This Week:

1. This week I have assisted in (mostly watched) the data processing and now have a (beautiful) well located bathymetry map for the North Gorda area to work on.
2. I have begun working on the video from the dives in the 1996 eruption area pinning in the boundaries of the eruption.
3. I have completed a literature review on the North Gorda area.
4. The project objective is now pretty much defined- I'm going to look at dyke propagation for the North Gorda and other historic eruptions, examining how fissure eruptions can be discontinuous despite being fed by a continuous source.
5. Gave a short presentation to my research group on my previous research to show them what I've worked on as part of my PhD

Next Week:

I'll be continuing to review video data for the chosen eruptions, looking for evidence of eruption flow directions and flow boundaries to pin in fissure locations. I'll also be reading up on previous dyke propagation studies and adding to my literature review.

Going well/Not going well:

Everything is going pretty well. I'm glad to have the outline of a project in place. I have had a few problems with the spatial analyst tools in ArcGIS not functioning properly. I tried emailing somebody at MBARI (who I was told was bit of a GIS guru) but I haven't heard back so if anybody can help/knows somebody who can it would be much appreciated!

THIS WEEK the ESP lab was challenged by the beloved instrument Moe, which was deployed last week.  A displaced puck is preventing the instrument from collecting any samples and can only be properly realigned manually (this was discovered after countless command efforts).  The instrument is being retrieved today and the next ESP will be deployed in mid-July.  While we will have a gap in our time-series, the discontinuous data will still provide invaluable information.

I have been continuing my work with gene sequencing and the MFB2 device.  I have run nifH templates through the PCR at various concentrations and will determine a standard curve to compare to future environmental samples. 

 And lastly, I finally met Chris Scholin!  He is the President and Chief Executive Officer here at MBARI and head of the ESP lab.  I am very honored to intern in his lab.

GOING WELL Everything has been going great!  I am looking forward to next week!

This week after countess emails and on-line searches, I found the on-line program that seems to be a great tool for disseminating the EITS video data- Voicethread (www.voicethread.com). It will enable clips of video to be packaged for students (and the general public) to view and share their comments and even drawings

Linda was a tremendous help in getting the video watermarked and packaged for uploading. Danelle has been invaluable with her expertise and advice. We met with Erika Raymond and her intern Gregor Bwye. He will be reviewing the video from the last deployment and sharing "exciting" clips (of course, they are all exciting). I would also to thank Mark Chaffey and the crew of the RV Point Lobos for letting me tag along on their cruise last Friday. And finally, thanks to the Aquarium's WATCH program and the students at Pajaro Valley High School for letting us kayak with them on Monday.

I've coerced some young folks to trial the first run through with the videos. I have a phone call meeting with one of the co-founders tomorrow to try and see how this will all work in a public forum and work out some glitches.

I wanted to have the EITS video portion completed by tomorrow so that I could work on the supplementary materials, however, this might stretch into a few more days.

All in all it has been a good week.

This week:

 I started to work in lab. First, I transferred my two isolates into new media so they can grow happily. Also, I checked for my media for any contamination. Then, I did some fluorescence microscopy and saw the isolates are both a mixture of photosynthetic eukaryotes and heterotrophic bacteria.

Next week:

 I will start doing genetic test on these two isolates by first harvesting their DNA. Also, I will prepare some antibiotic plates to grow my E. coli clones the following week.

Well/not well:

All well.

This Week:

This week I have worked on the PUCK implementation for the TCP protocol and I finish the first draft of the C code. I implement the TCP/IP PUCK protocol as a generic code that can be used with any micro-controller which implements the lwIP stack for Ethernet communication ( is an open source code micro-controllers), and FatFs file system (open source code for file system implementation on micro-controllers and is Windows compatible FAT file system ). I implement the PUCK memory on a SD card using this file system and so it can be easy read and write on Windows PC.

I also start to program the java host tools for the TCP PUCK protocol based on the last version for serial communication. And with this software I can debug and verify the functionality of the protocol.

And until tomorrow I will also write my web page

Next Week:

I will be continuing to finish the java application and testing the puck protocol that I created for Luminary micro. Also I will start working to implement the ZeroConfig on lwIP for service discovery and multicastDNS.

This week

During the past week, I have developed an in-depth understanding about my project.

I am currently working with Jim Barry (supervisor), to develop a database using Google Earth to display the locations of current and previous ocean acidification work.  This website will also provide a web-based entry system allowing researchers to manually enter information that is of concern.  The goal of the project is to provide a brief overview of ocean acidification research.   This will be of value to those that would like to liaise with other professional organizations and to those that would like to find out more about ocean acidification. 

What have I done?

Have spoken to and receive help from various individuals.

           A special thank you to Nancy, Tara and Mike

Developed a basic database

Started to learn the basics of web design

Challenges

Since I have a poor background in database construction and web design, this will be a difficult task

Next week

Will start my web design component

Finish developing the database

This week

I went aboard the R/V Zephyr to observe/take images and videos of the Gulper AUV just three miles off the coast of MBARI. 

I have been busy updating the CANON website including information on field work, an April workshop presentation, and individual team member contributions to the CANON initiative.

I have been busying updating the AUV website including information on LARAUV, artificial intelligence/autonomy/T-REX, and the Upper Water Column Vehicle/Gulper AUV vehicle. I am also coordinating with Francisco Chavez of the CANON initiative along with Kanna Rajan of the AUV project team.

Next Week

 I will start to develop in detail sections for the AGU poster, a high res image of the T-REX block diagram, and information on the decision support system for the AUV website. I hope to have a better and more in depth comprehensive review of the various case studies for the CANON workshop.

Going well/not going well

Creating and editing content on Dreamweaver has been going fairly well. The real challenge will be to  coordinate with the various MBARI staff into getting their content onto the web, while being scientifically thorough and accessible to the public.

This week

I had a day on the Point Lobos with the midwater ROV team.  It was great getting to watch the trip from the surface to 1000 m, and I got to drive the ROV!  Also, thanks to Linda's drug cocktail I didn't feel sea sick at all, although we were lucky with the weather.

I have been learning more about VARS and am making a collection of VARS images of all the fauna I am likely to see in the MARS area.  I've also started writing a literature review so currently wading through a sea of journal articles.

I also had the chance to go kayaking with MBA as part of their summer teen program.  It was a great day with lots of sea otters, sea lions, harbour seals and pelicans.  

The intern's blog is now up and running!  

Next week

Hopefully my images will be loaded onto VARS on Monday, then the serious annotation work starts!

Going well/ not going well

Everything is still going great.  It makes such a great difference to have the chance to meet high school kids, aquarium staff and other staff members at MBARI whilst working on the internship project.  

This week:

 - Began to prepare for the pressurized gas samples that are to be analyzed with the laser Raman system however there was a leak in the pressure cell so the cell had to be shipped out and repaired, delaying this project

- Instead I began to prepare background buffer solutions of pH ~4, 6, 7, 9 that will be used as a reference when saturated with H2S

- A new set of these samples will be saturated with H2S (g) and their spectra observed at the varying pH

- Peak ratios will be determined to visualize the cross sections of the H2S, HS-, S2- species 

- This lab data will be taken on the cruise and used for the marine pore water analysis

Next week:

- Hopefully have a repaired pressure cell to be able to run gas mixture samples through the Raman spectrometer (mixtures: CO2/N2, CH4/N2)

Going well/not going well

Everything is going really well. Aside from the set back with the pressure cell, things are beginning to come together nicely for the cruise in July. 

This Week:

• Completed schematics for a 3-Axis Magnetic Sensor
• Completed schematics for a Inverting DC to DC Switching Regulator
• Completed schematics for the Daughter Board Select Logic

Next Week:

• Schematics for the FOCE Environmental Sensor Board should be completed early in the week
• Layout process for the PCB will begin

Going well/not going well:

• Everything is going very well aside from some strange incidents with prototyping

This Week:

• Decided to use GWT for the project.
• Identified the component needed to be learnt.
• Went through a few tutorials to learn about GWT and RPC.
• Got TREX running on the system.
• Went through the previous work done on Visualization using Swing.

Next Week:

• Get the basic skeleton ready.

Going Well/Not Going well.

• Things are pretty good.

This Week:

• Had a meeting with the VARS team to figure out exactly what they wanted on the Deep Sea Guide, and where on the page they wanted it.
• Came back to my desk and coded and coded. 
• Talk to Nancy Barr about external design guidelines and how to input the Deep Sea Guide into the the external website.
• Got the website done in HTML5 and CSS3, and got so enravelled in the beauty of the new CSS attributes like rounded borders and columned text that I forgot how crappy Internet Explorer is in regards to compatibility. ARRGHHH.
• By tomorrow I will probably change everything back to CSS 2 so at least some IE browsers can see some stuff. Rounded borders I'm keeping just for Mozilla, Safari, and Chrome users. 

Next week:

• Finish Image and Video Gallery page/CSS
• I want to have everything cleared by the VARS team and my mentor Brian, and then any changed needed will be implemented
• I would love to start using the Wicket framework with Brian right after this and begin the real work!

Going Well/Not Going Well:

• I hate IE.
• I love CSS3.
• Drawback--> I don't know JAVA and for this I will be wasting Brian's time in trying to follow everything he says. I am going to read tutorials etc at home.
  

 ***Note: I realize most of us don't even know the jargon in each of our updates. I'm personally sorry about that in my update as well >.<

THIS WEEK: I met my mentor, and we started putting ideas on the table about the project. I have started to review some more literature and, most of all, develop some pieces of software I will surely need. I have been also checking a piece of software my mentor provided to me, since I have to use it as part of my project.

NEXT WEEK: I will try to give a small presentation about my previous research to a small group, and I will compile a tutorial about the technique I am planning to use in my project, to give  them an idea on how it works. I will surely continue developing pieces of software as I need them.

WHAT IS/IS NOT GOING WELL: My mentor has been very helpful and interested in what I was doing, and I appreciate that. He is very open to any ideas I might pose and we are both trying to define a good goal for the project. Everything is going well, except I am advancing slower than I would like to (no one said this project was an easy one).

The current week was spent finishing the designs for a pressure test assembly. Today was a ship day for me. I went with Larry Bird to observe the deployment and operation of several instruments he has helped design. The mission was, for the most part, a success, some problems did show up and can now be remedied. The Materials/parts for one of my test assemblies arrived this afternoon which means I will be able to begin machining tomorrow. There have been no real setbacks yet, with the exception of the lag time on parts. Next week I will finish the pressure test assembly and begin trials. I will be going back and forth between the pressure test trials and a thermocouple design starting next week. All in all things are running smoothly and I'm reaching my goals on time.

This week:

I met with a few of the ROV pilots to show them my design for the shackle. I got the thumbs up from the operators to go ahead to the next phase of work which will be to run the tensile and yield strength equations of a few different materials that will be used for the MARS link application.

Next week:

I will build a prototype for some preliminary trials out of 50 series aluminum that can be milled and formed easily. This will make the 50  series aluminum perfect material for a prototype model.  

Well/not well:

I got to go out on the Lobos Thursday to see the ROV Ventana in action and see the MARS platform. This was excellent for me to actually see where my shackle will link up with MARS and the operations of the Ventana in real time. Awesome!

Isobel: If you were trying to contact Brian- he is on vacation. Jenny is great at GIS too, but is away right now, yes? Talk to me today, I may be able to help.

Everyone: Be patient with yourselves. Learning means, well, learning. If you already knew how to do stuff, you wouldn't be learning!

This week: I spent the beginning of this week outlining how I was going to construct my 1d turbulence/NPZD model. I wanted to base my model on the PWP model, but I was having trouble locating all of the required data. I began to explore other options, and in my search I found that the GOTM (General Ocean Turbulence Model) has test case scenarios where you can integrate a NPZD model. I decided that using this model would be most effective. I have since been learning about how this model works. I have also compiled some data from the M1 mooring to use in the model. I am now working on developing my own scenario for the Monterey Bay.

Next week: Although the biogeochemical model has default values for nutrient, phytoplankton, and zooplankton concentrations as well as plankton metabolism, I want to bring in values that have been observed in Monterey Bay. In addition, I need to learn about the various options that are built into the model. The model has many different options for the turbulence model used, so I will go through the literature to find which options are the most appropriate. In addition, I want to learn more about the internal wave models. Eventually I want to be able to use this model to look at the effects of more episodic mixing events in the bay on turbulence and nutrient/plankton dynamics.

Going well/not going well: At the beginning of the week I was feeling a bit overwhelmed about constructing this model and finding all of the appropriate data. I'm really happy to have found GOTM because it allows the user so much flexibility. 

This week: I have continued my work on converting the program from the Benthic Rover to facilitate the Sedimentation Event Sensor. I also had the chance to work with Alana Sherman. One of her current projects involves testing an acoustic modem to see if it is able to transmit through one meter of sediment and still produce a quality data transfer. Very fun tests. One new, semi-fun, semi-ughh thing - The Point Lobos. Mixed reviews on that trip.

Next Week : I will be working with Rich Henthorn, Alana Sherman, and Paul McGill. The first few days of the week involve working with a stepper motor that will be used in the Sedimentation Event Sensor. More etsting with Alana Sherman is possible. And of course,  further progress with the SES program.

 Well/Not Well: Everything seems fine. The trip with the Lobos killed my dreams of being on Discovery channels "Deadliest Catch". The water was calm and i still didn't feel well.