This week

I finish the java tools for Ethernet PUCK and make tests with it.

I found a couple of bugs and I fix them.

Tuesday I have been to some project presentations and I learn more things on technological and scientific projects that are running in MBARI. 

I also start working on ZeroConfig implementation.

Thursday I will be on LOBOS

Next week

Continue the work on ZeroConfig protocol!

Going well/ not going well

Everything is still going great.  

THIS WEEK I learned how to clean different 'PigTails' on the MFB2, make the appropriate Primer Probes (PP) and Master Mixes (MM) for the GrpC and Tricho nifH gene templates, and do DNA extractions.  I also continued running GrpAnifH templates on the MFB2.  I am going out on the Lobos tomorrow (Thursday) for an ROV deployment.

NEXT WEEK I will continue my analysis of the GrpAnifH templates in Excel and start testing the idiA primers I designed last week.

GOING GREAT!

This week

-By Friday last week I got all screenshot mock-ups out to VARS team.

-Mentors were very busy preparing for DOEST, but I spent Monday fixing small errors and adding a sidebar to the Image Gallery page in order to open room for MARS and EARTH gallery integration.

-Tuesday= DOEST and first met Nancy Jacobsen Stout for the first time, matching the voice to the lovely face =]

-Today was amazing. Brian added a few pieces of code into his JAVA and voilla! The pages became active, lol. Now we're going to start the ball REALLY rolling.

-Tomorrow is Point Lobos.

Next week

Use those 3 days to finalize a working output of Deep Sea Guide, from then on it'll be about testing, changing, and adding!

Going well/ not going well

All is awesome, time is flying! I want to be very helpful this summer and maybe go beyond just helping the internal release of Deep Sea Guide, maybe really expanding it!

This week

• Wrote code for the server to communicate between TREX and Client Browser.
• Debugged the code and resolved all visible networking and configuration issues.
• Got the basic first cut of the Visualization Running.

Next week

• Improve the Visualization, by implementing more logic to handle additional cases, and adding more features.

Going Well/Not Going well

• Everything is Great!

This week

I kept on working on the path planner tool.

I found a couple of bugs in my code and I fixed them.

Tuesday I attended to several presentations to the board of directors.

I had the chance to talk with some board members, who were amazingly kind with the interns.

Thursday I will be on Point Lobos research vessel to deploy the benthic rover

Next week

I wll continue working on the path planner, adopting maybe another approach.

Going well/ not going well

Everything is going well so far

This week I have:

developed an online working database which is now linked with Google Earth.

developed a basic template and rough website map.

embedded Google Maps within a webpage.

The rest of this week and next

        1.  Will experience the rock and roll of the Lobos

        2.  Obtain constructive feedback from my mentor

        3.  Improve the appearance and visual appeal of my website

        4.  Make the website more user friendly 

The BAD

I still haven't acclimated to the Monterey weather despite the rather chilly laboratory conditions.            

The GOOD

My project is coming along quite quickly.

No other complaints

This Week: I have continued working with the GOTM (General Ocean Turbulence Model), and I have been looking at how the various physical forcings affect the biogeochemical model. I have also been putting together a Powerpoint presentation to present to my mentors as well as my advisor at MLML. I met with Josh Plant and he helped me with some data collection programs in Matlab so that I can use NCEP data in my model. I attended the DOEST and enjoyed the presentations. Tomorrow I am going out on the Lobos, and I'm excited for that.

 Next Week: I want to conclude my work with the GOTM and move on to answer some more specific questions based on what I've learned from the model. I want to be able to describe how vertical mixing and turbulence are affecting primary productivity. 

 Going well/not going well: Things are going well and I'm happy with the progress I've made. I still feel like there is a lot to be accomplished and the weeks are flying by.

This Week:

1. I have read a number of papers on dyke propagation and rock fracture dynamics
2. I have spent quite a lot of time in the video lab watching videos from dive 886
3. I have mapped in most of the eruption boundaries for the 1996 flow
4. For the areas of flow I have mapped I have pinpointed the eruptive vents
5. I have added the geochemistry of all the samples to the Arc Project and distinguished those which have 1996 chemistry from the others
6. I have identified the samples with 1996 chemistry which lie outwith the lava boundaries and begun to analyse their chemistry to see whether the could be a different flow or the same one and therefore whether the boundary needs to be shifted
7. I met with Bill Chadwick and discussed the project. He was the first person to attempt to map the 1996 flow so this section of the project builds on his work. He has offered to help us get hold of some camera tows and submersible footage from the same area. This will be useful in areas where we have gaps in data but the navigation is not as accurate as that of the more recent studies so it is less reliable

Next  Week:

1. More reading and add what I have already read to my literature review
2. Finish dive 886 video and finish mapping in preliminary flow boundaries
3. Compare these boundaries to the geochemistry
4. For outlying samples analyse the geocchemistry and revisit the video to check for other flow boundaries, adjust 1996 flow boundaries where necessary
5. Begin to look at the distribution of eruptive events in relation to the dyke point focusing problem
6. Find other examples

Going Well:

 Everything is going well at the moment. It's great to be finally working properly on my project and Dave's been really helpful. The data is fantastic too which makes my job easier...

Not Going Well:

Nothing

This week

• After GIS mapping the Smooth Ridge site I will be working on, Linda and I used VARS to pull a list of all the species I will be likely to see in the Rover images, then I used VARS again to hunt for good, close up images of each species.  This will help me get my eye in for the fauna in the area and hopefully make image annotating more efficient.  These images will also be added to the research team's google page about the area.
• Before the images could be uploaded to VARS the TIFF and B16 files had to be converted to JPEGs, this is taking a little longer for the B16s but the TIFFs all went up successfully so the annotation began.
• I'm currently working my way through the images, documenting everything I can see in them.  For the first week Linda and I will be going back through what I've done to make sure I'm picking out everything and identifying correctly.
• The blog continues to go well!

Next week

• Continuing to work through the Rover images, we have around 350 to annotate then I can start comparing annotation methods and linking what I've seen with environmental conditions in the area.

Going well/ not going well

• I'm excited the annotation has begun and I can start doing some serious project work.  I'm being well supported by my mentors and still have no complaints!

This week

•  After saturating the buffer samples with H2S gas before the weekend, their pHs were measured on Monday only to discover that the buffers were actually titrated down to a slightly acidic pH
• The experiment had to be repeated on Monday by adding base to the buffers to get the desired pH and then analyzed by the laser Raman system
• Their spectra was annotated (deconvolution of peaks, integrated peak area, baseline correction, etc)
• After the experiment was run for the third time, and after some confusing calculations Ed and I finally set up a spreadsheet to determine the ionic strength, pK, and relative molar Raman cross sections of the HS-/H2S species
• Two different buffers were giving different values so today the experiment will be repeated with one buffer to come up with the desired values

Next week

•  Next week is only a three day week, so I will spend most of my time preparing for my cruise on July 9th-21st, making sure that I obtain the necessary data needed for the Raman analysis of the pore waters off of southern California

Going well/not going well

• Ran into issues with the experiment, but it seems we're getting where we need to be for the cruise next week

Happy Canda Day to all

Even though I have committed to using Voicethread (VT) as a tool for dissemination, I still feel like email conversations were a constant during the week. I put together four mock-up VTs to illustrate the EITS footage and also the VT tool. I also put together a "How To" for using it, based on questions all the "volunteers" have had as they trialled the mock-ups.  This morning we participated in a teleconference with the cofounders of VT in hopes of understanding where their technology is headed and how it best be used to benefit MBARI and ORCA (Ocean Research & Conservation Association). 

Allowing the interns to participate in DOEST on Tuesday was a great way to experience the collaboration between scientists and engineers outside of our own study areas. Being able to interact with the board also brought home all the talent (science, engineering, support) that works together to make mbari innovative and successful.

Next week I will finalize the mock-ups, work on how best to present this technology and data to the participants of the EARTH workshop the following week and figure the best method for getting feedback from all parties (teachers and "EITS") to move forward with disseminating the footage to a larger audience and if there is time, work on a "How to" for making your own VT.  It would also be interesting to pursue how this technology enhances the National Science standards both in science and technology (that might have to wait until after Oregon).  

Thanks continue to go out to:

Danelle for her guidance (and home grown avocados and plums),

George and Linda for, well, everything (I know that's a cop out)

Erika, Duane and Greg for their input and ideas

Van Pool 3 for providing am and pm entertainment (it was too quiet with most of you on the boat this morning)

And, again, MBARI for allowing us to participate in DOEST and this intern program (esp' Conner who went out of her way to introduce us to board members) Everything seems to be going well (perhaps the calm before the storm). The only downside is that both the EITS footage and VT are engaging and it is difficult to stay focused on one application (many educational tangents).

This week
Continue to identify the two isolates.

• Cultures were transferred to new medium to keep the algae cells happy
• DNA was harvested for both
• PCR was performed on the universal marker for eukaryotes, 18s, to try to ampify the genes.
  • One of the cultures did not amplify at expected temperature of 55C, but did at a lower temp 45C. This means the eukaryotes in there is either too little because they get outcompeted by bacteria OR this may represent a new group that the amplification does not work so well.
  • The other isolate did not show any amplification at both temperatures. This means the isolate is most likely all bacteria.
• Try to clone the gene for sequencing next week as an identification tool for the ??? eukayote.
• Another fluorescence microscopy was done on these cultures at the same time as the DNA harvest.

Culture collection check

• Two strains in the culture collection may have contamination. We want these to be composed of only 1 strain/species of eukaryotes.
• DNA was harvested for two strains.
• One culture's composition will be checked using quantitative PCR. This is a very sensitive and accurate method to identify the percent composition of targeted groups.
• The other culture's 18s was amplified and cloned. Waiting for sequencing.

Next week

• Sequence the clones I got this week for genetic identification.
• qPCR on one of the culture collections.

Going well/ not going well

• All very well. The experiments are ramping up and getting more and more exciting!

This Week:

• Ordered and received parts for prototyping a bipolar current source and magnetic sensor set/reset
• Prototyped the bipolar current source successfully and attempted to characterize its output
• Revised schematics with new set/reset circuit
• Fixed all DRC errors in schematics
• Sketched footprints for circuit components
• Began locating order numbers and locations for electronic components

Next Week:

• Review schematics with Chad and adjust any changes suggested/recommended
• Locate order numbers and locations for all electronic components
• Begin drawing footprints for surface mount package types

Going well/not well

• Everything seems to be going well except I cannot find some of the equipment that would have been helpful for my prototyping

This week:

There was some extra machining that I had to complete this week before the pressure test Assembly could be put together. The flanges for the assembly are finished and need to be welded to the body of the pressure chamber.

Next week:

My goal is to finish the welding for the PT assembly and get the center block for the rangefinder made up. I would like to start familiarizing myself with the rangefinder output. Depending on how much I can get finished during the short week I may be able to pressurize the assembly by Friday.

Things are moving along, maybe a bit slower than I had planned but I'm still in the clear. The shop has been busy and so the fabrication is just taking a little more time. Everyone is getting what they need when they need it so there are no problems.

This Week

Developed a working slideshow for the AUV section of the website.

Put up flash video clips for the CANON website.

Used photoshop to fix the distorted images on the website as well as to reduce their size so that web pages took less time to load.

Developed a section that relates to CANON's fieldwork.

Got several powerpoint presentations from the DOEST to work with for the website.

Developed a section on the T-REX system and automated intelligence for the AUV.

Next Week

Thoroughly edit all of the scientific content that I have written so far to make sure that it is within MBARI web guidelines.

Going Well/Not Going Well-

Everything is going fairly well at the moment and I am progressing at a sufficient pace.

Need to improve the communication between me and the respective AUV and CANON teams.

This week:

My first design was to machine my prototype part out of a solid piece of aluminum 6061 and then use the break to put the necessary bend angle on them, however, I ran into a problem with the shape of my clip making the bend difficult. The solution was to add another piece that will be welded on rather than putting a bend on the part.

 Next week:

Ordered springs on July first that should arrive next week. I will be able to assemble my mars tether clip and submit to the ROV pilots for iteration. Then it will be back to the drawing board to make adjustments for the final product.

All is well on the western front!

This week : I was able to work with a couple of electrical engineers (Alana SHerman and Paul McGill). The have me helping with the testing of an acoustic modem as well as testing a stepper motor to see if it is capable to be used on the SES. Although they have wroked with this motor in the past, they have thrown it in my lap and asked me to "reverse engineer" it., meaning figure out its fundtions and potential without any paperwork. Very fun.

Next week: It will be a very short week so hopefully i will be able to progress in the testing of the motor.

Everything is well. Looking forward to the 4th