This week

Unfortunately, after a lot of work learning the DISTANCE program, we have decided not to use this software.  Oh well, these things happen, maybe knowing about line transect theory will come in useful at some point in my future career!  We are going to use PRIMER for the statistics instead so I've now started reading the manuals for the software and Linda is going to give me an introduction tomorrow.  I've also been learning about similarity indexes so I understand the theory behind the tests we will be running.

My data from iVARS has been exported so I've been wading through massive excel spreadsheets a lot this week - rearranging and sorting the data, fixing problems, adding CTD data from the MARS site and producing graphs of the abundance of the most dominant taxa for each transect.  I've also started pulling out some good images to use for my presentation.

Next week

I am hoping to get all my analyses finished in a week.  This will include getting my head around PRIMER!  We hope to construct multidimensional scaling (MDS) plots from Bray-Curtis similarity indexes and link these with the environmental data from the MARS CTD probe.  If this is all finished, leaving me a week for final write up, I'll be very happy!

Going well/ not going well

I really enjoy doing stats so I'm quite happy learning these new methods and I'm really looking forward to having a go at PRIMER tomorrow, it's a program I've read about in a lot of papers but have never used.  It's very satisfying to be finally pulling some results and graphs out of the project and I'm excited to see what they come out like!  Although it's being to dawn on me that I'll actually be going home soon which isn't such good news! 

This week I faced the fact that the sequences derived from my clone library were not what we were hoping for.  In an effort to trouble shoot I have been trying different combinations of the 5 primers I designed for PCR.  My gels are showing non-specific amplification and so I will need to perform a gel extraction to isolate my targeted idiA gene.  On a lighter note, I spent Tuesday at UCSC with my mentor to attend a site visit for representatives from the Moore Foundation and MEGAMAR.  It was nice to learn about different projects currently being funded and I got to chat with more graduate students, post-doc's, and other people associated in this field.

Next week is the last full week!   I am really hoping to successfully clone my idiA gene because although 'bad' data is still data, it is much more satisfying to leave a project having achieved what I set out to do. 

Going well/ not going well Things aren't exactly on the schedule I prefer, but I still have faith in this project!

This week

• I spent this week taking spectra of H2S saturated 0.5M NaCl and nanopure water solutions at an acidic and basic pH
• I had to figure out how long to saturate the solutions to get a desired pH of about 4 (took about 4 minutes) and how many drops of 10M NaOH to add to raise the pH to a desired basic value of 10 (22 syringe drops)
• Today I will run these samples once more to make sure everything is correct. Because later today and tomorrow I will be sealing the septum vials and adding base through a syringe
• The total sulfide of each solution will remain constant and ZnS will be precipitated out of solution using ZnCl2, dried and weighed to determine the concentration of total sulfide. I'll then do some math to figure out the concentration ratio of [HS-]/[H2S] at a given pH and thus hopefully be able to determine the pH of pore water from the molar Raman cross section

Next week

• sifting through data, calculations, and organizing my presentation and paper
• this is the last full week so I hope to have all the data collected by early next week so that I can just work on processing and putting last minute things together

Going well/not going well

• Time is running out and I'm hoping the experiments go well...

This week

I've spent most of this week trying to organize the pieces for a last VoiceThread (one that allows all the people involved with this project to explain what they have done). I also am putting together a generic science introductory VoiceThread using clips from EITS. I've recruited teachers from Oregon, California, North Carolina, Missouri (me) to add a discussion element for our students. My presentation is next Tuesday so I have started working on the final paper and then will put it together for a presentation. I also continue to add resources to the wiki and am encouraging teachers who have used EITS lessons to upload their materials.

Next week

My final week. Presentation on Tuesday and tying up lots of loose ends. 

Going well/not so well/thanks

I've enjoyed riding in two different van pools and my time with a friend's family. My family left yesterday so that would be in the not so well category.  Time is becoming scarce.  Linda is fast becoming my idol with all the clips she's put together as supplementary information. Thanks also to Van Pool #5 and #2 for the pickups and drop offs. Danelle, as always, has provided lots of valuable insights. Thanks also to Erika and Gregor. And, of course, George is beyond value. Thanks to you all!

This week
This weeks been a lot of fun watching the processes in the development of my clip*. * The machine shop has put a lot of time into my clip this week, and it will probably be done by the end of the week.  I have continued fine tuning my presentation/paper which are for the most part complete.

Next week

Finishing up my paper/presentation is my priority.  The development of a locking mechanism for my clip will be my final project for my clip next week.

 Going well/not so well

All is good! I am looking foward to seeing the final proof of my clip this coming week.

This Week:
This week i decided to write my update more like the science kids. I began the week by discovering that I had routed my PCB with the wrong connector and as such I spent Tuesday morning reworking my layout. However, I am not completely finished with circuit design and layout and as of 2pm today, my board was submitted for fabrication. My mentor also ordered the parts for my board on Monday and both the board and parts are expected to arrive by next Tuesday.
Other than that, I have spent the entirety of the week working on my report. Its slow. And tedious.

Next Week:
I will either be populating my PCB myself once it comes in or I will be having on of the ET's do it because they will do a better job faster. Once that is completed, I will begin testing on my analog circuits to make sure they are working. In the time between I will be finishing my report in all its glory.

Going Well/Not Going Well:
Turns out the test tank is 53V as compared to ground. I got to watch the FOCE CO2 apparatus dissolve in salt water which was exciting.

This week:

• I have done a RS232 connection on the development kit to be able to use a real instrument in the video.
• I wrote a good part of the final report.
• I tried to integrate the SID Interpreter (Sensor Interface Desctiption) from 52°North but it is not finished yet and they have to repare the bugs. I will use for now a Java API for SensorML that I have done, but this should be replaced in the future with the interpreter from 52°North.

Next week:

• Make the final demo and edit the video.
• Finishing to write the report and the presentation.

All is going well. Time is running out and in 2 weeks we will missing this time here ...

This Week

• Read about how HMM's are used to detect a feature of interest for the AUV.
• Brushing up C++.
• Started messing around with the code of TREX a little.

Next Week

• Try to implement a reactor which can handle observations from a HMM with more then two states.
• Learn more about TREX internals and the role of HMM in detecting the feature of interest for an AUV.

Going Well/Not Going Well
Everything seems to be fine.

This Week

Continued to work with Paul McGill on the mechanical process of the Sedimentation Event Sensor's carousel. The locations of each station have been set and the testing on the time vs speed vs torque has been completed. An updated power budget should soon be completed.
NOw that the mechanical aspects are complete, work on the software end can now resume. Rich Henthorn is once again my primary mentor, and we have been developing the behaviors that will guide the carousel autonomously.

Next Week

Continue developing the program to drive the SES. Also, continue working on my research paper and my presentation

Going well/ not so well
Need more time. A meeting with the SES team has determined that the project will be put on hold. Can i come back for a thanksgiving or christmas internship?

This Week

•  Emailed the first draft of the AUV website to everyone involved.
• Created five new pages for the AUV mission website.
• Edited 28 pages worth of web page material from both the CANON and AUV websites
• Written 14 pages for my intern project paper
• started on the presentation
• Fixed the mapping AUV web pages

Next Week

• Edit both sites entirely
• get feedback from scientists and work with that
• Finish the internship paper
• Finish the internship presentation

Going well/ not going well

I am on track with respect to completing both the CANON and AUV websites.

This week:

Lots of sequences...

All the sequencing I did in the last two weeks are back, so I have been analyzing them to see what my isolates are. A couple very interesting ones that has no cultured representative.

 Also, I will send Alex a short report on one of the contaminated cultures in the culture collection.

Plus, working on my lab presentation next Monday...

Next Week:

Lab presentation and final report.

Well/Not well:

All well!

This week:
I have been compiling information about the various components of my project into a powerpoint, and after meeting with my mentor on Monday we discussed what to include and what not to include in the presentation. I made a rough draft of the slides I want to present. I will be going over some of the previous work that has been done on the subject. I hope to show that assigning a bulk diffusivity may be appropriate in some cases, but really there should be a time-varying diffusivity. From my model results, I have calculated diffusivity, and it's been interesting to see how this compares with some of the values reported elsewhere. Previously I had thought my data wasn't accurate and I was going to use values from other studies, but after doing some smoothing and averaging, I'm happy with the results. I can use these diffusivities with the nitrate gradients to compute nitrate fluxes. Basically I have spent much of this week putting together the information for my presentation and finalizing decisions on which figures to include.

Next week:
Finish the presentation and continue on my report. I'm concerned about the amount of information I have and fitting it into 12 minutes. My work here has existed in parts--looking at GOTM, calculating gradients in AUV nitrate measurements, and resolving temporal and spatial scales from these exercises to inform sampling strategies. I'm a little concerned about thoroughly describing each of these components and fitting in descriptions of instrumentation. It will be quite challenging.

 Going well/not going well:

Things are going well! 

This week:

 I have been working in parallel on both techniques to solve the path planning problem. The main tools to run those path planners are mainly done, so now it comes the time to test them with different scenarios and conditions and fine tune whatever that doesn't give the expected results. I am using different sources of data, satellite data for fluorescence, model outputs for currents fields, ... it seems everything is starting to come together so I can see if my development is actually working.

Next week:

I should finish the details of the code, run it the different scenarios, save results.  Meanwhile, I should write the report and prepare the presentation too.

Well / Not well

Running out of time, but everything is going well.

This week:
Brian is back! For now. My mentor has loads of projects to deal with, but through our meeting at the beginning of the week I was able to understand a little more Java. This allowed me to do the following stuff:

+ All secondary images coming up in mini gallery on Main Concept Page now!
+ All titles based on ConceptName have been added as well
+ Linked all the jumps on Main Concept page
+ Linked jump images on Search Results
+ Added all header and footer includes

There are a few more things I will be trying to add in the Java today. If I can't do it I will have to wait until the last week I am here to sit down with Brian and sift through it all at once. Which is fine because he's so smart! But I'm a little anxious!

Next week:

• Mock-up a whole Concept page for my presentation, with the help of VARS team!
• Start my presentation and finish it.
• Finish my report (this may not happen until the last week)
• HOPEFULLY receive T-shirts, if quick, if not, then we should receive them at the beginning of the last week.

Going well/not going well:

Pretty much going well, I just want to finish things but there are some things I cannot do without Brian so I have to be patient for the last week.

This week:

Waiting for the circulation system to be built

Revising protocols and experimental design

Next Week:

Conducting experiments

Writing report and compiling a power-point presentation

Concerns:

Webpage has been neglected, will not have time to finish both experiment and webpage

Concentrating on these task so close to the end will also give me very little time to prepare a good quality paper and presentation

Izzy's update

This week:

1) Finished Report with exception of two figures
2) Have a good hypothesis for why dykes are point focussing at depth
3) Looked at volumes of flows and lengths of seismic swarms to work out an
approximate eruption rate and found it to be comprable to Hawaiian fissure
eruptions (this is exciting!)

Next Week:

1) Finish final two figures
2) Put together presentation

Ship Update:

We completed our first dive yesterday. We'd initially been worries that we
were collecting only the thick manganese crusts that cover the rocks and not
the rocks themselves but when they came on deck we found that actually all
but 2 of the samples had rock cores, so that was good. The second dive
hasn't happened yet today because the weather is too bad. It's unclear
wether it will clear up later today allowing the dive to start then or not
so fingers crossed. We've sent in the first blog update I think and it even
has a bit from me in it.

Izzy