Monday and Tuesday this week I spent at the Romberg Tiburon Center in Tiburon, up in Marin. It's a beautiful research station affiliated with SF State University. If anyone's interested in a PhD in ecology or eelgrass restoration, there's a wonderful woman there who does cool work named Kathy Boyer. It was a productive visit, I had 4 interviews. I spent Wednesday responding to a request from the Exploratorium outdoor exhibit group for a real-time salinity map of the bay. A map like that would be useful for many of the managers I've been talking to, so I think that is going to be one component of my final project.Thursday I had a phone interview with the Manager for the SF Subtidal Habitat Goals Project, which went well.

This afternoon I'm meeting today with my mentors to present what I've learned so far from my meetings, and discuss my final project ideas. 

The summer is going so fast! The work that I'm doing could take much much longer than a summer, so I think it will be useful for me to try to set boundaries on what I want to accomplish, so that I can get a final product produced by the end of 10 weeks. 

This week was super busy for me, and I definitely put in way more hours than I would have liked, but right now it all seems to be worth the hard work (such a satisfying feeling).  Thanks to everyone who helped with George's birthday extravaganza.

I've been working alot on aligning my 16S mystery bug sequences and comparing those sequences to other potentially similar organisms.  Looking at these alignments will help me to design qPCR primers, which I'm hoping to send in to be made today.  Eunsoo Kim, the seminar speaker from Wednesday, is helping me do this.  I also gave a presentation on my project yesterday at a lab meeting.  It was kind of stressful to prepare, especially with all the other stuff going on, but I think it will really come in handy when it's time to do the final presentation.  I'm really enjoying working with Eunsoo, and I can't believe that she's using my data!  I also had dinner with my advisor and some people in my lab last night and had alot of fun.  I don't want this summer to end!

So this week has been an interesting one. Hit a snag with the illustration that I initially thought was going to be the easiest! Hey ho, have revised my ideas and sent them of to Bruce and Rob for feedback, so fingers crossed it all works out in the end. I've revised my schedule so that I have a week dedicated to each project I'm doing. That should help me maintain my focus as the 'level of hectic' increases later on. My OMF illustration is still in the planning stages which is frustrating, but I should get that sorted out today/early next week. The idea is that my design for each piece is complete by the time I come to the week I've dedicated to it. That way those weeks can be spent on final rendering not preparatory research.

Thanks so much for all the hard work for George's birthday Julie. It was lots of fun!

Excited about learning to scuba. Let's hope I don't suddenly discover that I'm terrified of being underwater!

To increase the size of the test set and still have enough images for training, we randomly selected 10% of the events for test and 90% for the training step. We did it a lot of times. Depending on the events that are placed on each step, results get better or worse, but on average more than 90% of the events were correctly classified. And this is true for all the classes. Using the old algorithm (only grayscale information), one of the classes had only 63% of correct classification. Danelle, one of my mentors, asked me to start writing the report. Writing the report will also help me understand better some parts of the algorithm that I've modified

I can't believe today is the end of the 6th week. Time really flies by when you are enjoying things! This week has been very fruitful. Keith Grochow got back to me regarding the problem I had with COVE. He said and I quote " I have the crash fixed in the newest build, but there's still something pretty wrong with the vertical section" so I had a discussion with my mentor and decided that eventhough COVE is a very promising and useful tool it is better to leave it for now as it seems to be unstable. With this, Google Earth got my full concentration. I packaged all the MATLAB scripts that I have written so far for Google Earth into a neat GUI based application and moved onto programming the GE plugin in a javascript based html. My goal for this would be to interface the html with TREX and show what is happening inside TREX and the geospatial context of the AUV when run under simulation. I have completed a small version of this application that shows the geospatial context of the AUV in GE just using the generated log files. Next week I will start working on TREX side, diving deep into it trying to get a low level understanding of how it works. Then I will try to figure out how to put a component in there that would publish its internal status in the manner I can interface with the javascript page. 

Also yesterday my mentor  Kanna Rajan left for India and won't be back before I finish my internship. But he has made sure that I have the right people to help me if I stumble into something on top of the regular conference call I am gonna be having with him.

Trucking away with the Ocean Acidification Discovery Lab creation - I finally got in a "story board" to Laura for the creation of molecules in motion in the ocean.  I met with Jim Barry and talked for two hours about what we've done so far.  His input as a researcher in this area has been very valuable.  The challenge of teaching the topic is that it's emerging  and there is still so much that is unknown  We want to make sure that what we are planning on teaching the students is valid and that it is a realistic portrayal of what the concerns are, what the result are so far and what actions they can take as citizens of this planet to help in the slow down of carbon dioxide emissions.  All this in 45 minutes!  We're still going through images to use for our introduction video... I am hoping we will avoid using too many of the typical "Al Gore" images of factories and exhaust fumes which I think people have seen enough of and  which don't really have much impact any more. If we do use them, the trick is to make them relevant to a high schooler - my next move is to photograph my own teens as they leave phone chargers in, computers on, TV on, etc...should have no problem finding those opportunities .  I've finished my staff training outline and started the Power Point I will be using for it.  This weekend I break out the C-MORE OA kit and put it to test so I can use it for the staff training days - nothing like the smell of active yeast!  Headed to the aquarium this Friday for some aquarium catch up and work with staff involved in this project. 

Have a great weekend!

This week I've just been trying to pinpoint the reason why my I'm not getting much amplification with the PCR unit on my ESP. The first thing that came to mind was that there was no lucky mascot, so I fixed that by zip-tying a tiny frog to the MFB. His name is Lucky. It worked, but it was short-lived...one PCR reaction long to be exact. I haven't lost all faith in him yet though...Lucky the frog WILL come through in the end. Meanwhile, I'll be running a series of reactions to systematically find out what the deal is.

I was also able to extract DNA from a filter through which I filtered 1 liter of Santa Cruz's finest boardwalk water (thanks to Roman...Wise Roman, not Young Roman). I'm going to test the filter for bacteria today. Hopefully all that sea lion poop will finally be put to good use.

This week for me has been interesting and exciting. I started out with maybe a total of 15 frozen tomopterid eggs and larvae. I chose 8 samples first to try and amplify DNA using PCR. The first and the second gel for that did not turn out so well. None of my samples worked on the spetrometry so we did a spec DNA to see if anything is there to work with and there was none. Plan B into action, I chose 5 more different tomopterid samples. This time we checked with the spec DNA first before actually doing the whole PCR and two samples looked promising. The end result was only that one sample worked and it is currently being sequenced. Most of my samples I could match to live video footage which is also cool.

 Learning lab work is a little tricky ,but its still great to have an opportunity to learn. Plus my lab mentor is fun so we have fun!  

Really happy with the Ysi driver. Only needs a few more modifications and it's all done.

The arm processor is another story. I can finally boot the kernel and my linux choice. Currently I'm trying to run the 'official' sun embedded java interpreter. Not much luck so far, but confident I can get it running soon.

Next week will be building SIAM for the arm board, RXTX libs, and more Ysi coding.

Processed the oxygen sensor test data, read more papers on oxygen sensor test methods and met with people who have experience with oxygen sensors and test measurements. I have been able to get some valuable data from our tests but most importantly I have been learning how to improve the test techniques. Worked on my oxygen sensor evaluation presentation.  Met with the Mate people with some other interns. I enjoyed talking with Joel, Michelle and Kathryn about thier projects.

Next week I will continue to meet with oxygen sensor experts, finish my first draft to review with my mentors and perhaps start on the ESP project.

Hope to continue my conversation with Michelle about her rain forest biology experience. Also looking forward to seeing what Joel discovers in the chl a database. Meeting with Young women in science on Tuesday.

Starting to feel like the end of the internship is coming too soon. I am really enjoying the internship experience and I am learning a lot.

So I have gotten remote control of the boat's rudder working. I also managed to break the circuit board that drives the propeller by frying a couple of passive elements on there. I'm hopeful we can repair it, but I have a similar board that I can use to develop while we figure out a replacement. It only provides 1/3 of the power the board I broke had, but that's not an issue for development as long as it can turn the motor.

I have also found a couple of bugs with some software in my development toolchain and I'm working with the developer to resolve these issues and improve the software as a whole.

Next week I'm going to resolve the motor driver board issue and finish integration with the propeller with the replacement board I have. I'm hopeful I can fix the last rudder issue on Monday and start initial work on the waypoint guidance. Tuesday I'll go up to campus to work with my lab group to determine what can be done with the propeller driver board and fix or replace it.

This week flew by!  This Monday I started working through qPCR primer/probe design-- unfortunately the biliphytes are SUPER diverse-- which made the design process pretty difficult.  Also-- the majority of the biliphyte sequences that have been created are about 700 bp long and contain two areas of high variability.  Thanks to some more ARB lessons from Chris Preston, and a good switch to SYBR green from Taqman-- the primers were designed.  I ended up creating a few different options to try to figure out what is best; it ended up being impossible to hit all the biliphytes with one primer set.

 I will be doing some qPCR runs just to figure out what is working etc. etc.  Next week I am growing up my plasmids to get ready to make a good standard curve for qPCR. 

Beyond the realm of the lab: I ran the wharf to wharf race today... tons of fun!  Super crowded though...

I finally sent out my teacher surveys and started getting some valuable feedback for my HAB page.  The EARTH teachers have been somewhat more responsive than some of the other people I was trying to get a hold of, so it's been great hearing some of their input.  I also met with some of the tech guys to talk more about the design and content of the webpage as well as Raphe who is the expert on HABs.  Raphe does a lot of the data collecting for the Santa Cruz Wharf, so hopefully we'll be able to use some of his real-time updates and link that with satellite images of chlorophyll concentrations and SST.  Jason was also another researcher I started corresponding with this week.  He's in charge of all the data in Monterey Bay, so it's been helpful hearing his input too.

This next week I'm going to be writing a brief report on the history of HABs in Monterey and the different types of red tides that have been identified in this area.  This will be the introductory content that'll be up on the webpage, along with a few helpful links to phytoplankton identification guides.  I also have to research a couple of case studies the teachers can work through with their students and maybe a few tutorials on how to read/ make graphs with the data.  It's going to be a busy busy week!

This week I was in contact with a company that handles the 3D printing for my project trying to get some new pelton wheels in for testing. Hopefully the new wheels will be in next week.

The orifice testing continues, I was able to collect more data this week that supported the theory that higher flow rates could be achieved (over steel orifices) by using sapphire orifice inserts to create a water jet. It is my hope that by combining the sapphire orifices with the newly designed pelton wheels I will be able to achieve a substantial increase in the efficiency of the system. I calculated the ideal flow rates for the orifice diameters I am using so I have something to aim for and to compare my data with. At this point though, the data I have collected is not as close enough to the ideal data curves as I would like so hopefully the new wheel will give me the boost I need.

As the program begins to wind down I am stepping back, in an effort to outline the part of this wave energy project that I will be talking about and writing my paper on. This is the most difficult task in front of me right now. Because this is a fairly broad project I have decided to focus mainly on orifice optimization and pelton wheel design/optimization (to a point.) There is plenty to do still, next week I would like to test the new wheel (if it arrives) and collect more data so that I can compare it to my calculated data.

Great week working with Francisco.  He doesn't answer questions with answers.  Instead, he reframes the original question making my problem no longer relevant and giving me the freedom/ responsibility (AP) to choose the best method.  Its awesome.

I put some biological variables into Matlab from the data base.  Now I can look at Carbon/ volume of many different species and groups of species for the study area and possibly correlate these with larger processes.

Also, I'm now looking at line 67, from Moss Landing out around 150 km into the Bay, for some distance from shore revalations.

I got the transformation on ESB working. Since all this time I was working on static configuration, Kevin decided to switch to the JBI configuration which is the most appropriate way to do future work on service mix. After a little digging in the book and testing the ESB, I got NMR working. By the end of the weekend I was stuck with the transformation because the code looks fine but somehow the transformation didn't work.

Today morning Kevin emailed with his latest updates on the build.xml for service assembly and he got it working. Excellent!! This week I will work on security, both authentication and authorization issues on ESB.

I am very excited about SCUBA... hurrayyyy... I will be in the ocean very soon   

The goal for last week was to implement a checkbox system where you can select which jellies you want to see on the map; for example, if I only wanted to see moon jellies, I would click the "moon jelly" box and then only the moon jellies would show up on the map of all jelly sightings.  I'm also working on porting the makers over to a system called Marker Manager, which handles google maps that have >10,000 markers on them (we hope to have that many sightings in the future!).

Last week what I DID get accomplished was I figured out how to easily change the icon associated with each species, such that it can be edited in the database rather than hand-edited in the HTML somewhere.  

Picture-uploading functionality coming soon!

This past week was spent troubleshooting my problems from last week--I used a new protocol for protein purification, but there was not fluorescent protein to be extracted from my cells. I did another digest of the PCR product, ligation into the pQE vector, and transformed that into chemically competent cells. Again, these didn't fluoresce when I plated them. SO, it was time to find out whether or not these clones had the vector with my insert in them. I digested all old mini-preps from the pBAD vector to cut out my insert. I then ran these on a gel, which at first didnt work, but on friday I saw that there were indeed inserts in the mini prep samples, but still not being expressed! I also picked 32 new colonies with the pQE vectors for mini-prep. I sequenced those and analyzed the sequences. While doing this I learned that this FP has two varieties: one with a tyrosine in the chromophore and one with a cystine in the chromophore. No FPs without the tyrosine have ever been known to fluoresce. So it seems that when I do PCR only the cystine variation is being amplified and transformed. So next step is to find out how to amplify the tyrosine variation rather than the cystine one..