Over the course of this week I have used other taxonomic materials and more lab photos to add the described cydippids into my key. In it's current state it is capable of resolving pretty much all described and undescribed genera of cydippids. As the cydippids form a major component of the diversity of the phylum ctenophora, I have made good progress toward a key for the whole phylum. My remaining task is to incorporate the other major group (the lobates) as well as a few oddballs. This second stage is likely to be slower due to the high number of species already within the key, and fitting the more derived species into the framework built for cydippids.
The result would be a complete key for all ctenophores we currently are aware of and would be available in two versions. The first version would be a full version with all described and undescribed species (that we have reasonable detail about) and would only be available to MBARI. The second version would include only described species (to not steal our thunder so to speak) and would be freely available on the web.
So my main task over the coming week is finding ways to integrate these derived species (like cestids and benthic ctenophores) into the framework, and scoring them.

For the record todays kayaking was amazing. Firstly we saw a relatively long (8cm or so) chain of Thalia democratica (a pelagic tunicate), which is the first time I've ever seen a salp (particularly cool as they are the fastest growing animals, increasing up to 20% in length per hour!). Also being surrounded by sea nettles like that, and getting to see them in the wild for the first time really is a high point of the internship so far for me.

I worked on the rest of the urchin specimens through out the week.cleaning, dissecting, bleaching, drying, mounting on epoxy and finally grinding took lot of time. but final results were amazing. I have already finished the specimens from last cruise. but I have some extra urchins from previous experiments. so, I'll  continue the same procedure over the next week too. hope to finish all the specimens by the end of next week.

kayaking was really great. it's my first time, I enjoyed a lot. wow, Otters, I like  them lot.

This week saw some steps forward as well as a few steps backwards. On Monday I designed a new valve block for our sensor integration in order to include a standard sample of CO2 to be run through our system while it is deployed. Our original valve block has only four valves, so I designed a new block that had five. On Tuesday morning, after finishing the new design, we realized that the new valves would not work with our controls, therefore we had to resort to our older valve system that is used for our moorings. This block is very large, however by taking a little off from all sides of the block, I am confident the older valve system will work. Because this valve block is designed with only four valves, we have decided the fifth valve will be separate and will come directly off of the standard. In addition to designing this new layout, we will need an additional Chamber Controller board because we have run out of I/O bits. Also on Tuesday Gernot Freiderich returned to our lab, so he has provided us with insight into what needs to be done to incorporate the equilibrator as well as the CO2 standard, which is much larger then the one that we had originally thought we would be using. On Wednesday I designed a new mounting board for the duel Chamber Controller, and adjusted the entire layout of the dry box to incorporate the larger CO2 standard. Today I will be working on attaching the plumbing from the valve block to the internal instruments. This should take me at least a day.

Next week: Will hopefully begin wiring all of the components together, that is if our design doesn't change once again. Once this has been completed, or better yet, while this is being completed our communications with the Wave Glider Comms. and Controls will hopefully be established. If all of this is done within the next two weeks, then I will have the final week to make sure the system runs properly before our presentations on the 17th. My fingers are crossed....which makes it hard to type.

This week I finished the lab work and most of the sequence editing for the two mitochondrial genes I am looking at. Today and next week I will be learning some computer programs to analyze the sequences and build haplotype networks. This week I also got some preliminary results for two nuclear genes that look promising. Next week I will look at those sequences to see if there are any polymorphic loci (because we need some variation to compare sequences) and re-design primers if necessary. If that all works out I will run the PCRs and sequencing reactions for those genes on the remaining samples.

By the end of the day I'll have hopefully finished off the videos from La Jolla, the most complex and most stunning of the SoCal canyons, the topography is amazing! This afternoon Lonny is also going to show me VARS for images and some of the mosaicing tools that he uses, this was initially what my project was going to consist of so it will be interesting to see how all of this works. When Charlie gets back from Scotland we're going to discuss the way forward with all my data and whether or not looking at the PV slope dives would be useful for comparisons.

Next week will be mostly data manipulation and habitat classification based upon video observations and bathymetry data, that's assuming I can get benthic terrain modeler installed on my computer.

So I do believe I have been productive this week- although it is hard to remember the week sometimes. I have finished all of the measuring and am working with Linda on the stats and number crunching. By the end of today I will be set up to just finish a few things and then start on the graph making next week, which Paul will be helping me with since excel has been thumbing its nose at me lately. As soon as the graphs are made and interpreted, I will be starting on the paper..... which will be interesting.

Yesterdays kayaking and aquarium adventure was the high point of the week; sea otters, Jelly fishes, seahorses, sunshine and fog, all in one day! The BBQ on Wednesday went off well, with lots of work from everyone. We had so much fun we've decided to have a Cookie break on Monday. 

My projects have been going really well, and are very interesting. I've plotted temperature vs. pH data from 13 transects stations along the West coast from Canada to Mexico. I then compared that relationship (equation) to the daily averaged relationship between temperature and pH at a mooring in Northern Monterey Bay over a 2 month period. Surprisingly the relationship between Temperature and pH didn't vary as much over distance as it does over time.

Next week I will spend some time with those equations, and trying to apply one equation to satellite temperature to predict pH. I'll also start applying this technology to CeNCOOS and helping shellfish farmers.

This week I have been importing a whole heap of results which have been spat out from the batch classifier. There are still lots of misclassifications but there have been a lot of bugs both within the files which were processed and the classifier itself.

A lot of these problems are being exposed by the amount of visual noise the EITS dataset contains which can not really be altered as they are THE results. It is a very interesting learning curve however to observe what the classifier categorizes as noise. The results from each day show varying levels of noise which is ultimately dependent on the size of file (clip duration).

Unfortunately, there hasn't been a sniff of any squid interactions but it is also interesting to ask why there havn't been any. At the same time, it is also important to ask whether this is viable..how accurate is the machine?

On a light note, there have been some very cool things in the data set which aren't directly relevant to my current project but are interesting nevertheless!Hope to may be share some of the cool clips from the data set with everyone during the seminar!

This busy week, so many stuff went through
Monday: we have to do some shopping for Wednesday BBQ in Costco and Safeway, and design the intern T-shirt for sale on Wednesday, too. After that, I have been at work for the rest of day.
Tuesday: I was at work for the whole day, talked with mentor Gene for around 2 hours and planning the installation of all hardware for McStar

Wednesday: I was at work for the whole day. At Noon time, we serve BBQ for MBARI employees and show our design of T-shirt. Have a meeting with Gene and Wayne, work on the McStar together. Work on Mechanical Engineering design and electrical engineering stuff, that is cool.

Thursday: George took us to MBA before noon and kayaking in the afternoon, be back to MBARI after 3:30pm. Exciting adventure

Next week:
Update all the documents
Have meetings with Mentors and plan the final experiment preparation on Wednesday.
Start to work on the final report

Apologies for the delay.

This week was frustratingly unproductive. I spent most of it working on a journal submission about the algorithms I've been working on. Discovered a couple of problems with it that I need to try to fix. I've also been working with Sergey to try and integrate my gradient-detection results with his LCS analysis of surface currents to see if we find good correlations between the fronts detected by his method and the ones detected by mine.

 The coming week will primarily involve more of this.

Last week I wrapped up the bulk of my project concerning CO2 replacement in CH4 hydrates and am now trying to get as much out of the data as possible, which is always a tricky game but I'm feeling good about what I've produced so far. The results I've gathered disprove a recently published paper, so it's been fun working on a complete and effective counterargument. I've also spent a lot of time with Peter Walz designing and building various instruments in shop for our cruise in two weeks, which is still my favorite part of this job. Everyone has been incredibly patient and supportive of my fumbling around with tools and machines I've never used before, and I am so grateful for that. It's been a steep learning curve but a fun ride. This week I plan to start my last project, looking at sulfide hydrates, which will serve as a foundation for the work I will be doing on the Flyer in two weeks. In addition, I have to prepare my talk for next week and begin my final report! Looking forward to a busy week ahead.

I know I'm really late on this one, sorry everyone! Last week I wrote my first ever Javascript and this week I finally got it working! It allows the user to automatically enlarge a table row to read the full description for a concept in the comparison table (this will all make sense in my presentation - that's the thing with explaining web development and programming, it's much easier with visuals!). I still had an unknown problem with the page that allows the user to browse the VARS tree, which I worked on this week as well (and apparently fixed...I don't quite know how). I fixed a couple of bugs in the searching and made some layout changes that the video lab suggested. I really enjoyed kayaking, and didn't fall out of the boat, which was a first for me! This week I am working on having the DSG generate sets of "representative" images for higher order concepts (such as kingdoms and phyla) so that there are fewer pages with "no image available." These sets are randomized, so for high order concepts with lots of options (such as Eukaryota), the generated slideshow will be very different every time you refresh the page. I've also been taking lots of screenshots for my presentation for pages that take too long to load so I won't have to wait on them while presenting. Brian's been doing a lot of cleaning up and condensing the code and working on the data artifacts (graphs, etc.) which I hope to be able to integrate into my comparison table before I leave.

This week was a whirlwind! With the BBQ and the MBA/kayak tour it was a bit difficult to focus, but I managed to get a decent amount of work done nonetheless. I got some slides back from the histology lab at CHOMP, only certain sections of the trailing tentacle of Atolla, and began trying to identify the cell types and annotate the internal anatomy. I also took some photographs of the Atolla eggs collected a few weeks earlier. There are a few eggs showing potential for development so stay tuned. Hopefully I will get more slides back next week, as I am incredibly anxious to compare the internal structure of the trailing tentacle with a marginal tentacle. Hope you had a good weekend!