The majority of my week has been spent running PCRs and gels.  Since I ran a PCR on some environmental samples on Tuesday and got some pretty ambiguous results, I've spent most of my week trying to coax the best results out of my samples.  The best part is it's possible that my results are actually supposed to be that weird, so I might have run 3 gels and 2 PCRs too many.  But practice makes perfect, and I am having a lot of fun getting to know the people in my lab and the lab itself.  I have also been working on those readings I mentioned last week, and they're actually starting to make sense!
I had the pleasure of meeting Marcia McNutt yesterday, and she might be my new favorite superhero.  She is the president and CEO of MBARI (aka VERY successful), yet she's still incredibly friendly and amazingly fashionable...I'm sufficiently jealous.  If you haven't met her I'd definitely recommend it.

My mentor still has not returned (I possibly scared her out of the country this time), but we've been communicating through emails, and it's been really helpful.  I'm excited to show her all the work I've done since she left.

I assume that next week I will be continuing with my reading and possibly getting a head start on the introduction for my paper.  Maybe I'll get another email from my mentor telling me the weekly agenda.  (It's so great, and it makes me feel like one of Charlie's Angels...or I guess Alex's!)

Hope everyone had a great week, and enjoy the weekend.  Hopefully the weather will be a little nicer.

My Second week@MBARI,
         After meeting my mentor Kevin Gomes,  I came to know that my project is changed from connecting the ROADNet(middle ware frame work) and ESB, to testing the features provided by the ESB. Even though there are many flavors of ESB available in market, the popular open source ones are MULE,
and Service mix. The one I am working is the Apache service mix. There is this beautiful book "OPEN SOURCE ESBs IN ACTION", the best resource to work with my project.However, I still have to do a lot of reading(get  used to the technology) and practise (exercises given in the book) before I can actually do any of the testings to the ESBs.           
Next week:
Get to know more about the ESB
Hoping to start the actual testing.

Best thing about this week is the Board of directors meeting I attended. All experienced people with different areas of interest sitting together sketching the future of a challenging company like MBARI. Its amazing!
Now I know the answer to the puzzling question in my mind. What am I going to be after 40 years?

This week I started working with the MBARI visual event classifier. It takes a grayscale image as input, creates a feature vector which describes that image and then compares this feature vector against feature vectors from known classes (Rathbunaster, Leukothele etc) in a database. I've made some modifications to the code and now it takes a true color image as input and then generates the feature vector based on that. Then I ran both classifiers (grayscale and color based) on a small set of images. They gave different outputs but the results are not conclusive, we have to test them on a larger set. This is the plan for next week. Reading more about the "boxes" of the classifier is also on the plans. This week I had the chance to go to the sea, in Point Lobos. It was very interesting to see how they deploy Ventana, control it remotely, control Ventana manipulator etc. The bad side is that I got terribly seasick. I should have taken some medicine . I am getting more comfortable with spoken English (still not so good).

I've been making a new layout for the website (Jellywatch) this week. My mentor and I came up with a pretty snazzy banner for the site, now all I have to do is change the site's style sheets such that the new design is implemented. I also need to come up with a nice color theme; right now we have a purple-ish theme with some seafoam green.

Over the course of next week (probably more like "next few weeks") I'll be improving the "Mark New Sightings" page where users can put in a new jellyfish sighting into our database. Right now it doesn't record the date of sighting. Also, right now the only way to put in the location of the jellyfish sighting is to either enter the latitude/longitude (who would know that?!) or to zoom into a google map and add a marker on the sighting location. We want to also let users be able to enter in a marker based on a text location (like "marina state beach"). I'll also be implementing a picture-upload feature, so users can link a picture to a jellyfish sighting. If we can get it working, it would be really cool to have users upload their cell phone pictures to the site.

We met with the web design people at the Monterey Bay Aquarium, they want to link to Jellywatch from their site. Cool!

This week I have, more or less, accomplished what I was set out to do. With the help of Fredric, I have successfully installed TREX on my system and it is up and running. I corrected the coordinate transformation error on the script written to visualize the trajectory of the AUV in Google Earth and now it is right where it should be. I have also modified the script to show different actions taken by the AUV (get GPS fix, Fire a gulper..) with different place-marker icons. I met with my actual mentor and along with the autonomy group , planned what my main project would during my stay. I went out on a sea cruise on R/V Point Lobos and saw ROV Ventana in action. Did my best to stay in the control room and follow up the things that were being done...too bad...couldn't do that for more than a couple of hours .

I have already started reading about COVE: A Visual Environment for Ocean Observatories, which I might be using to visualize trajectory and state of the AUV. More or less my task next week would be to do an in-depth study of COVE and decide wether to use it or not. I am planning to go on the sea on R/V Zephyr on July 1st for an AUV mission.

This week has been very full! I got to participate in the teacher workshop (EARTH) on Wednesday, which focused on ocean observing. Then, Thursday and Friday I have been at a workshop in Pacifica focused on recent advances in coastal monitoring and management. I've met so many people working in coastal management in California, including people from the Coastal Commission, the Army Corps of Engineers, consulting firms, local governments, the Bay Conservation and Development Commission, SCCOOS, the Southern California counterpart to CeNCOOS (my group), USGS...and on and on. It's a crash course in who's who and getting a feel for the culture of the different agencies and what their roles are. I'm still at the conference now, just taking a moment to fill out my update!

Next week: follow up with some of the contacts I made here at the workshop.

I really enjoyed meeting the board members and hearing about how they ended up where they are. And, it's been awesome to be at this conference, too, and meet so many movers and shakers.

Because of the success of my PCR run with my primers and plasmids, I went ahead and ran PCR with my primers against a series of environmental samples taken on two cruises (CN107 in July 07 and CN207 in October 07).  Surprisingly-- the PCR appeared to work really well-- my gel showed only one band at the right size for 18S.  So, we went ahead and TOPO cloned the PCR products and prepped them for shipment off to SeqWright, where a clone library will be created and the clones sequenced.  Much of my week has been spent on the phone with SeqWright and in consultation with various lab members trying to figure out what primer should be used for sequencing.  The sales reps from SeqWright recommended using a primer specific to the sequences that we have in our library-- however the sequences we used to amplify the samples hit a part of the vector.  So-- I ended up deciding that I would go ahead and use M13 (a common primer specific to the vector) for the sequencing.  Funnily many people I spoke with said that they had better results with using reverse primers, so I went with the superstition and chose M13R. It will be very useful to have one entire library which is particular to my bug (the Biliphyte)... and I think it will help my project out a bunch.

Aside from this-- ARB is still not functioning, which is frustrating.  I think that I am going to try to download it on the Mac associated with the lab.  Most of the people, who I know that use ARB run it on Macs-- so I might be able to get more guidance if I switch to that operating system.

I also finished up all the reading that I have been trying to complete-- meaning that I can really focus on writing up my literature review now!

This week I worked on transforming and expressing a fluorescent protein from a siphonophore (Diphyes). I used first strand cDNA as well as double strand DNA that Meghan (the grad student I'm working with) had previously sequenced. I used PCR to amplify all the cDNA she had accumulated of the ten combinations (5 sets of cDNA and 2 sets of primers) only three worked. So, I digested those three and purified them. Then, i ligated the gene into a vector and transformed them into bacteria cells. After plating them, I only got a few colonies, which was strange; we think the competent cells are bad by now. Also, the colonies did not glow so much at first. So, I had to do a few things to figure out what was wrong: I did another transformation using more of my ligation, and I plated these cells on both charcol and regular LB plates to see if the concentration of charcol in the plates was toxic. This morning I had some growth, but still very few colonies and the colonies grew on the non-charcol plates just as well as the charcol plates, so its not toxic to the cells. Next, I'm going to transform into a different type of competent cell that I just made yesterday (making competent cells is a whole day ordeal, but I'm really glad I learned this new technique), and I also have to test that the competent cells I made yesterday are acually competent! I also think that a few of my colonies are glowing, but I need the expertise of some of the other lab members to tell me if I'm right or just seeing things.

 So, I have quite a bit on my plate: testing the competent cells, using the new competent cells for a transformation, expressing the protein and getting my colonies to glow, and sequencing some of the colonies to see if my insert is even in there. I think I'm close to getting these colonies to glow, and I'm pretty excited about it!

p.s. i have no idea why some of my first paragraph is crossed out, i couldnt change it...

Second week:

Project:  with my luck, the Pt. Lobos arrived on Monday with the F.O.C.E. flume just when I could get out and  photograph it being put on the dock.  The flume has been brought back due to some water being detected within the  electronics and also needs some structural repair.  Lucky for me, this misfortune has allowed me to be able to take a very close look at the equipment and learn more about it.  Ed Peltzer was kind enough to give me "tour" of the flume and I was also able to take very close photos of the individual components!  I must remember to take a voice recorder with me so I can go back and write down what I was told!  I now have to go back to the notes I took, head over to the webpage and jot down an accurate interpretation of FOCE that I can use for my project!  

Tuesday was great!  What a unique experience it was meeting board members and eating great food at the reception.  I was able to talk with Julie Packard, the CEO of the Monterey Bay Aquarium, about the internship program.  She was happy to know that one of her own is an intern this summer.    This was also when I was finally able to meet Ed Peltzer and Peter Brewer, both of the High CO2/Low pH team.

I've spent the rest of the week in the E.A.R.T.H. workshop. Wow!  There have been great speakers like Heather Kerkering and Matt Binder who spoke about Ocean Observing Systems, Raphael Kudela whose focus was Harmful Algal Blooms, John Horne on DEIMOS and acoustics in the oceans, Edith Widder on bioluminescence and Erika Raymond taught us about the Eye In the Sea - Phew!   All of these presentations were accompanied by ideas for how to use the information in the classroom.  While participating in the workshop, I've been in contact with my team mates at the aquarium, giving them ideas for our own teacher workshops. 

Next week, I will be off site at the NMEA conference, helping with the running of it. I only get one day at MBARI! 

It's been a very busy and stimulating week and thanks to my mentor, I have learned tonnes!

This week I met with several  scientists to get input from them on AUV projects they need engineering to work on next year. I met with Steve Haddock, Ken Smith, Charlie Paull, Bob Vrijenhoek, Zbigniew Kolber, Julio Harvey and Chris Scholin. It was very interesting to hear about the projects they are working on and to check out their labs. They all have very diverse requirements for the AUV. I evaluated several different optical imaging systems and wrote up a brief summary. I continued to summarize all the instrumentation requests in a matrix. Met with an Engineer to get information on Disolved oxygen probes.

Next week I will  meet with a few more scientists and complete the AUV project proposal summary. I will get started on an oxygen probe evalution.

Attending the board meeting presentations was very interesting and helpful. I also enjoyed meeting some of the board members.

Well it's my first week on the job and I'm still adjusting to the time zone.  To be honest, my biggest challenge this week is staying awake!  (Right now I'm using lunch breaks to catch up on some zzzZZZ's). 

That said, I'm in the process of delineating the details for my internship.  It looks like I'll be working on a project with HABs (harmful algal blooms).  This entire week was spent looking at relevant websites, familiarizing myself with current HAB issues, and attending presentations to glean more background info. 

I actually did some research on this topic last summer in Hawaii with NOAA (National Oceanic and Atmospheric Administration), so the concept is familiar --even though I'm working on a much larger scale with CeNCOOS (Central and Northern California Ocean Observing System). 

Next week I'll finalize what angle I'm going to pursue.  I have several options ranging from public outreach to economic analysis.  It's great that my internship is so flexible and that CeNCOOS hasn't done much work with HABs yet, so I have lots and lots of options.

The only thing I have to complain about is that I'm still sleep deprived, but as the week goes on, things are getting better.  I'm also a little overwhelmed with all the material I have to tackle, but this project will shape up in no time!

If anything, I'm just really excited to be participating in this program because it's my first "official" internship.  It's great that I can not only contribute to someone else's research, but also develop my own intellectual skills as an undergrad and someone who is interested in environmental/ conservation issues.  Ultimately, I would like to expand upon my knowledge from last summer, meet pioneering experts from the field, and hopefully discover that lifelong passion I've been searching for.

Anyway, thank you so much for this opportunity and I really look forward to getting to know all of you!

P.S. George, maybe I can meet with you after Monday's meeting to take my picture?  Sorry I've been hiding from you all week.

Hi everyone,

hope you're all settling in well.

Cannot believe it's the end of week 2 already!
Thus far things are progressing well here in the illustration cubicle  I've completed a set of roughs for Bruce Robison, Rob Sherlock, and the midwater ecology group. The piece will probably be fairly data heavy. It will illustrate the oxygen minimum zone and its expansion in Monterey Canyon. It's been fascinating to see just how much data scientists have to get to grips with here. Huge amounts of information, it's just incredible. Anyway, we're batting ideas back and forth on the back of my initial designs, so things should firm up sometime late next week and then I'll get started on the color study.

I'm also working on a piece to do with technical geekery and computing. I met with Kevin Gnomes who very patiently described MBARI's Observatory Middleware Framework, and explained what kind of illustration would be most useful to him. This one I expect to be difficult, especially in the initial stages, simply because I don't understand the subject at all well, despite Kevin's (very good) explanation. There are a lot of overlapping systems, that appear to have some kind of ethereal presence in lots of different places. So I'm expecting next week to be a tough one as I'd like to try to at least get to grips with the subject some more before I attempt to put pen to paper properly and think of a way to visualize all those ones and zeros.

For those of you who don't know, I had a vomit-inducing trip on the Lobos and have therefore decidecd not to pursue a career in the navy, I'm sure they're devastated....

Otherwise things are fine here. I loved meeting Marcia and the board members and it's been great to settle in and start to get my teeth into stuff.

See you all soon!

P.S Hi Taryn, welcome! Good luck catching up on your sleep. I'm sure the weekend will help.

P.P.S Marco, I know how you feel, the Lobos broke me too  and your english is great, really great, so don't worry!

This week has been very interesting. My mentor Tom sat down with me on Wednesday to go over control flow of SIAM and its protocols. They have been developing on this for quite some time so their code libraries are extensive; sometimes it's overwhelming as to what I should exactly implement or even use.

Right now I'm trying to write a service for a menu driven instrument. This is a huge pain as the control architecture seems to write extraneous bytes through the outputStream, thus losing its place in the menus. Currently I'm using a serial port analyzer on a separate laptop (which just crashed and Tom has the password - I can't find him) and it is extremely helpful.

Also, I have mainly done command line programming but Tom feels that an IDE may be a better way as it can provide useful debugging features. However, after wasting most of my morning solely on the setup I gave up and am now 'manually' debugging.

Next week the Great Lakes Environmental Research Lab (NOAA) will be sending the PC-104 arm processor (they promised it will be here Monday) and that will be a nice break from this instrument service. I'm confident I can get SIAM up and running fairly quickly and can extend the power control to a stackable relay board.

Over the course of this week I tested the internal systems of the boat and found that everything that would need to work is working fine, so the propeller spins and the rudder turns. The control system that was on board had power disconnected and when I attempted to connect it the magic smoke came out...so I think we'll just leave it as we're going to replace it anyways.

One of my advisors for MBARI, Kanna Rajan came back and my advisor from UCSC came down yesterday to meet with me regarding my progress. Both got a chance to see the boat are we're all on the same page. A near-term plan development plan was drafted up and diagrammed for reference. As part of that plan I made a list of the parts we will need to buy for the boat this summer as well as prices for all of them. As long as the solar panels work (which would give us 1.3kW of power and save us $4000) we're only looking at $500 in parts.

We discussed how to implement some of the systems we hadn't been sure about (recharging the batteries from land and a solar charging/monitoring system) and now have a clear path for a little while.

Right now I'm starting on the software part and this will continue through next week. I've been busy today just trying to setup the development environment and get started on that. I'm working on both a proportional heading controller and a remote controller for the boat. The first step on this is to get remote control of the boat working and we plan to do that with our dsPIC board and a standard RC transmitter and receiver. The plan is to be done with remote control of the boat by the end of next week so we can go out and drive it around the harbor.

I will also be meeting with my primary advisor, John Ryan, as well as Kanna to talk about everything on Monday.

After continued wrestling with Access by way of Matlab via Excel and many such format changes, I'm finally satisfied that the data has transferred properly.  I've made some funny plots to try to guide me where to go next in the search for meaning (for this is the primary occupation of life). 

Met my other advisor on Monday of this week (Francisco Chavez) and he suggested another possibility dealing with Nitrogen isotopes and their meaning for the project I'm working on now.

I went to sea on Tuesday with my research group.  No ROV but many insights into the sources of my data (CTD, bottle samples etc.).  I collected bottle samples, dropped the secchi disk (vague measure of water clarity), and helped out with the general operation of the data collection.  Ate lots of food and had a fine time looking out over the water and thinking about the usual things.

Trying to come to peace with the fact that all places once were wild, bureaucracies do not make enlightened decisions, and that poorly place suburbs are like pug dogs; not themselves deserving of blame.

This week I ran PCRs on the MFB (microfluidics block...the part of the ESP that sets up and performs DNA extraction and PCR). I'm currently testing the efficacy of the MFB in amplifying two types of bacterial DNA that will be used to test water quality in the field...at some point. I've been able to amplify all the samples I ran this week, so next week I'll be loading all the reagents onto the machine. I'll also be running quantitative PCRs to see how much DNA is amplified from known starting concentrations.

I've started working on my final presentation. I know it seems early, but I realized that it's going to take a lot of graphics and animation to keep people from dozing off or just losing their minds during my talk (not that it's not interesting...just complicated). Hopefully it will be perfected by August.

I'm really excited for going out on the boat on Monday! And the four-day weekend! Next week is going to be awesome.

          The beginning of this week was spent number crunching. I had some good data but it needed to be processed before I could really use it. My main goal with regard to the data processing this week was to figure out which design is going to be most applicable to my project. Once I figured that out I was able to draw up a sort of "road map" for the project. I re-examined the existing project specifications and I was able to come up with a few more parameters that are critical to the success of my project. Having a clear idea of what I need to do is crucial to the success of this project. I had to prioritize; With only ten weeks to spend on this assignment I feel it is important to make meaningful headway on as much as I can rather than spend time on all aspects of the project and not really accomplish anything. With that in mind, my first task will be to get at least forty percent efficiency from the pelton wheel. In a perfect world with a perfectly designed pelton wheel efficiencies of up to ninety (+/- 5%) percent can be achieved so I know I should be able to reach my target.

                The second half of the week I spent testing the brass orifices I have on hand. I have narrowed the orifice diameter down to what will most likely be the final size, 0.06in. Now I can begin the process of maximizing efficiency for the 0.06in orifice. I will test different pelton wheel diameters and make numerous other adjustments in an effort to generate the most power I can within the bounds of the project. The testing process is very messy so I have mainly been working outside.No major snags as of yet, things seem to be running smoothly and I'm happy to keep it like that.

Week 2

I finally have narrowed down a topic on Tomopteridae (polychaete worm) eggcases. Mostly my work time is spent in the video lab using VARS Annotation on beta and HD video tapes. I am looking for possible footage of the eggcases that sometimes happen to fly across the screen and then try to get the best frame grabs. The more I watched videos, the easier the eggcases were to differentiate from other objects on the screen.

In the upcoming weeks I hope to gain more information about these polychaete worms regarding to their reproduction cycle and seasonal changes. Next week I could possibly be doing DNA analysis which should be oodles of fun because I have never done that before. Looking forward to learning more and completing my project.

This week, although short, was quite productive. I did a lot of sequencing, and took quite a while to analyze my data, but it turns out that only one sequence was complete, with both the beginning and ending sequences for my protein. I simultaneously learned how to purify a protein from a bacterial culture--this process was quite time sensitive and required actions after 5-8 hours and then 16-20 hours, which meant I had to come in at 9pm to lab. Unfortunately, I added 1/1000th dilution except 1/100th dilution of arabinose, which was not enough to induce my cultures. SO I had to repeat this whole procedure on Wednesday and Thursday (yes coming into work on my day off). I'll find out today whether or not it worked! If it did, then I'm on my way to characterizing this elusive fluorescent protein