This week

I finished annotating all my Rover images.  Linda and I had a few sessions going through everything I had done, checking the species' IDs and any queries I had marked.  She was also able to tell me that the strange purple blob taking up most of the bottom of my last image was an Opisthoteuthidae or Dumbo Octopus - quite unusual to see sitting on the sediment! 

I also completed a literature review of previous methodologies and taught myself about line transect theory.  This will help me to understand the statistics I will be using to analyse my data.  I installed the computer program DISTANCE and have begun to work through the user's manual, ready to make a start on my data once it has been exported from VARS.

Next week

The first step is to use DISTANCE to calculate the densities and abundance of the most dominant species in the area.  I can then compare these with the MARS CTD data and other environmental parameters. 

Going well/ not going well

I'm glad I have the chance to learn about statistical techniques and computer programs I've never used before.  I am beginning to get a little worried about the amount I have to learn with such a small time period left, although I suppose that is quite normal at this stage in the internship!

This  Week:

1. Finished Report Introduction and Methodology
2. Mapped in flows for North Cleft
3. Calculated Volumes for all North Cleft and CoAxial flows
4. Failed to calculate depth the NGorda dyke wold need to be to not fissure the surface but have emailed a few people so will hopefully get some help with this
5. Formulated several dike point focusing hypotheses:

• Convection within the dike causes and irregular surface topography which mean that as the dike propergates the crack forming is wider above these convection cells and hence penetrates further upwards through the crust and is thus more likely to intersect the surface
• That convection withing the dike allows cooler and hotter areas to form hence lavas may solidify non-uniformly along the length of the crack meaning that the dyke is split into a number of dike 'fingers' which reach the surface      
• The magma body feeding the dike could also undergo similar processes which mean that as a dike is first initiated it is non-uniform width along it's length

6. Begun to look at validity of these hypotheses. Already the third one seems unlikely as very thin dikes are rarely observed suggesting that most of the dyke must (initially at least) have been over 0.5m in diameter. 

Next Week:

1. Write results and some of discussion section for report
2. Continue to look at hypotheses and maybe formulate others (looking for geochemical differences etc)
3. Look at differences between volumes/geochemistry etc for pillowed mounds and shield volcanoes, could shields be an extreme form of a point focused fissure? If so why does this happen with larger volume eruptions?
4. Load Western Flyer for cruise
5. Go on Cruise (to Taney Seamounts)

Going well/not well:

NO TIME!

This week

I finished the EITS wiki (http://eits.pbworks.com/). The hope is that this will act as a discussion board for lessons tried from the EARTH lessons ([www.mbari.org/earth]) as well as examples of student work and lesson adaptations. I invited past EARTH educators to the site and will also link it to the EARTH Facebook page. The more participants the better so I encourage anyone with access to educators to spread the word (K-community college). I also am working on two Voicethreads. One allows all the players in the latest EITS deployment to share their reason for being involved and what they hope to learn. The other will compare the EITS camera with a similar deep sea device from Dr. Justin Marshall's lab at the University of Queensland.

I enjoyed speaking with the group of girl scouts along with Izzy, Sara, Hana and Roman. Dijanna Figueroa's talk was interesting especially compared to the modified talk she gave the girl scouts later in the day. There is always something to learn from how people adapt their talks for different audiences. 

Danelle and I met to go over "best practices" of Voicethread. At the Wed morning meeting, Erika shared possible plans for a redeployment of EITS in late 2011 (possible grant funding).

 Next week

Believe it or not I will need to start/finalize my paper and presentation for August 10 (I much prefered when it was nine weeks to the end as opposed to nine days).

Good/Bad/Thanks

I ran into a bit of snag this week with uploading video to Voicethread. Although earlier VT have been compatible with .mov files, the latest watermarked clips from EITS were not (they were too distorted to use). Susan Von Thon worked and succeeded in fixing the problem. THANKS! Also Linda has been adding to the MARS observatory photo gallery to reflect what is seen in these clips. She is also compiling short video clips of the organisms in color to go along with the black and white footage.  George has passed along many links and ideas to incorporate into EITS dissemination. Danelle has provided lots of feedback and unique questions on the project. Thanks to Larry Bird for giving a great tour to my husband and kids. Thanks also to Patrick Whaling (not only for some interesting stories) but also for trying to get hold of a Tanner crab this fall/winter to use in class.  Thank you all.

This Week:

• I finished the Layout process of my circuit board
• I held a design review for my schematics a little later in my design process than I likely should have but all is well and i shouldn't need to make any changes
• I calculated my PCB's power requirements to be about 0.7 Watts without the use of the microcontroller
• I began work on my paper

Next Week:

• Create prototypes for all circuits that I have parts for so I can take pictures of O-Scope graphs for my paper
• Continue checking suggestions made at my design review
• Submit my board layout to a fab house
• Order parts for my board

Going Well/Not Going Well:

• Everything is good. Knowing about needing images of my prototypes would have been useful before i took them apart but no use crying over it.

This Week:

I finished the Java API for the automatic discovery and data publishing
Tuesday I made the last demo and I will prepare a video for the OGC community and instrument manufacturers with the same demo.
I also work on the final paper.

Next Week:

Continue writing the final report.
I will refine some components of the project.

Going Well/Not Going Well:

Everything is good. I will need to see how I can make the video recording of the demo and maybe Linda can help me with this.

This Week

• Finished the visualization of future projection of a plan.
• Finished the visualization of constraints in a plan.

Next Week

• Study the use of Hidden Markov Model (HMM) to help enable the AUV to adapt its behavior based on feature
  detection.
• Look into TREX in more detail.

Going Well/Not Going Well
Social Security Number still hanging

Well, I just wrote out my update but confluence logged me out and lost all of it so its going to be short this week...

THIS WEEK I had colonies and created a cloning library.  I went to UCSC to meet the Zehr lab and carry out a DNA extraction. While waiting for the sequences to be sent back to me from Berkley, I have been on puck patrol and switching out coils on the MFB2.

NEXT WEEK I will be analyzing my sequences on a phylogenetic tree and testing different assays for my idiA gene.  I will also join my mentor for a Moore Foundation conference to learn what fellow scientists are currently working on and what upcoming projects will be.

 ALL is well

This Week

• Thorough editing of both AUV and CANON websites (editing slideshows, finding higher resolution images, wrapping text around images properly)
• Used apple Quicktime 7 pro to edit an over five minute video into an approximately one minute video. Used Adobe media encoder to convert .mov video clip into an optimized flash video (.flv) that I could put on the website. Thanks to Lonny Lundsten for the training.
• Added web pages related to the AUV in Gulf of Mexico mission, Lau Basin, and ALTEX.
• Started writing the abstract for the final project paper.
• Used track changes feature this week in microsoft word to coordinate with John Ryan and Nancy Barr
• Wrote an entry for the 2010 Summer Internship blog.

Next Week

• Will send out an email containing the first draft of the AUV website.
• Will continue editing both sites.
• Hopefully will have an opportunity to put together a slideshow of images the imaging auv has taken of the seafloor.

Going Well/Not Going Well:

Going pretty well.

This week

• I spent some time setting up more experiments to be run with the laser Raman spectrometer.
• I'm working on preparing high and low pH seawater samples saturated with H2S and observing the respective HS- and H2S species in their Raman spectra.
• I'm working under temperature controlled conditions and will be precipitating HS- out of the solution to determine the concentration both through conventional wet chemistry methods and Raman quantitative analysis.
• My mentors and I are hoping to use these two extreme end points to be able to determine the cross section of where these species exist to determine the pH of pore water that was collected on my cruise.

Next week

• perfecting my technique--I need to make up a 10% seawater solution possibly because adding base to seawater results in too many precipitates that interfere with the results
• meeting with Bill Ussler to discuss my project  

Going well/not going well

•  everything's looking pretty good as of now--I hope next week will be the same

This week:
I have calculated vertical and horizontal derivatives for nitrate using AUV data. I have also interpolated the nitrate data so that it is along isopycnal surfaces. This allows for a better estimate of the horizontal gradients because it tracks lateral mixing along isopycnals. Instead of using a depth-coordinate system, it uses a density-coordinate system. I have continued reading about methods of measuring turbulence. Previously I applied my time-varying eddy diffusivities to an averaged nitrate profile, and now I'm working on ways to apply this to a nitrate profile over the Monterey Bay. While I hope to use the entire data set that spans 40 km and 100 m depth, I think it may be more meaningful to stick with the averages. 

Next week:

I will finish up the initial stages of my powerpoint presentation to show to my mentor and start writing up the final report. I want to thoroughly describe vertical, horizontal, and along-isopycnal nitrate flux, and the dynamic range over which mixing and turbulence change.

 Going well/not going well:

Not enough time left! 

This week

• Created an Image Search Results page with CSS-coded hover image + captions
• Created secondary images gallery on main concepts page
• Got intern shirt orders ready

Next week

• Order t-shirts
• get all java coded up through Brian who's coming back Monday!
• make any last corrections
• then if i have time I will add content for mock-up pages to show all of you!

Going well/not going well

•  it all depends on how much gets done next week since Brian has to leave again the week after!

There was some troubleshooting for the rangefinder that needed to be done and that took up some time in the shop. The modifications for the mounting block were finished at the end of the week. Connecting up all the sensors and instruments filled up the rest of the week. next week everything will be running, hopefully as it should. Also next week the thermocouple machining will begin. The part will be a bit tricky so it could take up a big part of the coming week. other than that everything is going well with the project and things are starting to come together into something recognizable.

This week:

Made a ton of head way on my presentation/write-up.  The material arrived on Wednesday for my clip, and the machine shop begun milling the block down for the bale. One interesting note: the machine shop is experimenting with a new high speed carbide pocket end mill.  This new technology has not been used here at MBARI so it was interesting to see the machinists experimenting with different feed rates and end mill rpms to dial-in the new cutting tools ability.

Next week:

I will continue with my presentation/write-up.  Keep tabs on the clips progress. Plus, depending on the progress of my presentation/write-up if all goes well I will try and design a locking mechanism for my clip just as an added safety feature to ensure that there will not be an accidental release of the clip. 

Everything is going great!

This week:

 I have been working on a new version of my first technique (A* algorithm) to solve the path planning problem. As the whole planning takes too much time to be computed, we have decided to make it in steps. So, instead of planning the best path for the next ten days, we will plan the best path for the next day ten times (which might look similar but it is not). Unfortunately, the pieces of software written so far do not adapt very well to that, so I have started rewriting the code to adapt it to the new situation.

Next week:

I will keep on adapting the code to the new situation and make some tests once it is finished. Hope to start writing the report too.

The time is getting shortened somehow.

This week:

Made a lot of progress!

Two initial isolates:

Got all the 18s (eukaryotic marker gene) and 16s (bacterial/mitochondrial marker gene) sequences back.

Culture collection:

From the qPCR I did previously, there was for sure large amounts of contamination of Ostreococcus in a pure Bathycoccus culture. I took this a step further and performed this week sequencing on this culture. The goal is to identify where the contamination came from by the sequences, because we only have two strains of Ostreococcus in the lab.

 7 more algae isolates:

Performed the whole culturing/cloning protocol to identify these cultures via 18s gene sequencing. Took most of the time because now every step along the whole protocol I have over 100-150 samples to deal with (to reach at least 10x coverage for each isolate). Gets really tedious after a while... HOWEVER, the sequences came back on Friday and hopefully I dont have to do this again.

 Next week:

Now lots of sequences to analyze from above!

Well/Not well:

Tough week but I managed to get through it...

This week:

• Became familiar with the following techniques

              Preparation and analyzing samples using the spectrophotometer

                      Successfully tested the internal pH of a sea urchin

              Preparation of DIC samples

              Experimental design

• Web design:

              Formed an excel database based on the data provided by the members of EPOCA, SOLAS and IMBER.

Not going so well:

• Need to revise the software used to create the database

• Sea urchins respired more than I expected.  This was enough to significantly drop the pH below two treatment levels.

             Thus there is a need to construct a manifold that enables the environment to be continuously flushed with treatment water

Next week:

• Start the main experiment

• Start writing the final paper

• Continue with the website