This Week:

1. I have finished watching all the dive 886 videos and am now retuning to specific parts to look at sedimentation of certain sample sites and compare these observations plus those of contacts with the geochemistry to pick out individual lava flows. So far I have identified 4 potential flows alongside the 1996 one using predominantly the rock sample geochemistry as it is the most reliable.
2. I have mapped in all of the preliminary eruption boundaries for the 1996 flow and am beginning to map the possible boundaries of older flows.
3. For the areas of flow I have mapped I have pinpointed the eruptive vents

Next  Week:

1. More reading and add what I have already read to my literature review
2. Continue with identifying and mapping in boundaries for the older flows in the area
3. Begin to look at the distribution of eruptive events in relation to the dyke point focusing problem
4. Find other examples

Going Well:

 Everything is going well at the moment.

Not Going Well:

Nothing

This Week

Currently I've switched focus from how to disseminate the EITS footage to how to present it to teachers at the EARTH workshop next week. Danelle and I met to talk about objectives for EARTH and the limitations of Voicethread. Erika Raymond (post-doc) and Greg Bwye (Erika's intern) met with us to talk about the footage from the 2009 deployment on MARS. They both have also agreed to provide the voices/expertise/doodling for a Voicethread mock-up for EARTH. The hope is that uploading EITS footage to Voicethread will provide a collaborative tool for classes all over the country/world to discuss what they are seeing and to motivate them to further study (and conserve) the ocean. 

Also attended Ari Daniel Shapiro's seminar on Spinning Science Stories. His thoughts were right on target as we try to get the EITS (and data from ocean observatories in general) out to classrooms and the public. Great seminar!

Next week

Danelle and I will present the footage to the group of teachers and gather lots of feedback about its usability and how well it meets the objectives. Hopefully the feedback will lead to minor revisions and not a whole new platform. 

Going well and not so well

Time, I suppose could be an issue. I hope to have some more clips to bring up to EARTH so that teachers can use their creativity and energy to spread the word.

Thanks to

Danelle, George, Erika, Greg, Ari and all the INTERNationals

This Week:

1. I have read the documentation for domain name service (multicast DNS) and service discovery to be able to implement this for instruments. With this information I made the plan to use the parameters from Puck data-sheet and so to register the mDNS with this data. With this all the instruments will be unique identified into a local network and so they can be called using a real name and not an IP address.
2. I have prepared a demo for IP Puck for tomorrow with Headley Kent and Edgington Duane.

Next  Week:

1. Continue to get more information to make the implementation of ZeroConfig protocol.
2. Programming the multicast DNS and DNS service discovery for the Luminary micro-controller.

Going Well:

 Everything is going well.

This Week:

Proceeding to sequencing from last week. Isolated the plasmids (small circular DNA) with the eukaryotic marker inserted. Preping the sequencing plate soon and will sequence whenever the machine is available.

Culture check: continued qPCR to identify the culture composition from one sample in the culture collection. Results are in and waiting to be analyzed.

Next Week:

Prepare sequencing of 16s DNA of the two isolates I have. Procedure similar to 18s I did last week. This will give more information on what the culture composition is with respect to which bacteria are in the culture besides the algae and identify more specificifically the algae species.

Well/Not well:

Going very well after an AWESOME long weekend!

Short Week 4:

The welding for the PT Assembly is finished and the Rangefinder block is well on the way to being done (probably Friday). Some minor design changes had to be made but everything worked out fine. I'm waiting on parts for another project to arrive; they should be in next week. I will be leaving next week to go out to sea on a 9 day voyage.

I was able to get what I needed to finish this week done and get back on schedule. When I return on the 21st I will be in a good spot to begin the next phase of the project. 

This week:

• Mainly I've been assisting in the preparation for the first leg of the Western Flyer So.Cal cruise leaving tomorrow
• This has involved unloading and setting up lab equipment and making sure the instruments we'll be using are working correctly on the ROV (laser Raman, CTD, etc.)

 Next week:

• My cruise begins tomorrow and sampling sites which involve sampling at the Santa Barbara Basin and Santa Monica mounds, among others

Well/not going well:

• Things for the cruise seems to be in order but my project of determining the relative molar Raman cross sections ran into some problems that will hopefully be fixed after the cruise

This Week:

• I submitted my schematics to my mentor and am waiting to hear back about them

Next Week:

• Fix any problems with my schematics that my mentor finds
• Design footprints for unusual package types

Going Well/Not Well:

• Everything seems to be going well. The down time that I get waiting for approval on my schematics has given me some time to write up a bit about my project for the intern blog

This week:

Prototype finished! The Western Flyer is headed out manana, and I finished just in time to show the ROV pilots my shackle before they shove off for for a few weeks. My mentor Larry Bird helped me out big time since this week was a short one with getting my shackle desgin milled/assembled. I was stoked with the feed back that the pilots gave me on my design, and I will be submitting my drawings to the machine shop soon for the next fabricating phase.

Next week:

Get the Finished product started in the shop, so can start doing some load testing in a couple of weeks. I would also like to start my presentation/paper to get a good start on the final weeks of my internship.

Going well/ not well:

Only six weeks left for the internship! Where did the time go? 

This week

• Fixed a few synchronization issues in the code.
• Completed the most basic version of visualization and tested it.
• Discussed with mentor what additional features to add to the project.

Next week

• Integrate the visualization code with DSS.
• Add more features to the code, like zoom in, zoom out, left shift, right shift, tool tip for tokens etc.

Going Well/Not Going well
Everything is Good.

This Week

Met with David Caress to discuss updating the mapping AUV section of the MBARI  website. I have modified the D. Allan B. vehicle specifications and uploaded the most recent maps that the mapping AUV has taken. I am working on a soundslide plus slideshow for the AUVs, which will show the different kinds of AUVs with captions to describe them. There is a small possibility that I might be able to do a podcast and combine that audio media with the AUV slideshow.

 Next Week

Will be editing all of the new material that I have uploaded so far and I will be meeting with some more AUV team members.

Going Well/Not Going Well

The challenge is to be able to get recent information on autonomous underwater vehicles and CANON now. I cannot wait until week eight to receive new information since that information needs to be thoroughly edited and reviewed by scientists. Everything is going fairly smoothly.

This week:

• I introduced the previously implemented heuristic function to the algorithm.
• I have found and fixed a few bugs.
• I am adding code features for debugging and checking the properties of the cost and heuristic functions I have defined

Next week:

• I will fine tune the cost and heuristic functions to speed up the searching process
• I will try with another approach to solve the same problem

Going well / Not going well

• The internship is being a very interesting experience. However, almost 4 weeks out of 10 are gone. This is really short.

This week: I showed my mentor, Sergey, my Powerpoint describing how the GOTM works and how the biological model responds to the various physical inputs (heat flux, shortwave radiation, wind, etc.). Today I met with my lab back at MLML and I discussed the model with Larry Breaker who is pretty familiar with General Circulation Models (GCM). He helped me gain a better understanding of how the model works and offered a lot of guidance as to what I can do in the next few weeks to thoroughly understand how much the physical inputs contribute to turbulence. I have been reading about the model from books on marine turbulence as well as articles that describe how the turbulence closure models work and how the ODE (ordinary differential equations) solvers are applied to the biogeochemical models. Lots of very complex stuff! I have also using Matlab to collect data from the M1 mooring (meteorological observations, temperature and salinity profiles) and getting it in the right format to import into GOTM.

Next week: I will put together a report or refine my presentation to show the various scenarios where I have added/removed different physical inputs. The goal of this will be to better understand which forcings are producing the greatest amount of vertical mixing. Wind is likely the most important factor, but it will be interesting to see the importance of heat flux and pressure gradients. Once I have plotted these different scenarios, I will then examine how much that input is contributing to turbulent kinetic energy and dissipation, nutrient flux, and phytoplankton growth. This will help me connect the GOTM with the original goals of the internship: to improve quantification of vertical mixing, and subsequently refine estimates of primary productivity.

Going well/not going well:

Things have been getting better as I learn more about this model and how I can use it to understand vertical mixing. I'm excited to see some of my results for next week. I really enjoyed Ari Shapiro's seminar this week!

This week

Currently working on last week's 'to do' list

          1.  Webpage design and layout (colour, pictures and text)

          2.   Webpage security          

With help from a fellow MBARI employee, we were able to successfully develop a secure login page that restricts unauthorized individuals from entering information in my web based form.

Next week

I will put together a facts page

                Read and sift through the literature

I will further improve the design and layout of the website

The not so well

Haven't made much progress during the past 2 weeks.

Having trouble getting back into it

This week

• Got to see Brian's fast-paced output of some Java coding for the site. 
• I didn't do much because I wasn't here yesterday and on Wednesday I was only able to change the search and search results pages a little bit.

Next week

• Really should be the week everything should be coming together, from design to Java, and then hopefully we'll only need to change what asked to change

The not so well

• I didn't get much work done this week, but I'm going to make up for it next week!

This week:

My images were loaded onto VARS so I have started annotating.  There have been a few issues trying to improve the brightness of the images for greater detail and I have recently come across a problem with the timecodes.  But I'm really enjoying these little daily challenges and compiling a method development for the image annotation process.  

Next week:

Annotating takes some time and I have around 340 images to go through - I'll probably be at this for the next few weeks.  Although both Linda and Alana have other small jobs for me if I need an afternoon away from the computer screen so hopefully I'll get to try my hand at some other projects as well.  I might make a start at the introduction and methods sections of my report, the time is flying by!

Going well/ not going well:

I still have no complaints.  I'm really enjoying my project work and I love the other opportunities that are arranged for us here - meeting board members, seminar speakers etc really adds to the experience! 

THIS WEEK I had to re-run my GrpCnifH and TrichonifH negatives on the MBF2 because of a  type-O error put in last Wednesday (my fault, and Thursday was on the Point Lobos).  I created GrpC- and Tricho- nifH templates using the primers I designed and was able to run a PCR experiment (not on the MFB) on environmental seawater samples from Santa Cruz.  Unfortunately our agarose gel standard was old and we could not determine if the primers properly amplified our idiA gene.  We switched to  positive synechoccus controls (cultured synechococcus) but unfortunately the NanoDrop indicated that our DNA extraction experiment did not have a high enough concentration of DNA from the cultured synechococcus (probably due to the age of the culture).

NEXT WEEK will be dedicated to re-doing this 'primer-testing' procedure.  Hopefully we can find a positive control for idiA and my primer design will successfully amplify the proper DNA!

NOT SO WELL- DNA amplification, MFB2 negatives, primer testing- much hope for next week!

This week : It was a short week and both mentors were out on holiday. I worked on the stepper motor that would be used in the SES. The programming aspects as well as the mechanical operation of the motor need to be solved by the time Paul McGill returns from his trip to Texas.

Next Week : Work will continue on the stepper motor. 

Not so well : I have had to visit the doctor twice so far. This is a huge inconvenience due to the loss of health and the loss of work hours.