This week I designed an additional mounting board fro the dry box lid, which will allow for easy access and maintenance of the A to D board and the Chamber Controller. Included in this process was the overlapping of these two circuit boards using stand offs and spacers, which proved to be challenging due to limited space. I also attached a pump to the mounting board as well as the Oasis 4 board which is the most critical component of the integration process. With these main components attached (the Li-cor, Oasis 4 board, pump, A to D, Chamber Controller) it appears that we will have sufficient space for the remainder of our needed components. On Monday Francisco and I also met with a Liquid Robotics employee, Luke (a former MBARI employee), and discussed potential fusion of our OA sensor package with future Liquid Robotics Wave Glider deployments, particularly a mission that entails one Wave Glider traveling from the US to Australia and the another from the US to Japan. It would be extremely exciting if our package were a part of that mission, which is set to start in September!  Today I will begin wiring the parts together by following the OA sensor suite that was designed for the OA moorings. Yesterday I went on the MARTIN and helped cast a CTD for sampling of chlorophyll, O2, nutrients and POM at five different locations within Monterey Bay. During this process I filtered the samples collected by the CTD while the ship moved to different sampling locations, which proved to be tricky due to swells and brief gusts of wind. All in all the cruise was super fun and I learned a lot! This afternoon I will be testing some of the chlorophyll samples with a fluorometer down in the Rad Lab.

Next Week: I plan to complete the wiring and will hopefully be able to mount a soda lime (to strip the CO2 from air within the drybox), a dryer (to remove moisture from the dry box), a CO2 sample, and the critical air filter block. Once these are installed and wired, I will need to install bulkheads to the top of the lid, which will be used to link our internal plumbing and wiring from inside the dry box to our external surface and subsurface sensors.

busy week. I managed use the polishing equipment at mosslanding marine laboratories.It made me easy and quick. managed to complete more specimens. Though out the week I was preparing specimens for polishing (dissecting, beaching and drying). now i'm on the process of photographing and counting bands in urchin plates.also trying to induce spawing of urchins using thermal stress method.

next week i'm planning to work on rest of the specimens. also hope to start writing.

Most of this week I spent on the computer program Codon Code Aligner editing sequences that were run last week, which are mostly looking good, although there were a few sloppy sequences for which I had to run new sequencing reactions with an internal primer. I also finished DNA extractions on the samples I have to work with. Today I am completing two plates of sequencing reactions to run in Lola tonight.

Earlier this week Shannon and I designed some Tevnia-specific primers for a heat shock protein gene from a sequence she found in BLAST. We also ordered one additional nuclear gene primer, so for the rest of the day and next week I will be doing PCR and hoping that I can get results for some nuclear loci. We also got more cytB primer, so I can finish the PCRs for the remaining samples for that gene. There will also be much more sequence editing for me to enjoy.

By the end of the day I will have hopefully finished the tapes from Mugu Submarine Canyon, only La Jolla left to go! Once that is done I'll have a nice dataset to play around with. During the process of reviewing the dives I have been classifying areas sampled into various types, this will hopefully allow me to factor in at least some of the heterogenity that is seen within submarine canyons when I am doing my analysis. I've also sorted out my ArcGIS maps so that I can easily generate profiles of the canyon at various sites along the axis.

Next week I'll hopefully finish off La Jolla, and address any ID issues that still remain. Then I can start playing around with my dataset and determine what environmental factors are affecting the faunal composition of the canyons.

Harry Potter tonight! {~8-D) 

This week I've been working on validation. Turns out my previous approach was a total dud, so now I'm working on something new. I've also been working on geolocating my results. Currently they're just based on distance of the AUV track. Now I need to move them to Lat/Lon and come up with a way of spatially matching different fronts.

This week has been a spotty one, because I was out sick, but an exciting one nonetheless. I have managed to isolate several, possibly fertilized, Atolla eggs from the kreisel in which I had both male and female specimens. I put a few eggs in multiple types of media from plastic to glass with multiple substrates and filtered seawater. So with fingers-crossed I am anxiously awaiting any development of the eggs. As far as the adult Atolla, there are only two specimens still alive and they are looking a bit decrepit. Due to their current state there is not much else on the experimental front that I can do except try to keep them alive for as long as possible, however I have made some interesting observations that will be discussed in my paper and presentation. I am still waiting for my slides to return from the histology lab at CHOMP so that I can get a closer look at the trailing and marginal tentacles. It looks like I will also be running some extractions on some frozen Atolla samples in the near future and looking further into the genetics of these jellies.

Have a lovely weekend and enjoy the final installment of Harry Potter!!

This week has been great! I managed to get the batch classifier up and running and finally get to test how the "man vs machine" contest would pan out. Nothing is conclusive yet, as (like always with science) I had a couple of issues with some of the batch processed data. It turns out there were a few bugs with voting method (the way in which the classifier finally decides on what it classifies) which was causing some errors in the batch results.

Another issue is the rate at which these files are firstly being processed for analysis and secondly the time it takes for the batch classifier to get through one file. So, many hands make light work...I now have another loaner laptop which is essentially doubling the classifying speed as I can run two directories at the same time.

The problem with this is that it needs data to classify, and this is a slow process. I am waiting for enough data to be ready to use so that I can run the batch classifier and leave it to run overnight/over the weekend. My mentor is helping me by setting up more computers to process more files..but this slows down the speed it takes to process one full complete file. Still, time to start writing.

Next week I aim to start writing whilst these files are being classified, the results of which I will put into a spreadsheet and separate them by day. It sounds complex, and it is! I also plan to meet with a Stanford graduate from Hopkins Marine Station on Tuesday to talk squid which I am thoroughly looking forward to!

HP tonight (Sorry guys - forgot my cape) and camping in Big Sur. Recipe for a great weekend. Hope you guys have a good one!

Disection, Purple hair, and Harry Potter.... oh and lots of staring at a computer screen click clicking at the key board- that pretty much sums up my week right there.

This week I have continued measuring the sea cucumbers from dive 232. By the time I am doen I will have over two thousand of them. Today I disected the sampled cucumbers from the last cruise that Ken went on. I discovered mostly females with full gonads which is a good sign of maybe getting results one day, but I won't assume anything now. Next week I will begin some work with the data and statistics. Since most of my mentor team is leaving next week, I pray pray pray, that I understand what I need to do and where to go from there.

The last week has flown by, and I'm not sure where it went!

I wrote up my notes from the workshop, and pulled together some of my research on Ocean Acidification for Heather's talk next week at the Coastal Zone conference. Simply reviewing the workshop notes gave my plenty of food for thought. Monday afternoon Francisco and I met to talk about pH, global circulation, spatial variability, biology, and many more interesting topics. Since then I have been working on comparing temperature versus pH along the wester coast, from Canada to Mexico, and trying to define the relationship between the two and how it varies spatially. 

I've also sent out a survey to the shellfish growers on the West coast to see how pH is affecting the,

Next week I expect to fly past as well, with more work on my spatial variability project, and hopefully more surveys to compile, and exciting things to learn.

For anyone interested next Friday my MLML lab mate is defending her masters thesis on O2, pH and temporal variability in Monterey Bay at 4pm. I will send a follow up email next week. 

This week, not too much have been done, because the programming is still sucked. On Monday, work a little bit on the hardware wiring and test the Bluetooth, battery, and beagleboard. We find the beagleboard which is used is broken for some reasons, we are not sure. So we started to build another board but cost some time. So that makes the field test delayed.
Next week, I turn to my mentor and give a hand to build this new beagleboard, and install in the McStar system, and try to run this system directly , try to fix some bugs. After completed all the stuff, we will plan to do the field test and get some acoustic data for analysis. Plan on Wednesday depends on the software process.
Also, Monday intern meeting, Wednesday intern BBQ, Thursday intern tour to aquarium and maybe Kayaki one day. Look forward to that.

This week has just been more coding, some of it successful and some not so much...Brian has been in meetings a lot this week, so he hasn't been around to help me fix certain things (especially the Browse Tree page, which is no longer working on my computer). I had a very long meeting with the Video Lab group on Tuesday in which they detailed exactly what they want the DSG to be like - "the functionality of google with the layout of the mbari home page." So that is what I'm shooting for. They also found a lot of little bugs and some layout inconsistencies that I have started fixing. I also finished the first draft of the comparison table page and have made it so every search bar in the upper right corner does the same kind of search as the page it's on. Also, if you enter something in the main search page and click one of the top links, it does that action with the keyword (think google - if you enter something and hit "Images," it does an image search).

 This week I will be making the comparison tables update-able (so you can select exactly which groups to compare), working on making all search boxes autocomplete, and working on making the browseable tree collapsible, once I get it loading again. I'll also be polishing the layout on several pages.