This week I sent out my first emails to marine managers in SF Bay proposing uses of CeNCOOS data. I am wondering how many to send out (and what percentage will write back). I am following up with contacts I made at the California Shore and Beach Preservation Association workshop last week. I'm hoping to meet today with my mentors to go over the ideas I've brainstormed for the different user/manager groups.

This morning we got to check out the Western Flier, which was really cool, especially seeing the Doc Ricketts and the pilot room.

Next week I hope to hear back from some managers, schedule some meetings, and start honingin on an organization to create a product for. I am also going up to Oakland next Thursday to attend a Harbor Safety meeting, and after that gets out I'm meeting with someone from the exploratorium to look at their future outdoor exhibit site at piers 15 and 17 in SF. I may help design the ocean observing component of the exhibit as part of my summer work. I'm excited to learn more about that project!

Things I really enjoyed this week:
-seeing the Western Flier
-getting out my first contact emails

This week went fairly well (as short as it was).

 I got ARB to work!  Which is amazing... I have been struggling with it for about 3 weeks.  It is probably the most ornery program ever designed... but it is working now.  I was able to create a few databases and align some sequences (though it isn't optimal yet).  I have my biliphytes pretty well set up-- and the parsinophytes are the next to get set up.

 I shipped off my DNA samples to SeqWright on Monday (at least I thought I did...), unfortunately there was a mix up in the mail room and they didn't get shipped until yesterday.  Hopefully the DNA will still be viable.  If not, I suppose I will redo the ligation (etc.) which is slightly problematic as the sample are pretty precious, and I am not sure how much DNA has been extracted for the different sites.  

Aside from that-- I have been working on my literature review-- which I am supposed to be done with by tomorrow.  

Next week I am going to be working in the lab with Alex-- possibly working on some flow sort samples to try to figure out where biliphytes are located on the read out.  As it stands right now, no representative biliphytes have been cultured-- so no one is sure if they are autotropic or heterotrophic.  We stained some of the samples with lysotracker green-- so if they are heterotrophic (and have acid food vacuoles) they will show up at 531nm.  If they aren't heterotrophs then we hope to see them on either the chlorophyll (692nm) or in the orange range (575nm).  They were thought (originally) to have orange fluorescence because of some observations made with FISH-- but now it is thought that they might have just eaten a phycoerythrin possessing phytoplankton.  FISH protocol unfortunately causes the chlorophyll to be knocked out... so that was never observed.  Needless to say-- these results should be interesting.   

Regardless-- I am looking forward to the fourth! 

Even though it was a short work week I feel it was very productive. Today I finished the base framework of my instrument driver and, with the help of my mentor, integrated the output stream into data turbine [http://www.dataturbine.org/]. However, there are a few issues that need to be addressed with the data structure as well as more robust control methods, but what I have now works well for a prototype. Oh and lots of documentation...

The R/V Western Flyer tour was great. Goosebumps when I saw 'the Doc'. Definitely want to sit down and talk shop with the ROV guys.

Hopefully today I can get the PC-104 ARM board booted up and running. I received it yesterday and haven't had a chance to play with it yet. The next steps are to install Debian Linux on the board and then SIAM as well. We'll see how that goes.

It's nice to be alive and well, but I still feel like I'm floundering around since I don't have an exact emphasis for my project yet.  For the past few days, I've been aimlessly researching websites and public outreach organizations that might be interested in HAB (harmful algal bloom) data.  One of my goals this summer is to develop and update CeNCOOS's HAB webpage, but I'm finding real-time data (on HABs in particular) is not very common...and most of the information is obsolete.  

However, this morning was fairly productive.  I met with Steve Ramp (one of my mentors/ director of CeNCOOS) and we started contacting some people who might know a little bit more about obtaining real-time data for HABs (e.g. Chris Scholin) and also brainstorming ideas on how to get a hold of some teachers.  Another goal for the summer is to expand CeNCOOS's educational outreach and HAB program for younger students (i.e. middle schoolers).  So Steve has a couple of people in mind, but I'm also looking to meet some teachers MBARI might be affiliated with.  That said, I will be coming into work tomorrow (thank you, Michelle!) to attend the MBARI tours and hopefully meet the 70+ teachers who will be attending.

Next week will be a continuation of these endeavors.  It looks like I'll be contacting more people and searching for more relevant/ up-to-date information to post up on CeNCOOS's website. Aside from work, I am so stoked for the intern BBQ, Laura's t-shirt design!!, and maybe attending some of those open Ocean Studies Board meetings.  Hopefully my other mentor (Heather Kerkering) will be around, so I can bounce some ideas off of her.

But things are going swell and I'm really enjoying MBARI's atmosphere!

Hi everyone,

This week has been pretty hectic and progress slowed to a crawl for a while there! This week has been mostly attempting to understand OMF and generally getting my head around the second main piece I'm doing, which is much harder to visualise than the midwater ecology illustration. Got some encouraging feedback on that first one, so I'm pretty happy with that and have left it on the shelf for a bit while I tackle the complicated second piece, which I hope to have some understanding on by next week (fingers crossed.)

As well as that, this week's been BBQ prep and getting on with the intern t-shirt design. The one thing I've not had time to do is my webpage. Sorry about that Linda and George! So that's something I must get done by end of day Monday next week.

Have a great 4th of July everyone, enjoy the long weekend!

Laura

My3rd week@MBARI:

   Monday I was on the R/V Point Lobos.It was a quite amazing experience except that I was sick half of the time. Tuesday I was supposed to sit with my mentor to understand the flow of the code with in the ncsa project. Unfortunatley my mentor was sick, and I didn't get chance to meet him until that evening. However, he gave me a quick demo and files from the repository. Today, I went through some of those files, and got hardcopies of few others hoping to finish them this weekend. Nextweek I will work on the code, and I will start working with the ESB

Continued to talk with people about AUV instrumentation proposals. Spoke with Jules Jaffe from Scripps, John Ryan, Bruce Robison and Kim Reisenbichler. Jules is an imaging expert and a lively character. He is working on an ultrasound imager which may be suitable for AUVs. He is also working on a laser line scanner which may be suitable for a larger AUV. Bruce would like an AUV to be able to identify an interesting biota and follow it. He talked about an interesting small animal that can build a large 1 m mucus filter. No one has ever seen the filter being built. He would like an AUV lock on to it and watch the process.

Went to an interesting presentation by Julio Harvey (genetics group). He probed the AUV water samples taken from Monterey Bay for invertabrate larvae and copepods. It was interesting to see that there were no rock attaching shallow water larvae like mussels in the deep water.

Worked on an evaluation of Disolved oxygen sensors. Spun my wheels for a while with the usual software hicups. Went to the castroville warehouse to look for cables. Lots of interesting stuff piled high there.

Next week I will be going out on the Point Lobos to test oxygen sensors and will complete the AUV proposal summary. Will meet with my mentor for the first time.

Pros for the week: Enjoyed the tour of the Western Flyer. Learned a lot about acoustical and optical imaging.

On Monday, I was a bit confused about how to test the classification algorithms on the large image data set. So I sent an e-mail with some questions to my mentors. For my surprise, they prompt arranged a meeting and prepared a complete presentation (datashow, white board...). I was given the task of labeling about 7000 images according to their contents (fish1, fish2 ...). Spent a long time doing this. This is necessary to compare what the computer says to what a human says about each image. Then I wrote some code to make the test results more readable (make a spreadsheet). Matlab didn't get a holliday. It's now working for me, running the algorithms. Let's see what it find out next Monday. I wrote a very short description of my project in my webpage, I'll improve it next week. The Western Flyer tour was very cool, specially the Doc presentation.

This was an especially short week week for me. On Monday I was out to sea collecting sea urchins. The trip was really interesting even if it was a little shorter than the normal day trips. Our early return worked out well though as we were able to make it back for the cookie break, YES! It was good to get out on the Lobos for an ROV deployment and see how much work goes into getting the Ventana into the water.
Back on land I had some success with the pelton project. I have been working on improving the design of the pelton wheel itself in an effort to squeeze every last bit of power out of my setup. my new modifications gave me a little bit more power but not quite as much as I needed, so I will have to try some more modifications. Larry Bird has been a huge help, assisting me with all the machining associated with this project. Next week will bring continued testing. My sapphire orifices are due in next Monday or Tuesday so I expect to be busy mounting them and testing them against my stainless orifices. Overall things are still going well but its clear that I have a lot to do in the coming weeks as I'm sure everyone else does.

This week was spent developing the software for the control system for the boat as well as determining what hardware we will need for the boat. We've developed a nice list of hardware that's needed and even started to order some of it. The software is nearing completion for allowing remote control of the boat.

 Next week we need to talk to the harbormaster about where we could test-drive the boat. It shouldn't need very deep water, but he'll be the person who can help us find a suitable test site. I also hope to finish up with the remote control code Monday or Tuesday so that we can get it out in the harbor driving out to get a sense of how fast it can go and how quickly it can turn along with a general feel for the boat. I will also be starting the basic waypoint guidance system for the boat so that given GPS coordinates the boat will motor over there and rest on top of that point. Depending on how our harbor test goes, I hope to make some good progress through that. We will also finish ordering the parts we need so that they'll be on hand when we need to make use of them.

This week I finally had an opportunity to go out on the Point Lobos which was collecting sea urchins. I was very excited to be out in the ocean and see sea otters, seals, and other animals. I love animals. It was also interesting to see how all the equipment is used in the control room as well as seeing how the crew works together.

As far as my project, I am still in the process of scanning videos for the polychaete eggcases. It is sometimes tiring, but I am also learning a lot about the uses of each tool sled in the Ventana and the various species found in the deep ocean. So far my experience is still going well and I'm very glad everyone is so nice and helpful in this work setting.

This week was spent finalizing the layout of the Jellywatch site and then editing the page's style sheet so that the concept we came up with in Illustrator can be implemented on the site. One thing I was having issues with was trying to get the footer to "stick" to the bottom of the page, but after a few google queries and lots of trial-and-error, I finally got the sticky footer to stick to the bottom of the page. At some point we need to add modifications to the stylesheet so that Internet Explorer 6 can read the page.

For next week, I will start on the less-fun but more pertinent task of re-writing the "Mark New Sightings" page. This is the page that allows users to mark a location where they saw a jellyfish.

Last week I was able to go on the Point Lobos for an urchin collection trip. The "week" went by so fast that I completely forgot about updating everyone on the status of things. With the remaining two days I was able to finish preparation of MFB3 for PCR, and set it up to run three PCRs over the weekend. I'm going to look at the results in a minute, but you'll have to wait til my next update to find out the rest of the story...I know you'll be on the edge of your seat all week.

Analysis at last! At one point this week I had both of my advisors and another lab group member huddled around my screen discussing a problem.  Yippee! 

I looked at PAR (photosynthetically active radiation) from two different sensor types and found them to be curiously related (bimodal).  So I went back to the CTD data, found downcast data (every meter), and found the same problem with these.  In the end, I chose the cosine meter over the 4pi meter as the data were more self consistent over time.

Went to San Francisco to reconsider this country's revolutionary, war time, and beat past in the context of a non-american (Marco).

This week was a very short one especially since I went out on the sea on Wednesday on R/V Zephyr for a ''Front Following'' AUV mission and spent almost the whole day on the ocean. I must say Zephyr is better than Point Lobos, reason...I didn't get sick... So basically I did most of this week's work on Monday and Tuesday. As per my plan what I did is, did some investigations regarding COVE and started working on Google Earth in parallel. I met and talked with Mike Godin and Mike McCann on how to use Google Earth in smart and robust way to perform my task. They gave me very good and insightful ideas and guides. I would like to express my warm appreciation for the help and support they have shown and given me. I also discussed some issues that I had, with the task I am doing, with my mentor Kanna Rajan and Fredric Py.

Next week I am going to start communicating with Keith Grochow, one of the important people who developed COVE, and start inergrating Google Earth plugin and coding the visualizer I am planning to develop.

During this (very short) week, I focused primarily on reading a bunch of papers that will give me useful background information for my topic.  On Tuesday I headed over to the MLML library, which was very relaxing and a great place to focus.  I also heard back from my mentor, and I finally know what to do with my PCRs!  Wednesday, I woke up in the wee hours of the morning and headed out to sea on the Lobos.  The trip was focused on software programming, which was completely over my head, but it was great to see the Ventana in action.  I really enjoyed seeing all of the otters and sea lions on the way out to sea, and I even got to see some really pretty jellyfish.

This coming week, my mentor finally returns!  I'm really excited to be able to work side-by-side with her.  (No more long distance relationship!)  I plan to run one more PCR on some environmental samples using my specific 16S primers.  Then hopefully I will be able to run a gel purification and ligation reaction so I can get my sample sent off to be sequenced.  Because my results were so bizarre last week, I might need to work a little on modifying the primers in some way to make them more specific.  I also hope to get a jump start on the introduction to my final paper.  Hope everyone had a great 4^th of July!