This week I completed my routine for detecting upwelling fronts using any of temperature, salinity, nitrogen, oxygen, or density. I trained the system on 11 clear data sets and then applied it to all the Dorado data for the last two years. It's not perfect, but it seems to be okay.

 This week will be primarily working on improvements. Improvement #1 is to integrate lat/long data instead of just the distance metric it uses now. Once that is accomplished I will be able to combine Tethys and mooring data with the Dorado data. The eventual goal is to be able to also integrate satellite SST data and ocean current data from the HF radar.

A long week for me. my initial project changed as cruise got canceled. so I have to read lot on my new project as it is quite a new field to me. I'm going age urchins we got with the last cruise. I had to go on several trials. so starting with apical dics, then rotula and finally managed  end up with interambulacral plates with success.wow...improvement....

next week i'm going to start age determination of urchins of different diameters in different depths. I'm excited to see the results.

This week I finally got an answer on how to measure my amperima-peniagone complex cucumbers. I will be including the feeding tentacles and then drawing a line parallel to the body and ending at the posterior end of the cucumber but not on it so not to add extra length with a diagonal line. I have measured over eight hundred and fifty specimens so far, and will have plenty more done by tonight. If I do not finish all one thousand and five hundred tonight, I will continue next week wednesday, and most likely be done by then. My original problem with using the program I was in was never solved, but as I am averaging about ten measurements per every six minutes (when Grant and I are not feeling distracted,I have no problem continuing with the original program. If I have to measure cucumbers from more dives than this one, then I will run screaming to Dan Davis and beg for help. As soon as I am done with measuring Ken and I will most likely have a meeting about how to go about looking at the time lapse photography, and what data I want from the photos. Then I will go from there- I might even get out of the digital cave for a while and see some light

This week I have been going through videos in order to identify the various canyon habitats based on terrain, substrate etc., attempt to standardise the observations, and determine where transit occurs where there is no view of the benthos. It's been pretty time-intensive but I've finished off one canyon so far and have identified a few potential issues that may be reulting in the stark community differences between the two sample sets. Based on this I should hopefully be able to clean up the outline data, which is pretty comprehensive in terms of presence/absence, and then run some more analyses.

Next week; playing around with the data a bit more, roulette, more video analysis, hopefully some nice results...  

Despite only spending three days in lab, this week was a long one. Monday I finished analyzing the last of the standardized gas mixtures in the lab using the Raman system. Based on the temperature-pressure profiles I created last week, I have successfully shown that there is a linear relationship between the gas pressure, temp and raman spectra, as we hoped, but was not guaranteed with imperfect gases.

Tuesday I traveled to Palo Alto with Dr. Brewer to attend an all-day meeting with members of the committee appointed by USGS/NSF/BP to distribute funds for research concerning the Deepwater Horizon spill. This particular meeting was focused on developing a database to organize and archive all data acquired by such research, and was dominated by slick Silicon Valley data management companies giving demos to less than tech-savvy senior scientists. I came along to meet these scientists, spend time with Dr. Brewer in the HOV lane, and eat the delicious food they served us in the former Facebook offices. It was an eye-opening experience into the more corporate side of scientific research, and I'm very glad I went. I also received a wealth of advice about grad school from the few recent graduates also in attendance, which I always appreciate.

 The rest of the week has been spent working continuously with the laser Raman system and finishing off the analysis of sample gases obtained in Barkley Canyon last summer. Next week I'll be headed to the video lab briefly to watch the footage of the hydrates' capture and hopefully draw some conclusions about their dynamic phase change. I'm looking forward to the long weekend and spending as much time outside of the dark laser lab as possible before coming back to work on Wednesday. Have a great weekend everyone!

This week has been one of experimentation and creative thinking. I have been trying to come up with different ways to test the hypothesis that the trailing tentacle of Atolla is used for prey capture, but to little avail. After setting live mysid shrimp loose in one of the kreisels, followed by erratic avoidance responses from the Atolla, I realized I would have to be more invasive. So I removed the largest individual we have in the lab and put it in a pseudokreisel and proceeded to "force feed" the poor unsuspecting Atolla, by taking different potential food items in forceps and applying them to both the trailing and marginal tentacles. I observed some interesting behaviors when I tried to do this with a recently deceased mysid, followed by a recently deceased Gausia. I also tried krill, a Cyclothone (fish) chunk, and simulated marine snow. The results of this venture will be given in my final presentation, so stay tuned! I also discovered that at least one of the Atolla still has the ability for bioluminescence, suggesting that it is able to synthesize all the components it needs to create light, not relying on its diet. In other exciting news, Allison Gong, an expert on medusae (especially compared to myself), will be coming to MBARI today to give me some insight and suggestions for how to proceed with these amazing deep-sea jellies! Maybe she can give me some tips on how to prepare my preserved specimens for histology, which will hopefully be taking place this Friday.

Until Next week...Happy Fourth of July!

Cheers!

This week saw a change of project for me, and an accompanying period of reading. My new project focuses on categorising the all the different unidentified cydippid ctenophores that we have framegrabs for. To do this I began by spending Monday and Tuesday learning in depth the current taxonomy of the ctenophores (fraught with disagreements) and the nomenclature for their anatomy, so I could describe their features.
I am currently in the process of taking every picture we have of unidentified cydippids and assigning them to arbitrary groups. I am particularly fond of a ctenophore called Ctenoceros, and may focus the remainder of my project on this group.
By the end of today I will have categorised the remaining images.

Next week I will meet with my supervisor to go over the groups I have defined and increase my confidence in their boundaries. Following this I shall focus on a particular group (probably Ctenoceros) and attempt to determine how different the group is from other described ctenophore groups, and the morphological characters that define it.

This week I've been making more improvements to the Deep Sea Guide, including adding the image search and browse tree pages. The first shows images that are found by searching with a keyword (like squid), sort of like google images. It also has a list at the bottom saying which species matched the keyword but don't have pictures yet. The browse tree page (which will be up on the internal server by the end of today, hopefully) shows the entire structure of Knowledge Base, down to the phyla if the selected concept is under the "marine organism" heading or just the children of the main root (object) if it's not a marine organism (if this doesn't make sense, take a quick look at the VARS knowledgebase on seaspray and observe the tree structure on the left-hand side). There are still some layout problems with it and it is displaying way too many levels, but I'm working on that and hopefully will have it fixed today. If not, Wednesday should be enough time to have it totally done.

Once I finish browse tree, I will start working on my own page (all these pages have been implemented before - we are just improving them now and putting them on the new Deep Sea Guide, which is in a different programming language). I'm pretty sure we decided that I will be making a page that does comparison tables for groups of organisms, showing their images and other properties that might help determine what species they are looking at in a video (Linda made some of these by hand, but it would be useful to have it on the Deep Sea Guide so it will update itself whenever VARS is changed).

This week I spent some time on the computer editing sequences that were run last week. When my eyes could not take it anymore I returned to the lab and extracted DNA from individuals from a couple sites that I did not yet have samples for, and then did PCR for COI and cytB, the genes that I have already had working. Those results were positive, so I cleaned the products, did the sequencing reactions, and they are now spending time in Lola, the sequencing machine. I also finally got one nuclear gene working for a few samples, which was very exciting. Those samples are currently being sequenced, and the week after next (since my mentor will be gone next week) we will use those sequences to design primers specific for the tubeworm genus Tevnia. The primers I used for this original PCR were designed for a closely related genus, but since nuclear genes are trickier to look at we want to achieve greater specificity. I also tried to draw a picture for the intern t-shirt.

Next week I will complete the COI and cytB PCR's for the remaining DNA samples I already had available and have already extracted. I will also try to complete extractions next week, so that I have DNA for 30 individuals from each site. When I am not in the lab I will be on the computer editing sequences.

Week Three: I continued learning SolidWorks and successfully was able to incorporate the OA sensor suite into one of the Wave Glider dry boxes.  While this was done on a computer, it is uncertain if all the of the parts will truly fit with all of the plumbing and wiring that needs to occur for the system to work. However I now have a blue print and layout that should successfully allow me to place all of our equipment into a payload dry box. This was essentially the first step in my project, so things are heading in the right direction. In addition to working with SolidWorks and successfully designing a layout, my mentor and I drew out a timeline for when we hope certain milestones will take place. By the final week of the internship (if everything goes as planned) I should be able to demonstrate how the different sensors can obtain information, send that information to a satellite and then review that data on a computer.

Next Week: I will create a plexiglass mounting plate that will be used to mount the various sensors to, which will then be mounted to the payload lid. From there I will start to attach all of the pieces (wires and tubing). In addition to this I will start to review the communication system and determine the best way for our sensors to speak to the control and commands of the Wave Glider. This will most likely be one of the most difficult aspects of the project. Another major road block that will have to be resolved asap will be how to incorporate our plumbing and wiring in and out of the wave glider payload box (its a very tight space where many tubes and wires will need to come in and out).

This week has been a bit of a rollercoaster in terms of the success rate of AVED picking up squid. I have been editing the images within the training libraries by condensing the total amount of images the classifier works with and flushing out all the 'crap' image files. This helps the effectiveness of correctly assigning organisms when running the classifier. I am still finely tuning the libraries, testing them under different parameters to see what works and what doesn't. There have been a fair few 'this-doesn't-work' scenarios but hey, trial and error is important in knowing the limitations of a particular system!

I also queried the VARS database to see if there were any relevant pieces of information regarding my squid observations around the EITS site (MARS) in February 2010. I wanted to see if there were any notable clues which indicate their presence. I tried querying for hake aggregations as I believe they may be important in determining where the squid may be lurking and at what time of day. This may help me pick out which chunks of unannotated data from March 2010 I want to process and have squid around the EITS site. There is A LOT of data, so have to choose wisely! There is a high chance there will be no squid interactions, but if there any, I will be a very happy chappy and I can then document their behaviour! This is where the newly calibrated AVED will hopefully churn out some interesting results which may not take place till maybe next week if all runs smoothly.

A long week has passed in a short time. Cannot image the work was running so slowly.
1.Monday, Weekly update meeting and research proposal workshop. I am looking forward to the presentation coming next week, and try to follow some related projects. The rest of day, I work on some reading on Unbutu/Linux system.
2.Tuesday and Wednesday are bad days for me, spent most of time working on Beagleboard installation and booting, but always deal with some issues. Try to step by step, block by block, but always have new problems coming up. End of Wednesday, I can get the beagleboard booting, the monitor can show up the process, the bad side I cannot completely install linux system into the beagleboard. Feel sick.
3.Thursday, have meetings with Wayne and try to figure out the problems lying. Spend around 3 and a half hours (9am-12:30pm), finally we make the beagleboard and linux system running. Luckly. Sorry to be late for the communication with kids. After that, I go back still working on the board, try to make more update and installation. So far, not too far has been done yet. Otherwise, the system in the board is mostly crashed due to my continuous correction. NOT good sign at all.

Next week (another short week), try to make the board working well. Install all the system we need. Try to make this happen.
Work on the hardware update with beagleboard installation, make sure everything can go well before taking it out.
Work on the schedule for the McStar test in the coming week.

TRY TO MAKE A BIG STEP IN THIS SHORT TIME. COME ON!GOOD LUCK!