Kayelyn update 1: 

a) This week I have been reading many articles about various midwater species. Learning how to use VARS Query and VARS annotation to see pictures of midwater animals. I also have been to the aquarium which was fun and I saw a larvecean sample which I have never seen before.

b) Next week I could possibly be starting on a project...not real sure what my specific project will be yet

c)Everything is going well, the staff and the food is great. Can not complain at the moment =)

d) From this 10 weeks I would like to widen my perspective and knowledge about marine science. Also learn about different career options. Possibly advance personal skills in writing a paper ,presentations, and networking.

What I did this week,

settled into my cubicle and learned how to work the coffee pot!

I have met with Nancy (my mentor) several timeswho has been incredibly encouraging and helpful. I've begun research/prep work for an illustration for Bruce Robison and hs team on the topic of midwater ecology and oxygen minimum zones. I've also done a little research for my second piece, an illustration on the subject of SENSORS. This has mainly involved attempting to get to grips with the basic concepts of each research topic

next week: more work on the second piece and the rounding up of useful scrap materials and stock images for visual references.

going well....coffee pot mastery

not going well....navigation....

What I'd like to get out of my 10 weeks:

I would like to build up a good methodology for working with illustration clients. I want to learn how best to communicate my ideas/problems an process effectively and in a way that helps both me and the person I'm working for, to make the process as smooth as possible and so that the best result can be reached within the time-frame. Also I want to learn how to draw cool deep-sea stuff......

THIS WEEK
On a personal level, I'm incredibly proud of myself for figuring out where my desk and the lab are after taking only a mere 47398724 wrong turns.  I'm practically a human GPS machine with my excellent navigation skills.

                On Monday I had a chance to sit down with my mentor (Alex Worden) and talk about her research interests and potential project ideas.  I've been given around 120 pages incredibly complicated reading (I know that doesn't sound like much, but it really is hard!).  I've started to make a dent in those articles and will continue to wade through the readings next week.

                I was surprised how much work I was able to do in the lab Tuesday and yesterday.  I tested primers for my mystery sequence (which is described a little more in my 10 weeks section) using both PCR and gel electrophoresis techniques.  The results were just as I had hoped, so I'm excited to get back in the lab sometime soon.

NEXT WEEK

                My mentor left on Tuesday for a conference, so I'm not entirely sure what I will be doing next week.  Personally, I'm rather impressed that I was able to scare her away from me in one day.  I will probably continue to work on those readings and maybe pick up a few more.  I'm sure I'll be working on them for awhile, but 4 pages per hour is a good pace, right?

GOING WELL

                I'm really proud of the amount of work I was able to get done yesterday in lab.  I ran my PCR reaction and three different gels, all of which are very time consuming processes.  I'm getting super excited to my project and having fun meeting all the cool people I'll be working with.

NOT SO GREAT

                I feel particularly bad that I missed the seminar yesterday (sorry George!).  It seemed like a really interesting topic and I was excited to go, but I was so preoccupied with my lab work that I didn't get a chance to see the reminder email.  But I hope it was fun for everyone who went!  Other than that, I've been having a great time getting settled in.  MBARI is such a cool place, so I have absolutely no complaints.  The weather, however, could be a little nicer...

IN MY 10 WEEKS AT MBARI

                From what I can tell now, the main focus of my project will be to determine the unknown phylogenetic origin of a 16S plastid DNA sequence from a creature appropriately named the "mystery bug."  In general, I'll be learning how to work in a research environment that serves as an intersection for scientists, engineers, programmers, artists, and more.  I hope to really get to know my research topic from several different approaches by combining everything I learn in lab work, computer programs, and the readings.  I'd also really like to be able to take back the lab techniques and concepts I learn here to my biology classes at Smith and any research I may do later on.

                I'm having a great time meeting you all and can't wait to see what happens over the course of this summer!  AND we get tomorrow off...how could this get any better? 
P.S.  Sorry this is so long and potentially boring

This week:

Brought down the boat and built a lift harness for it. Scheduled tank time for next week. Started debugging the boat as it's not fully operating right now. Also sampled much of the cuisine on the island.

Next week:

Run the boat in the test tank checking for leaks and seaworthiness. Start to address any issues that should be fixed before the boat can be tested out in the ocean. Continue to develop new software control system in parallel.

What I'd like to accomplish:

Learn more about how oceanographic research is done at a company like MBARI and attend some seminars to learn about the latest research. Learn more about debugging complex electrical/mechanical/software marine systems and common modes of failure. Take advantage of the specific knowledge available in the staff here and pick their brains for further improvements to my project as well as life after grad school.

What I did this week

• I went on a research cruise with my group. I was too sleepy from the anti-nausea meds to do anything useful, but the trip was fun!
• I met with my mentor and talked about some things that need to be done to the website that I'm working on. I'm working on http://www.jellywatch.org, a website that allows users to put in where they have seen jellyfish sightings along the beach. The website was started by an intern last year; this year I hope to improve upon the website.
• Got a notebook and started writing down all of the improvement ideas I have for the site.

What I think I'm going to do next week

• Get more comfortable working with Drupal, the content management system we're using for the site.
• Start working on my improvement ideas, one at a time.

Going well

• I got a flatscreen monitor (yay!). I thought I was going to have to work with a CRT the whole summer. My eyes are thankful.
• I think I have a lot of useful user interface ideas for the site.
• I'm working with a great group

Not going so well

• Waking up early >_<

What I'd like to do with my 10 weeks at MBARI

• Learn a whole whole lot about good practices in web development, PHP, MySQL, etc.
• Meet people
• See more of California

This week I met A LOT of people who work on the environmental sample processors (ESP), from engineers to scientists. The ESP is a machine that is placed in the ocean to test water quality; MBARI has 6 ESPs. I've mostly been working with Julie Robidart, a post-doctorial student who is currently working on optimizing the ESP called Moe to look for certain bacteria in the water. We've run a few polymerase chain reactions (PCR), a process by which DNA is replicated, with known concentrations of DNA to come up with standard curves to which unknown samples can be compared. The idea behind this is that if we know that a certain concentration of bacterial DNA yields so much replicated DNA after the PCR, we can estimate the initial concentration of DNA in any water sample by comparing the amount of replicated DNA to the standard curve. I will mostly be working on the ESP affectionately referred to as Gordon. We've plumbed Gordon with all the necessary reagents for PCR and will likely work on optimizing PCR reactions next week. I've got no shortage of papers to read, so I'll likely be doing some reading next week as well.

The ESPs are run with commands that you type on the computer using a program called Terminal. When I first looked at the scripts that run the machines I thought it would be very difficult to learn, but I'm getting the hang of it. So far the work we've been doing on Gordon has also gone smoothly. The one thing that didn't go exactly as planned was the DNA extraction conducted by Gordon. It yielded about 1/3 of the amount of DNA that we were able to extract using a Qiagen extraction kit. Ideally, we'd like to increase that number to about ½, but it's by no means a huge setback. Overall, things have been going very well!

During my 10 weeks here, I'd like to learn as many laboratory techniques as possible. Since I'll be communicating with Gordon using the computer, I'm also hoping to improve my typing skills. Hopefully by the end of the summer I won't have to glance at the keyboard as often as I currently do. Most importantly, I hope to get an idea of the type of research I would (or wouldn't) like to do in graduate school. I think another important skill I need to improve on is explaining technical processes to the layman...which, as you can see from paragraph 1, I'm not so good at.

What I did this week:
-Met my mentor, Steve Ramp, and the other folks in the group.
-Got administrative powers on my computer and settled into my office
-Explored every nook and cranny of the CeNCOOS website to familiarize myself with the components of the observing system and the products we've got
-Made a list of top priority organizations in the SF bay that might want some CeNCOOS data
-Researched a grant opportunity through the SF Estuary Partnership
-Registered for a conference for next week Th and Fri in Pacifica (just south of SF, on the coast)

What I'm doing next week:
-Beginning research into the potential partners in SF bay
-Attend DOEST reception and meet some board members!
-Perhaps attend some of the teacher workshop on Weds, because it's focused on Ocean Observing, which is what my group does!
-Th and Fri, go to conference on "Recent Advances in Coastal Analyses and Management Affecting California" hosted by the California Shore and Beach Preservation Association. Hopefully meet some of the people I'll be talking with this summer

Going well:
-I'm starting to get a sense of what CeNCOOS does, and what the near-term goals are for the group
-Really enjoying my group, and they have a great attitude about having and utilizing an intern
-Found the tea cabinet in building G, and am enjoying it immensely! And, I think I'm the only one who drinks tea in the building...

Not going so well:
-Been looking at the computer screen a little too much. And, said computer screen is a deep one, and reacts with the fluorescent lights to flicker a little. It's not so good. The IT guy made it better by changing the flash frequency of the screen, but it could still use some improvement.

 What I want to get out of the summer:
-Meet a lot of people who do marine work in the Monterey and SF bay areas
-Help CeNCOOS put together a needs statement from marine users and managers in the SF bay, to guide CeNCOOS's growth there.
-Learn whether I like this role in marine conservation (talking to and forming partnerships with organizations)

THIS WEEK:
This week I had the chance to meet one of my mentors (Danelle Cline), a very nice and helpful person. The project I'll work in is a bit different from what we were planning to do before. So I have read some papers in order to understand the whole system and what is the part I will touch in. MBARI already has a individual visual classifier which works on grayscale images. My role will be add color information to that. Today I finally got Matlab installed... ufa!!!

NEXT WEEK:
I have the Matlab code and books and papers which describes the mathematical stuffs of each part of the code. I'll probably spend next week studying and testing the code.

GOING WELL:
I think that I am going well with my readings.

NOT GOING WELL:
Unfortunately I'm having some problems with the spoken English. It's my first time in the US, so it has been a bit difficult to understand what people say.

WHAT I WOULD LIKE TO GET FROM MY 10 WEEKS:
- A better understanding of the ocean sciences
- Make friends
- Improve the classifier
- Take lots of pictures of California

After settling in this week consisted of building and running Software Infrastructure and Applications for MOOS (SIAM) on Fedora RedHat. This was time consuming as I am used to the Linux distribution Debian and was impeded by minor nuances. However, the build is running and my familiarity with RedHat is growing.

Next week NOAA's Great Lakes Environmental Research Lab (GLERL) should be shipping two items; a YSI ctd and an ARM based PC-104 stack. The ctd will be used to implement SIAM services so that the device and its data output can be incorporated into a node easily. Also, the PC-104 stack is a GLERL upgrade for their monitoring buoys and we hope to integrate SIAM onto this stack to standardize remote observation between entities.

Other project goals consist of developing other instrumentation services for NOAA, extending SIAM for NOAA's offshore power needs, utilizing Data Turbine Java libraries for SIAM real time data access, and to setup a lab testbed to incorporate these new methods.

Here at MBARI I hope to not only see software development but its realization on hardware here in the lab and out in the field. I would also like to learn about the thought and planning process for new projects. My interests also lie with ROVs, tentatively AUV development, and mooring deployments.

Hopefully I can also show something for my work here in ten weeks.

I am very honored to be a part of MBARI(I know it is only for 10 weeks .....However, I have 400 hrs[formally] to explore .....)

This week activities:
I have been reading some papers and books related to MOOS system, MOOS SIAM(software Infrastructure and Application for MOOS) and SENSORS project. Reading all these papers, I have this feeling that I am going to do a real real-time programming here.
I was able to connect to the machine prey where an instance of our ESB is running. Thanks for Bob and Karen for helping me with this. Right now, I am looking at the documentation for Apache ServiceMix that I will be working here at MBARI, which is very unfamiliar right now.
 
Next week activities:
I will get familiarized working with Apache ServiceMix. I will work on connecting the ESB to the new middleware system, the UCSD's ROADNet.
 
By the end of my internship, I would like to see my self being expert in the ESB technology and many new technologies.
 
Things I like:
     My office, The ocean, Ventana and UAV's(looks cool from outside but a real bomb from inside), and friends.
Dislikes:
     The climate(I can't play in the ocean ), and the lazy sea lions 
 
 
 

Emmm...what did I do this week?
I met my mentors and people I would be working with in person and on a conference call. Angel Olaya (who is directing me currently) gave me an overview of how to get started with T-REX (the onboard autonomy system for the AUVs). He helped me install the software on my computer but still we haven't succeeded. I read three of the papers published on T-REX and other technical documentations provided to me. I started analyzing the log file generated and checked the code written to plot the trajectory of the AUV on google earth. The code has a bug and I have been trying to figure that out....still haven't. Installed all the necessary softwares that I will be needing on Mac (my first time to use a Mac and having trouble getting around.. )

Next week
My actual Mentor will arrive and we will discuss on optimizing things so that I can get the best from my stay. Hopefully I will have T-REX up and running on my system at least with the Pseudo Simulator. I plan to fix the bug and plot the actual trajectory on google earth. Once T-REX is correctly installed, run multiple missions with the simulator to have an in depth understanding of how it works. Read a couple of more papers on T-REX and on Automated Planning.

So far except for not being able to install T-REX on my system everything is going well. I like the help and attention I am getting from my mentors.

What I would like to get from my 10 weeks stay:

• Be experienced with onboard autonomy of AUVs well enough to help me with my Masters thesis and upcoming challenges in this line
• To know more about ocean science and oceanography
• Be able to communicate and disseminate my works effectively.
• Learn about a new Culture as this is my first time in the US

This Week

• Met with Brett Hobson to define a short term project: Putting together a matrix of AUV instruments to support the Biodiverversity and Perturbation Experiment Initiatives
• Learned about the long range AUV architecture from the AUV team
• Created a preliminary instrument matrix of instruments, function, wet weight, demension and power consumption
• Used the van pool and rode my bike home to Sand City

Next Week

• meet with scientists working on the initiatives to get their inputs on which instruments they need on the AUVs to support their missions.
• Complete the matrix

Going well

• Learning about really cool instruments from interesting and helpful people
• Getting to know people in the intern program

Area for improvement

• need to define longer term project

What I want to get out of intern program

• To be productive
• To learn about biological oceanography goals, methods and instrumentation at MBARI
• Develop skills
• Develop relationships with MBARI scientists and engineers
• Potentially identify a topic for my masters thesis and maybe even get started on it!
  

Project update June 18, 2009, Roman Marin IV

        This week was mainly a setup and familiarization week. I, met with Andrew Hamilton (my mentor) and reviewed the project material and the project proposals. It looks like my main task is to optimize a small scale hydroelectric setup (pelton wheel) to generate power for instrumentation onboard a vertical profiler. I was also made aware of the project goals, budget and general specifications. I was able to procure a workspace in the ME lab which will allow me to complete the testing for my project without having to set up the testing equipment more than once. I recalibrated the instruments that needed calibration and set up a system to run my first set of tests. I designed a test system so that vey little will have to be changed between each separate test. Next week I plan to begin formal testing. I will hopefully be able to complete the first part of my flow rate testing for my set of orifices. I will also be modifying orifices in an attempt to determine the most efficient design. The next few weeks will be spent testing various orifice designs and materials (brass and sapphire, possibly stainless steel.) in an attempt to maximize efficiency.

So far the project is going well and I feel confident that I can make some significant progress during my ten weeks here at MBARI. The project is fairly large and is made up of several "mini-projects" so I will have to work steadily. That being said, it will be difficult to make things like seminars a priority. Still though, I don't see myself having a problem making it to the seminars and other non-project related events in the future. After all, those things are just as important to me as my project, the intern experience wouldn't be complete without them. Everyone I have come in contact with has been very helpful; they have made my first week here great. I appreciate all the help I have received this week and my hope for the next nine weeks is that I will be able to complete my project successfully and give back to this wonderful group of people.

First week - done!  It's been great getting to know the land, the amazing and brilliant people who work here and my new computer, which I wanted to throw out the window for a bit but, all has settled down and we are now quite bonded.  The first couple of days were adventurous and, from what I hear, quite typical of an intern's experience (I think someone's making that up!)  - I got my mentor lost in Salinas after he phoned me to look up directions.  Not only did I do a comical interpretation of the mapquest map BUT I sent him to the wrong address... he is back however, along with the three interns who were with him (thanks to Alta!).  I enjoyed speaking with Janet Cushing about Fish Habitat conservation.  My project is finally getting off the ground.  My outline is done, my wishlist for video & print pieces is complete and I have a list of staff here at MBARI who, I hope, will be available to give me the information I need for both the Ocean Acidification lesson the Aquarium's Ed Programs team is creating and for the training module I will be creating for their staff on the topic.  I just added a new person to that list after seeing Steve Haddock present today - that was so interesting!

Next week, I will be assisting George in preparation for the EARTH teacher workshop which starts on Wednesday.  In the days leading to it I hope to read, read, read all about ocean observatories, which is the focus of the workshop. 

 My biggest challenge so far has been to set a routine of sorts that keeps me on track - there is so much to do and so many wonderful opportunities that present themselves, that I find it is easy to get side-tracked from my project.  I imagine that this is typical of the first week and that things will settle down somewhat.

This internship is a very unique and incredible opportunity for me as an employee of the Monterey Bay Aquarium, the Institute's sister.  I hope to soak in as much as I can about this wonderful place and take back eduational materials and information that can be used to further the mission of the the Monterey Bay Aquarium to inspire conservation of the world ocean!

This week I learned some Microsoft Access, some visual basic, and a bit about the network and database I'll be using this summer.  My advisor proposed four projects, two of which I rejected and then proposed one more of my own.  I've started one project, comparing bottle measure chlorophyll to flouresence, and trying to define the reasons for the varying raito (light/ nutrient availability, distace from shore, season etc.).  I've got 20 years worth of data so there are a lot of numbers to push around (~50,000 bottle samples and 2.3 million CTD data points)  Yippie!  I'm also trying to keep good records of what I'm doing, to keep myself in order and whoever else continues the project after me. 

Next week I'll hopefully shove something into Matlab.  Also going out to sea next Tuesday.

MBARI is awesome.  Housing is very Twilight Zone.  Horribly acute suburbia.  Whoever designed it must have had a severe trauma in their past and has now given up entirely on humanity.  Only in america.

In the coming weeks I'd like to solve most of the major problems facing the ocean today.  In the process I'd like to become more efficient in my code writing, learn about lots of new oceanographic methods and find out about interesting future work opportunities.  I'd also like to see some more sea otters and go to the farmers market. 

This week:

I was at the CIFAR (Canadian Institute for Advanced Research) Integrated Microbial Diversity Conference in Asilomar.  Aside from the food it was wonderful!  The talks were very well done, and the research was interesting.  So, I accomplished relatively little in terms of the work that I did on my project this week.  On Monday I finally located the plasmids that we have been looking for quite sometime, which meant that I could test out the primer that we have for biliphytes.  It appears to have worked, which is a relief.  On Wednesday during our break at the conference-- Rachel (from UCSC) tried to help me out with ARB, a sequencing and phylogentic software, but, alas, I don't think that I downloaded it correctly.  Chris Preston also said that she had similar problems... which is comforting, so I hope that I can figure that out. Then, on Saturday, I worked on my literature review for my thesis which Alex wants to read on July 3rd.   

 Next week:

I am going to be working with Heather and Julie doing some environmental PCR-- hoping to ultimately send my plasmids off to get sequenced soon.  I also need to start on qPCR design for the biliphyte sequences and OLI11305 (a prasinophyte).  

 Going well:

I found my plasmids!  Which was going to be a hindrence to my project....

 Not ideal:

ARB is a huge headache... but I hope that it will work out!

This week:

Tuesday- Research Cruise on the Point Lobos! This was a really great cruise into the Monterey Bay Harbor, it was wonderful getting to know my lab on the boat. I sat in the control room for a little watching how the pilot flies the Ventata (we were at mid-level about 500m) to capture specimens. We were looking for various jellies, and collected quite a few,  including tomoptrus and ctenophores, using both the robotic arms and the suction device. Overall, I'm really glad I got the opportunity to go out on the boat early on, because I got to see how the specimens I'll be working on are collected. Often when working in a molecular lab, you get disconnected from the field work because you spend most of your time working on the micro level with chemicals and whatnot, but I was really happy to see the field work that does go on!

Wednesday- Meghan gave a presentation of her work at our lab meeting, where I learned about her project and just the general concepts of luciferin/luciferase. Her presentation really put into perspective the type of lab work I'll be doing this summer, and I'm excited! Later that day I sat down with Meghan to talk about my project and we ordered some primers for me to use next week. Finally, I watched Meghan dissect a live ctenophore (in the dark) and observed the bioluminescence it emits. The tissue was frozen for me to work on the next day.

Thursday- Today I tried an assay of Calcium sensitive photoproteins from one of the ctenophores we collected on Tuesday and dissected on Wednesday. I made buffers and homogonized part of the frozen tissue in the dark, then I used an integrating sphere (that Steve made--cool!) to carry out my assay. I injected CaCl2 and expected to see excitement, but after multiple attempts and after consulting Steve, he said that it could have used up all its glow and so the Calcium wasn't doing anything.

Next week:

Next week, I'll be officially starting my project of isolating and characterizing the gene responsible for a fluorescent protein from Diphyes (a siphonophore). This will involve amplifying DNA Meghan has isolated, making a plasmid with the FP in it, putting that into a vector and then the vector into bacteria. If the bacteria glow, then the FP has been successfully expressed and I will move on to purification of the protein and ultimately characterization.

So far everything has gone just fine. Ultimately, there are many things I hope to get from my summer here at MBARI. I haven't been in marine research for 4 years, and I really want to get back in the field. Strangely, I am using many of the same techniques I used in my undergrad research, but on jellies instead of plants. So, I'd like to hone my molecular bio skills and learn new ones unique to marine science. I would love to do some scientific diving to collect samples, but Steve isn't sure if that's on the agenda for this summer. I also thrive in a laid back, friendly lab setting, so I hope to make some lasting friendships not only with the interns, but with my lab as well. I'm super excited and ready to take on the summer!