This week

I've finished annotating my images!  As Linda is still unwell, I'm now putting together a list of questions and directing her towards certain images that she can look at from home.  I've also been preparing for the analyses that will begin as soon as I'm at that point.  I'll be looking at how the abundance of the 5-10 dominant species has changed over time and relating it to environmental data.  Lots of searching through the methods sections of published papers.  I'm also writing up my introduction and methods sections for the final report.

Next week

If Linda is back on Monday, one session with the images should finalise any further issues and ensure we are 100 % happy with the annotations.  Getting stuck into statistics and write up is then the final stage!

Going well/ not going well

Although my mentor doesn't believe me, I haven't gone crazy from 3 weeks annotating and I've really enjoyed it.  I'm looking forward to learning more statistical methods and having a little more free time to follow Alana around and help her with the technical side of the job.   

This Week

Still working on the Acid Ocean Website

Starting a new experiment:

Investigating how well Allocentrotus fragilis (fragile red urchin) controls its internal pH when exposed to future changes in ocean pH.
Learning the following procedures:

                CO2 bubbling and associated calculations to alter pH in treatments

                Spectrophotometric methods for measuring pH. (Samples taken from the Coelom and water)

                The protocol to prepare, store and analyze DIC (Dissolved Inorganic Carbon) samples

Physiological analysis -size, wet wt, dry wt and ash wt

Altering and tweaking the above protocols 

Next Week

Will start 1, 4, and 7 day trials of 4 treatments (8.1, 7.8, 7.3, 6.8) and five replicates.

Continue working on website

The Good

The barbie was superb

                Have received many complements

All is well

This week has been frustrating!  After last week's break through of finally getting my DNA to amplify, I was looking forward to cloning my samples this week.  However, I have come in everyday this week only to find my plates without an adequate amount of cultures if any at all.  I have even carried out a PCR purification protocol prior to cloning in an attempt to eliminate contamination or inhibition, as well as quantified decent concentrations of DNA via nanoDrop.  Yet my cultures fail to make an appearance on the nice home plate I have provided.  On the bright side, I've really got the PCR protocol down and the MFB has been producing some nice results for the Tricho_nifH templates.

Next week I will have cultures.  Then I can move onto DNA extractions and sequencing.  My mentor wants to take me up to UCSC to carry out the DNA extraction so I can meet the Zehr lab (which was planned for today), so I'm really hoping my cultures grow soon!

The not so good -Cloning  -In-vitro customer support

The better  -plenty of room for improvement

The good - MFB data -Developing expertise for running PCR experiments on my samples

The great -my mentor who is also frustrated but determined to get cultures!!!

This week

Spent most of this week working on my powerpoint presentation/write-up.  This part is not nearly as interesting as learning the ins and outs of designing and building, but its nessary.  I did manage to get some help from one of the Mechanical Engineers, Gene Massion, to run a finite element analysis(solidworks program) on my clip/shackle. We checked stress on my part from a variety different of loads and materials. Overall my design preformed well with the material that I intended my design to be made of, and not so well with others.  The tests were very educational and I have some good ideas on how to beef up my design for greater load capacities.

Next week

Should have my material for a production part in hand some time in the next few days, then next week the machine shop can begin fabing out my pieces. As for me I will continue working on my presentation/report. 

Going well/ not going well

I'am really happy the way the BBQ turned out.  The feedback that I have been getting from many is that we did a good job and I thought the food was great.   

This Week:

• I have begun the layout process after a long and unexpected delay
• I have updated my schematics for the 50th time with more parts
• I have completed all additional footprints necessary for my layout

Next Week:

• I will be continuing layout with hopes of finishing it by the end of the week
• I have a design review scheduled for the 28th to go over my design with four other EE/ET's that work here at MBARI

Going Well/Not Going Well:

Everything is going well except for the continual minor changes in my design and tedious software thats has more bugs than a New York sewer

Happy Birthday George!

This week

I spent the first part of the week going over the feedback from last week's EARTH workshop. The gist of it is that Eye in the Sea is best when it is live. Since my project is to disseminate Eye in the Sea footage, I am now working on putting together a wiki that contains all the lesson plans (finished and rough) on the EARTH website, as well as resources and discussions for the lessons. I'd like to have a rough draft finished by tomorrow and send it out to past EARTH participants for comments and further construction. The talk by Dr. Mark Abbott was good (hit home the benefits of working at MBARI), the bbq was fun (how often can you food shop for 150 people?) and meeting with the high school group on Tuesday was enriching (they were enthusiastic and I can't wait to use some Ostedax clips in my classes this fall).

Next week

I'd like to integrate any feedback from the wiki and also look into possible grants to get EITS re-deployed on MARS (and with the ability to capture video clips for later). Danelle mentioned that a color camera might be in the works for MARS which might be counterproductive to EITS (bright lights for color camera).

Good and bad

 I'd say things are going well, however,  time is running short.

This Week:

1. Two algae isolates

Prepared the samples for sequencing, and the bacterial/mitochondrial marker (16s) is getting sequenced right now.

 2. 7 new isolates

DNA was harvested this week. The cultures were looked under fluorescence/live microscopy.

Next Week:

1. Two algae isolates

Analyze the sequences once they are back.

2. 7 new isolates

Try to sequence the eukaryotic maker (18s) gene of these isolates. Do the whole PCR, cloning, plasmid prep, sequencing run.

Well/Not well,

 Ran into a few unexpected problems in the experiments caused a delay in my schedule, but the project is still on track!

This Week

• Completed the basic integration with DSS.
• Added a new features to show different predicates in different colors to the visualization.
• Started working on the visualization of "future plans" of a reactor in TREX.

Next Week

• Continue the work in visualization of future plans of a reactor.
• Start visualization of constraints in the "future plans".

Going Well/Not Going Well
Social Security Number process not yet completed. Almost Six weeks!!!

This week

•  Our last dive on the Western Flyer with the Doc Ricketts was completed on Monday (short dive, only 6 hours) during which Dr Brewer's postdoc, Andreas Hofmann, was in charge. We did a transect of profiles using the Raman porewater probe at the NE Santa Monica mound through clam beds. We were using the in situ Raman spectrometer to analyze the concentration gradients of sulfide, sulfate, and methane.
• We finished the dive with a gas sample using the in situ Raman probe. We collected venting gas from the NE mound in a push core, formed hydrate, and brought it up to around 550, where the hydrate began to dissociate and a gas spectrum was taken--refer to the picture: http://www.mbari.org/expeditions/Southern10/Leg1/L1_images/hydrate2.jpg
• Wednesday I returned to work and have been going through some of the data obtained on the cruise.

Next week

• The lab experiments will be performed again under constant temperature due to variability in previous results
• Data taken from the cruise will be sorted and process so that in the coming weeks I can determine the pH of marine porewater

Going well/not going well

• Time is running out!

This Week

• Edited the entire CANON website
• Created new sections for the mapping autonomous underwater vehicle website
• Met with Jennifer Paudan to discuss the changes I made on the mapping auv website
• Made sure to copyright most of the MBARI images and use references
• Developed new slideshows for AUVs, DSS, and CANON
• Met with John Ryan to edit the fieldwork section of the CANON website
• Used new tools such as adobe illustrator

Next Week

• Will send out email to entire CANON team asking what changes they would like to be made on the website 
• Will work on fully editing the Autonomous Underwater Vehicle Website.

Going well/not going well

• Keep up the communication with various MBARI staff
• Be aware of current developments regarding the websites
  
  

This Week:

• I finished the Zeroconf protocol
• I create the java API for automatic recognition of Ethernet PUCK instruments and I integrated with the PUCK tools
• I prepare a new demo for Monday for Carlos Rueda and my mentors.

Next Week:

• Monday demo
• Start to write a java API for parsing SensorML data from PUCK payload and use this API to publish the instrument data with Data Turbine.
• Start to write the final report.

Well/Not well,

All well

This was a very short week for me. I got off the McArthur II Wednesday afternoon in time for the BBQ, very nice. I managed to pressurize my test chamber and discovered that one of the parts had developed a crack. I will spend the beginning of next week fixing that. All else is good.

This  Week:

1. I continued to research dyke width controls/convection and am beginning to formulate hypotheses as to how dykes could potentially point focus at depth
2. I have mapped a ridge segment at CoAxial (from video, geochemistry and bathymetry) and identified at least 12 different lava flows. I have calculated the volumes for these flows and Dave has given me some dates for them so I can start puting them in order
3. These dates have also allowed me to look at how fissure density could be used as a proxy for age but as I keep moving my lava flow boundaries I haven't put together the final version yet
4. I wrote my report methodology

Next Week:

1. Write report methodology and results
2. Map in flows for a third section at North Cleft
3. Investigate point focussing hypotheses
4. Attept to calculate depth the NGorda dyke wold need to be to not fissure the surface to put constraints on point fissuring processes in this are

Going well/not well:

 Everything's going well but wish I had more time before the cruise!

This  Week:

• Met up with some of the VARS team and got some advice, which was VERY helpful. I made the tweaks and major edits I needed DONE. Today and Monday I will be getting more advice on what I have so far, so I can make the final touch-ups on what is there.
• Today I will be meeting up with Lonny and Susan maybe or perhaps on Monday. In the meantime I will be working a little on the Deep-Sea Guide but mostly on starting my report!

Next Week:

• This will be a very important week. I will be try designing mock-ups on a Tree Browsing section and Image Search. With ideas from the VARS team, I will have what I need to do this.
• Once I have these done I will ask Nancy Jacobsen-Stout on how to add information to the temporary database to fill up a species concept page. This way I will have a page or two to show all the features of the Deep-Sea Guide to show all of you!
• I want things to be done and ready for Brian to do all the major Java edits once he comes back the week following the next one. That way the final weeks will all be about reports and final additions, etc.

Going well/not well:

• Everything is going super well after meeting up with the team! It really helped me because this is made for them (and others later) and so it's hard for me to fully improvise everything design-wise.

This week:

 I compared the results of my scenarios to see how the different inputs contribute differently. I have calculated the surface mixed layer for the different scenarios which has been really interesting. The no flux case does not have a surface mixed layer. Plotting the results this way has really helped me understand how the wind and heat are contributing to mixing at the surface. I have calculated eddy diffusivities from my scenarios, and I'm trying to get a better idea of how to interpret the results. I'm used to working with numbers related to the abyssal ocean--so in the surface I'm unsure of how high they might be. From my model, I'm making some statements about how the vertical eddy diffusivity varies with time so that the AUV group can take this into consideration. I have been reading articles about how AUVs collect turbulence measurements and also about horizontal diffusivity.

Next week: I will analyze AUV data and track vertical and horizontal gradients in nutrients. I will then take some of my estimates from my model as well as estimates from research done on the continental shelf to track nitrate flux over time and space. I will also track nutrient concentrations along isopycnals. I will continue to learn about how the AUV collects turbulence measurements.

 Going well/not going well:

I am happy to be done with GOTM. Earlier in the week when I was tweaking the time step of my model, it started running into problems I was unable to save it as I normally do and I was unable to generate reports which are an easy way to just visually look at the model results without running the model. So I'm very happy to be done with it!

This week

I kept on working on the second technique for solving the path planning problem. I prepared a short presentation of the ongoin work and the preliminary results to show to the seminar speaker Mark Abbott. He was very kind and showed interest for the idea of the internship project as well as for the preliminary results. We planned with my mentor to work also on the first technique, since it was very close to give good results too.

Next week

This week I have to work on the first technique to see if we can get good results with it. Then, I will tweak a little bit the seconde technique we used to see if we can improve results also. And finally, I will try to add currnents to the model so the path planner takes them into account when computing routes.

Everything is going well, slowly but well.

This Week

I was able to meet with Paul McGill after his lengthy vacation. He introduced me to another engineer, but this time mechanical, Francois Cazenave. Francois is working on the power buoy and needed assistance on the motor that he will use for one component of the project. I was able to work along side him for a few days this week and had a blast. It turns out he is an ex-intern turned employee! Hearing his story was great. After finishing up with Francois, i was able to work on the SES again. This time i was able to hammer down the exact positions of the assigned locations for each device that will be attached.

Next Week

Work continues on the SES. I will need to get the pin out of the hall effects switch and include it as the home switch for my stepper motor. Unfortunately, no one can give me any info on the switch in question. Little by little the SES is being completed and soon we will be able to write the program to control the device.

Everything is going well