THIS WEEK my mentor and I set up a side-by-side PCR experiment for our environmental samples and samples spiked with synechoccocus.  The PCR product was run through gel electrophoresis to test for DNA amplification.  Fortunately we did see amplification in some of our samples, which indicates that our idiA primer worked and we don't have to redesign primers for targeting this gene expression.  We have now moved onto the next step- cloning!

NEXT WEEK we will hopefully be able to work with our colonies.  We will also return to using the MFB2 block for testing our GrpC and Tricho templates.

All is well!!

This Week:

1. Identified and mapped in flow boundaries for 5 lava flows plus two shield volcanoes on the North Gorda Ridge
2. Calculated their volumes using two methods the first assuming a flat base and the second a tilted base and compared the results
3. Mapped in all the faults and fissures in the area
4. Mapped both fault associated talus and 'erupted' talus and calculated the volumes of both.
5. Looked at the percentage of an eruption which is accounted for by talus and found that between 11 and 25% of an eruptions volume may be composed of this talus like material
6. Calculated statistics for the area, including cones per km2, and looked at the distribution and densities of cone patterns
7. Spent an afternoon learning about MB system and how raw AUV data is processed (Dave Caress)
8. Continued reading on dyke propagation and dyke width
9. Identified Coaxial, Hawaii and several other areas as potential comparisons

Next  Week:

1. Continue research on dyke width controls/convection and formulate hypotheses which might explain deep point focusing of dykes recognised from preliminary work
2. Investigate hypotheses and (hopefully) reach some kind of conclusion as to processes controlling this pattern
3. Map one of the comparison sites and calculate volumes of eruptions and large shield like edifices, compare volumes (and faulting and fissuring patterns to North Gorda)
4. Write report introduction and possibly methodology

Going/Not Going Well:

Everything is going well at the moment. I'm feeling a little pushed for time as I'm off on a cruise on August 5th and back the Friday before symposium so need to be pretty much finished by time I leave - eek!

This week

Still annotating the Rover images.  It takes some time but I think I'm really starting to get my eye in for noticing things and it's great ID practice.  Will hopefully have finished all of them by the end of this week!

Next week

I plan to go through some of the images and discuss any questions with Linda.  I'll then spend a few days making sure everything is annotated correctly and to the lowest taxonomic level possible with her help.  After this the analysis starts!  Just what the next steps are will be decided at the project meeting next week.  We'll also be putting the Rover into the test tank at some point to take some calibrated images so we can calculate the area of the images - I'm looking forward to a day's practical work.

Everything is still going great!

This Week:

1. Two mystery algae isolates

One of the isolates was sent out for sequencing (eukaryal marker). The bacterial (16s) gene was also cloned same as the 18s eukaryal marker this week for sequencing. Currently working on plasmid prep and will carry out sequencing next week.

Because the other isolate did not amplify at normal PCR conditions, I tried gradient PCR at different temperature to see if anything show up. Result: no. Then, I tested for inhibition in the DNA extract by dilution + PCR. At 1:10 dilution, the DNA finally amplified which means there is indeed inhibitors in the extract. Will try eukaryal (18s) + bacterial (16s) marker gene sequencing on this isolate again.

2. Culture collection check

One of the cultures in the culture collection was suspected to have contamination. qPCR was performed and results indicate there is indeed contamination of coastal Ostreocuccus in the supposely pure Bathycoccus culture. Currently working on a short report to Alex and will do 18s sequencing as well on this culture to see where the contamination is from.

3. More mystery isolates

Everything planned for the summer project is almost done. Therefore, decided to look at 7 more of isolates from the same cruise last year. Protocols will be very similar to the previous two isolates. The cultures were transferred this week.

Next Week:

1. Two mystery algae isolates

 Analyze the sequencing results from the first run. Also continue the sequencing (16s for one and 18s+16s for the other isolate).

2. Culture collection check

Sequence the culture (18s) and report to Alex.

3. More mystery isolates

DNA extraction + cloning.

 Well/Not Well:

Everything is going well but the amount of work more than tripled this week for me (still very exciting though!).

This week

Finalized my stress calculation and concluded that my shackle will be burly. I finished up my mechanical drawing on Tuesday afternoon and ran them past the machine shop Supervisor Ray on Wednesday to double check if there would be any problems in the fabrication of my design.  Ray gave me the go ahead to proceed with submiting my plans and ordering material. Material should arrive some time next week.

  Next week

I will be eagerly awaiting my 1 1/2 & 1 inch stainless steel plate, but in the meantime I will be working on my presentation/final report. 

All is well and right on schedule.

THIS WEEK

I am still in the development part of the Zeroconf protocol which will take some more days.

After the presentation and the demo from last Friday with my mentor, Kent Headley, and Duane Edgington, I start to implement an automatic system using PUCK, Zeroconf and SensorML to demonstrate the functionality and automatic setup for a system with different instruments and services available into a local network.

NEXT WEEK

Continue programing the Zeroconf protocol for Luminary micro and Java API for Service Discovery.

All is going well

This Week:

• I updated the package types and part numbers for the components on my schematics
• I replaced vertical connectors with right angle connectors which are necessary for the chassis system
• I updated the bipolar current source because my original design wouldn't prototype
• I reviewed all of my schematics once more and had a few parts ordered to prototype
• I finished sketching PCB footprints for unique package types

Next Week:

• I will start the layout process by making the footprints and mapping the initial placement

Going Well/Not Going Well

• Everything is peachy and covered in corn nut powder

THIS WEEK

• I kept on working on the path planner.
• I finally could complete all the chain of tools needed for it (discretizing the domain, analyzing its properties...)
• The results obtained by the path planner so far are acceptable, but I think they can be improved.
• Since the tool chain is built, I have started to improve the initial step, where the domain is discretized, by another approach, more closely related to the domain properties. I hope this improvement will be propagated to the obtained results.

NEXT WEEK

• I will keep on improving each tool of the whole chain.
• I will probably revisit the cost and heurisctic functions.
• I will start another approach to the problem, based on a different technique (Genetic Algorithms).

Everything is going well. Since I want to tackle the problem with another technique than the one used so far, I will have little time to get deeper in the current one. I need to decide wether to test two techniques or improve one of them as much as possible. Will see with my mentor next week.

This week

This week is the EARTH workshop cosponsored by MBARI and CMOP in Oregon. Thirty plus teachers from around the country have gathered to learn about real time data and to incorporate it into lesson plans that are available on the EARTH website ( [www.mbari.org/earth] ) . I presented using Eye in the Sea near real time footage using the on-line collaboration tool Voicethread (www.voicethread.com). Although many teachers have expressed interest in using EITS footage, no groups picked this topic to expand into a lesson plan for this workshop (a few teachers and Dr. Antonio Babtista have expressed great interest in using voicethread).

On the good note, I've learned quite a bit both formally (presentations by scientists and experts) and informally (socializing with the group).  I also still feel that EITS offers a great visual, raw data entry into using real time data

Posting for Melissa...

This Week (at sea):
-We have managed to make it to three sites since our departure on July 9th: Station M, Santa Barbara Basin, and Santa Monica
-At station M we recovered Ken Smith's 'elevator' at a depth of 4000m, this dive was also used to make sure the Doc Ricketts was performing well and to ensure there were no problems with the tether
-In the Santa Barbara basin, the Brewer team performed experiments on squid using a D-sampler (detritus sampler) to determine their 'respiration index' by manipulating O2 levels, CO2 levels and thus pH
-There was also an exploratory dive of an asphalt volcano that Peter Brewer suspected to possibly contain methane and sulfide rich sediments. About 15 Raman Spectra were taken of this site and 1 push core. However, weather patterns required the vehicle be recovered immediately
-Inclement winds and currents required we change sites, twice. Santa Cruz basin was next on schedule, but it was too rough to launch the ROV so we moved onto Santa Monica
-We launched the ROV Wednesday morning near the Santa Monica mounds but once reaching a depth of 830m, the vehicle underwent a dead recovery due to leaking hydraulic fluid
-We hope to continue Raman in situ analyses of porewaters around the santa monica mounds and taking push cores to compare recovered data vs in situ data. A vibracore system will also be employed to create a profile of porewater (pw) samples.
-the vibracore will be analyzed both in the lab and in situ using the Raman pw sampler.

Next week:
-We will port in LA on July 19th and unload our equipment
-We are scheduled to drive back up to Moss Landing on July 21st
-We hope, if there is time, to return to the Santa Cruz basin site

Going well/not going well:
We are still ahead of schedule but we are hoping to have things run more smoothly with the ROV and hope that the weather remains favorable for future dives

This Week

• Finished adding all the necessary features to the visualization like zoom in, zoom out, left shift, right shift, tool tip for tokens etc.
• Started integrating the code with the DSS( Decision Support System)

Next Week

• Continue integrating with DSS.
• Explore addition data that can be added to the Plan Visualization.

Going Well/Not Going Well

• Social Security Number process not completed. Four weeks period expired this tuesday.

This week:

-Went on the Research Vessel Zephyr  to observe and take images of the benthic imaging autonomous underwater vehicle. I also discussed the benthic imaging auv with various scientists and technicians, including Brett Hobson, who invited me to the cruise. Thanks.

 -I launched a decision support system slideshow using pictures from David Fierstein that details the user interface involved for controlling the autonomous underwater vehicle as well as determining its location.

-I managed to access scientific illustrations on algal blooms, red tides, and ocean acidification created by David Fierstein and uploaded them onto my CANON web project.

 -I also edited all of the Controlled Agile Novel Observation Network pages.

 -I created new web pages, including one on data and information management for the decision support system. 

Next week:

 -Fully edit the autonomous underwater vehicle pages by Tuesday.

-Create a new slide show for autonomous underwater vehicles, listing the various slides.

Going well/not going well:

 -Everything is going fairly smoothly, improving communication with the CANON team as well as the autonomous underwater vehicle principal investigators.

This week:

I finalized all of my scenarios in GOTM and I have been bringing them into the first stages of my report. I have put together 17 different scenarios with varying physical inputs and have standardized my plots so that they are easily comparable. I am specifically looking at the components of the biological model, temperature (to get an idea of mixed layer depth), dissipation rate of turbulent kinetic energy, and buoyancy frequency squared. I will most likely weed out some of these scenarios to a more manageable amount. I have been trying to get the vertical eddy diffusivity from the dissipation rate of TKE and buoyancy frequency, but my numbers have been off, so I've been playing around with those data sets. I have also been looking at AUV data and and averaging the nutrient profiles to come up with one vertical profile. As another type of method of estimating the vertical flux of nitrate, I have come up with an eddy diffusivity as a function of depth as well as a time-varying eddy diffusivity. This will help with my understanding of vertical mixing on nitrate concentration and episodic mixing due to internal waves and other types of episodic mixing.  

Next week: I will analyze the different outputs of my model (nutrients, phytoplankton, dissipation rate, buoyancy frequency) and integrate them over depth so that I have a mean value over a time series. I will compare these time series with one another so that I can make some statements about how the physical inputs differ in their results. I hope to be able to use the eddy diffusivity and the second derivative of nitrate concentration to look at the change in nitrate flux over time. I will also begin shifting focuses from the model to educating my group about methods of measuring turbulence.

 Going well/not going well:

I have enjoyed working with GOTM...but I'm ready to be done with it! Every time I try to do a run through with a scenario it quits the first time I try to do a run through--so it has taken up more time than it should. 

This week

Improved the design and user friendliness of the Acid Ocean Website 

Through trial and error, I've started to learn and decipher css web code.  This is a lengthy and frustrating process.  However, with a basic understanding of this code, I will be able to improve the general layout and design of each page.

Next week

Continue with the above tasks

The Good and the Great

No major interruptions and breaks

This week

I did a lot of design editing and found that my CSS is conflicting somewhere on a few parts. I guess it serves me right for making it so long it's hard to keep track  (_)

We decided to use MBARI's external page's header rotating images, which I will be implementing fully next week. This way we have more leeway with the look of the site as long as that piece is actually connected to the main page.

Moved around navigation and changed colors, etc. Most of all almost everything is functioning good.

Next week

I will be under Nancy Jacobsen-Stout's supervision for the next 2 week because Brian will be out until the 30th and then he'll have to leave again I believe on the 8-17th? I think. So I will be working on adding more content to VARS in order to also present Deep-Sea Guide with some data inputted.

The Good and the Great

Different when making websites for others, I've always had this problem when doing them for others: It's hard to figure out what everyone wants so when you're left alone typing away you may realize the next day that that is not how they wanted it. Haven't had anything THAT bad yet, but I'm always ready for it!

I am currently out to sea assisting Tim Pennington with CTD operations. We have returned to the bay and will be following drifters until Wed. the 21st. Overall the cruise has been succesfull, no real problems to report. There was some good fishing on the way back in to the bay, two beautiful albacore are now smoking. The weather has been nice and the ship (McArthur II) is much larger than the Flyer so the ride is smooth. Looking forward to dry land and getting back to the rangefinder testing.

This week : This has been the most productive and entertaining week at MBARI as far as work goes. I met with Larry Bird to go over some mechanical aspects of the motor. If anyone hasn't met Larry, i highly recommend that you talk with him before leaving.The motor to the SES is now connected and operational. I have also put together a presentation for the development team of my project. Hopefully this will be highly useful for the project.

Next Week : Up in the air. Paul Mcgill will instruct me on further steps.

Not so well : Another trip to the doctor.