nice rough draft of my 18S prasinophyte tree, which I hope to show at the presentations.  Aside from that, I have been preparing stuff that I will be working on during the semester and planning out the lab work that I will be doing in January.  All seems to be going fairly well.

I can't believe that the summer is already over!  

The good news is that Jellywatch is up and functional!  We have picture uploading capabilities and a good moderation scheme to sniff out bad jelly sightings.

The bad news is that it doesn't work in internet explorer.  In IE 7 and IE 6, the main content box of jellywatch.org just doesn't show up.  like, at all.  This week I will be pulling my hair out trying to figure out why.

Recently I have been finishing up my paper and editting it as well. My presentation is coming along and I got some pretty cool video clips..or at least they are cool to me! Learning about reproduction in the deep sea has been fun and interesting. I have learned so much about papers and pelagic polychaetes, its amazing that my head has not exploded yet. I am thankful for this opportunity to work with some amazing and interesting people during this internship. 

The geology tour was awesome; however, I do feel sorry for those people who living on the fault line and their houses are slowly being ripped apart! So sad.The mission was beautiful and the Mexican comida estaba muy bueno!! Sorry if that was incorrect
Spanish Alena!

SCUBA was the best!! Glad I had the opportunity and too advantage of it. I saw so many cool things and I was even more excited the deeper we dived (thats what he said lol). Hopefully I can scuba more on the east side, preferably in warm waters.

It almost feels like we just started having fun and before you know it, your done(thats what she said)!!! Good Times...good times

It feels like everything I've done this summer has been done in the past week.  Lots of PCAs and now step wise multiple linear regressions (finally a matlab processes that takes more than twenty minutes).  Tim has been helping me define goals for the talk, some of which are showing that there is no correlation (read: many analysis are not working out). 

I woke up this morning at 4:30, unable to sleep any more.  I've entered exam mode and it will be nonstop from here on.