I spent this last week in the video lab looking at more videos taken at Station M. We redefined slightly the project by deciding to look at patches that occurs in transect only and so that will give quantitative data. I also look at all sponges occurring in these transect to try to detect the formation of patches. Apart from being in the video lab, I am still reading papers finding hard to have information on the natural history of Paradiopatra polychates which will make more difficult to understand the ecological role of these patches at Station M. I am looking at related genus to see if we can transpose some information to Paradiopatra.
And Ken and his team came back from the cruise at Station M. They collected some polychaete samples for me so I will have a look under a microscope. I will look if they all belong to the same species and compare it with species previously collected at the station. I have a quick look at the specimen and it seems that other animals use their tube to grow which is very interesting for our habitat study. I did not get the sediments associated with the specimens as I hoped for to look at macrofauna association. But it is something that should be done in the future.
Larissa and I had several meeting with Ken and Linda to update them on the projects. Also Ken told us we were going to be busy at the Open Day so even if we do not know yet what we will do, it seems we will have plenty on our plates!

I was successful in getting the motor and sensors wired up, I just need to get the go-ahead from my mentor to fire everything up. Since the bar stock we ordered have not showed up yet, I can't really work on integrating the motor to the actual benchtop assembly. The other notable event from this week for me was sitting in the design review for the Coastal Profiling Float project. It ended up being a very valuable experience; it was very instructive to see what kinds of questions need to be addressed both from the scientific and engineering side before moving ahead on a project, and it was very helpful to learn more about what design reviews generally involve.

Next week my plan is to get the motor attached to the benchtop assembly, and hopefully start to run some efficiency tests. In terms of open house, I haven't been assigned to any particular project, though the chem sensor lab has not totally worked out what they are planning to do...

This weekend has been mostly good. I have been able to get all the parts working together so now I completely have a sensor that can measure CO2, temperature and humidity and store those values of data in memory.  In addition, I built the whole circuit of the sensor and integrated it into a protoboard. The idea is to have the sensor to run independently (meaning without the use of a computer), so for that I had to integrate batteries into the circuit and a level shifter which just regulates the level of the voltage to a certain amount.

next challenges are to equalize the carbon dioxide into Teflon AF tubing which will go through the air pump and then to the carbon dioxide  which will make the measurements of carbon dioxide underwater. In addition I have to setup the radio communications between the node and a base station so the node can pass all the information that is on memory to a computer where the data will be analyze it.

Monday was spent calculating flow rates at the new pump speed and then optimizing/troubleshooting peak resolution with the new timings.  I ran into many issues with bubbles forming in the line which created inconsistent readings as well as hid data in the noise. I also ran into issues with the hose on my pump failing during an attempted standard curve. The tubing was quickly replaced but time was lost since the curve was not useful. At the end of the day I learned the protocol for creating our working reagent.

    After a consulting my mentor and the manual for our flow sensor we placed a back pressure valve on the fluorometer output. This creates resistance to flow and an increase in pressure within all of the lines. The reason for doing this is to minimize the formation of bubbles  within the tubing and various fittings. After we installed it I got the most beautiful set of peaks for our standards. It made my day. I spent the remainder of the day processing the data into various graphs and calibration curves. 

    The behind the scenes tour of the Monterey Bay Aquarium was really cool. Seeing the open sea tank from above was great even without watching the sardines get fed. We also stayed to watch Linda's talk in the auditorium. I read python manuals until the speaker Emily Carrington gave a very interesting talk about her research into Byssal threads. I went into the talk not expecting to be as interested as I was. Her approach and study of the material science aspect of biology was quite intriguing though. I really enjoyed her talk. As the end of the day approached I was able to get into the lab and make some headway on my project. Using python's matplotlib, csv, and numpy libraries I was able to process  stored voltage data and convert it into a series of graphs displaying each sample and the injection/detection reproducibility.  While the data capture side of my project is not as automated as we want it to be it's nice to finally have good data to work with and the ability to get the data stored on the computer.

EDIT: I forgot to mention my mentor has said I will have a task with them on open house day.

This week I've been looking into how pgbench-tools test work. I ran into some problems with this because the test I run from within pgbench-tools was taking a long time compared to other pgbench test I run last week. I tried to figure out if this is normal by looking deeper into the code the test runs, the documentation of pgbench-tools and then by doing some google searches. I found some useful information but not a definitive answer, until I accidentally ran the test when the postgresql-9.1 service was stopped. When I did this I got to see how many actions this test was trying to do, it was doing a lot of actions which is why it takes around 3 hours to complete. Now I need to figurer out why some errors are happening when the test is ran, that are causing the results to display differently then expected.

I have no current assignment for open house, my mentor normally helps with parking.

I have spent the better part of this week collecting measurement data on my holothuroids at Station M. I have also sent our species list out to someone who can provide ratios of biomass based on a sea cucumber's length. Hopefully, this will help me in a couple weeks when I start doing analyses.

The behind the scenes tour at the aquarium was very interesting. I thought that I may not get very much out of it because I am a volunteer there already, but I was wrong! I really enjoyed being able to see all the inner workings of the protein skimmers, pipes and tanks. When I lived down in southern California, I was an aquarium manager in charge of those types of workings on a much smaller scale. It was amazing to see all the mechanics scaled up to accommodate an aquarium the size of the Monterey Bay Aquarium.

This week was also filled with various meetings about my particular project and Station M in general. It looks like I am going to start splitting my time between taking measurements of sea cucumbers and creating a new ArcGIS project to display some of these data from Station M. This will be a great way for me to brush up on my GIS since I have not used in a little over a year!

As Clair and I asked Ken about what we are going to do for Open House, he gave a little chuckle. Let's just say it sounds like we are going to be very busy at the Smith Lab booth...

This week, I've continued to work on visualizations for a package of krill-eating taxa that might illustrate some interesting seasonal or periodic trends. Plotting and data manipulation in R has been the name of the game, and I've got a preliminary look at how these taxa have behaved spatio-temporally over the last 25 years! We've been working on normalizing our data - not all ROV time is equal - which has required some reconfiguring of the dataset.

I also was able to join the Haddock Lab on a Rachel Carson cruise yesterday - a great experience which I can't wait to repeat! We performed a midwater observation/collection dive at one of the stations - I spend the majority of the day in the control room, watching as the team collected ctenophores and maneuvered the ROV. We picked up a number of samples that will be used here in the lab later for molecular analyses.

Next week, I'll continue to work on our data visualizations, looking at how best to illustrate long term trends with such a massive dataset, while still being readable. No easy task! Preparations for our week long flyer cruise will most likely begin then too.

Re: open house, I'm currently signed up to help with the Jelly Watch table.

Hi All,

My week has been great! Another productive week on the fabrication front. Peter Walz and I (90% Peter, 10% me) finished fabricating the swing arm that will attach to ROV Ventana during our two one-day cruises this coming Monday and Tuesday. Bailey and Alba will be joining us (on Monday and Tuesday respectively) and I'm excited to tell them about my project and witness the Raman laser in action in the field. Peter W. and I (same ratio as earlier described) changed out the housing on the Raman laser to match the depth and temperature range it will be operating at during the upcoming dives. I learned the laser calibration and operation protocols that we'll be using at sea. I got at tutorial on HoloGRAMS, the software I'll use to do spectral analyses post-cruise and generate figures for the internship paper and presentation (and maybe research conferences?). We also prepped the hydraulic accumulator, which will hold a oil/gas mixture that will be the focus of our experiment. Most of today and tomorrow (Friday) will be spent mobilizing for the cruise by installing the spectrometer tool sled, affixing the fabricated swingarm, testing the hydraulic manipulator functions, calibrating the Raman laser, etcetera.

Outside of my project, I'll be participating in the Land Use Proposal panel today. This side project will be interesting for me because I have a background in considering similar environmental issues in many of my undergraduate courses. And the Behind the Scenes tour at the Aquarium was an exciting day! It was amazing to see all the technology that goes into maintaining the exhibits with all the filtration systems and numerous sensors. I also like how much the aquarium is focused on educating about fisheries sustainability and marine preservation. The ocean plastics exhibit and the Seafood Watch wall really caught my attention. Linda's talk on deep sea biology was also fascinating! George also took a few of us still around to the John Hopkins Marine Station down the street. It was amazing to see the number of oceanographic institutions in this area. It made me even more excited to start graduate studies this fall at UC Santa Cruz. I know there will be numerous opportunities for collaboration in this geographic area. 

 The Brewer lab has nothing planned for MBARI Open House, so I am free to assist where needed.

I've been continuing with calculations for the power required for the over all functionality of the AUV and pretty much reorganizing my calculations and troubleshooting in areas where values seem to not be correct. As Bill put it, I'm trying to scale the world down into one little box with a couple of different options for motors instead of looking at a ridiculous amount of options. Based upon calculations, I've generated some graphs that allow me to look at such things as the impact of propulsion due to hotel compared to the power consumption and well as the power consumption compared to the length of missions. This data is important to determine optimal power, velocities and the correct hotel power of the vehicle. Hotel being everything else but the propulsion system... such as any instrumentation that will be used in the vehicle.

 I had a blast yesterday at the behind the scenes tour of the aquarium and I definitely felt like a child again! I could spend all day in there, but being able to see what goes on to make such a great experience at the aquarium was really neat. We also made a quick trip to Hopkins and got to check out the library and a gentleman there was kind enough to show us a collection of whale baleen.

Next Monday I'll be joining Peter Walz and Wilson on the Rachel Carson and am stoked to go out to sea!

Oh and I'll be working for Nettie during the open house... 

This week has been very interesting in that there has been a lot of variation in what I have done. Monday and Tuesday I been spent out to sea with the midwater lab deploying and retrieving the MRS, conducting transects, and general hunting. We were able to collect one juvenile Chiroteuthis and had another generously provided for us by the Haddock lab. While out to sea, the aquarium featured us in a deep sea presentation by projecting the live feed from the Ventana (while I was operating the camera!) during the presentation and talking to us via the radio in front of the audience. It was great to have Kelly and VGjoin us out at sea as well! It was all very exciting, and since I have been in the video lab and trying to keep my Chiros alive (which I'd better go and check). I will be with my lab group for open house. The aquarium was also very cool!

This week started off having an interesting, beneficial lunch meeting with Anela Choy, George Matsumoto and Alba.  I obtained valuable knowledge that I am sure will be helpful in my scientific career and graduate school.  By the end of Monday, the supplies for my Y-maze were delivered to my office! Whool!  

The rest of the week included various conversations with my mentors about the design and function of my project.  We were able to knock-out most of the "twicks" involving determining my Y-maze dimensions, water flow in the wet rooms, figuring how to include my stimuli (food) and limiting contamination factors, eta. I now have a well set-up Y-maze!   Today, I will acclimate my Urchins into different pH waters to prepare them for further experimentation and their sensory response to acidic waters in relation to their attraction toward food (kelp stipes).  Next week involves construction of three more Y-Mazes in building D and taking-up a lot of room in the wet-rooms! Watch-out
This week also included an adventurous "behind the scenes" tour at the Monterey Bay Aquarium and visiting the Hopkins Marine Station.  All I could think about at the Aquarium was wanting to dive-down into those huge pools! It was amazing to see the "magic" that operates everything for the well beings of the marine animals, from enormous pumps to many filters and working hands.

This week's seminar was in particular very interesting as well! Emily Carrington's presentation, and obvious passion for her science, was inspiring to lesson to and jogged some further ideas in regards to my project.

Looking forward to another weekend exploring the cities, beaches and MANY activities in Cali! Watch out San Francisco, the 2013 interns are coming to visit!

MBARI Open House: I believe I will be assisting on informing visitors about the BRS project within my lab. If this is untrue, I will be sure to notify Linda! 

This has been a half play half work week for me. Monday I accompanied Ben on the Rachel Carson. What a thrilling experience! On deck I was amazed with the large flocks of Black Footed Albatross and a Humpback whale surfaced right next to the ship!  In the control room it was quite exciting "hunting" for Nanomia sp. for Bruce Robison's respiration chamber and then watching the ROV pilots hang it on the mooring. After that we hunted for Ben's Chiroteuthis sp. which was like a thrilling high speed chase, although the motion of the boat and the dark room made me want to fall asleep...I didn't though, I watched every bit of marine snow fly by. 

Then on Wednesday we had the behind the scenes aquarium tour which was so cool. I took a lot of pictures that I haven't had time to look at yet but I will post them of fb when I do.

As for work I have been developing my sketches for Ken Johnson's C-SOBOM float project in the Southern Ocean. I just had a meeting with him, and like the other two crews I am working with, he was very easy to please. He said he was very excited with what I had to show him. Working as an illustrator is so gratifying when I make my "client" visibly happy. So, so far so good with all three sketches being approved with some minor adjustments or additions. I am ready to make my second drafts of all three projects with more definition.

 During Open House I will be working with the ITD department at the information booth and at some point I will wander around and take pictures of people enjoying themselves for Kim Fulton-Bennett's photo archive.

This week I've been working on a combination of tools and content. I am learning HTML, CSS, and some of the Dreamweaver capabilities through online tutorials.  I am continuing to work on the write-up and page layout for the GOC introduction page.  I'm starting to identify some important concepts that will need explanation (particularly some of the chemistry and geology), and researching background information on the expedition that will be important to include. 

Wednesday was an excellent day with both the behind-the-scenes tour of the aquarium and YWIS. Boogie boarding with the girls and other mentors was a blast!  We even got a special lesson on the baleen in different species of whale while visiting the library at Hopkins.

For the Open House, I'm involved in two projects.  I'm taking lead for the children's booth, and am planning to brainstorm with last year's coordinators on Monday.  I've already heard from a few people who are interested in helping (including Bailey). I'll be helping with the social media booth as well, which I just found out will be partnering with the Jellywatch booth (hello Alex).  We have been tasked with recruiting interns; so, if you don't yet have something to do, please volunteer with us! Just shoot me an email

Email: nmcmiller@mbari.org 

My how this week has flown by. I have made progress on the biology side of my project, but really need more hours in the day to get the bench top set up for my ECO puck/LISST-100 experiment going. At the end of last week I met with Jim and Denis about a possible flow-through system, and this week I seem to be adding new pieces to my project. Today I discussed culturing options from here through next week with Sebastian. It turns out that a social life is not conducive to growing phytoplankton...as I will need to come in tomorrow and at least one other day this weekend to continue monitoring their growth.

I ran another DAPI stain this week and visualized some of my plankton, both for photography and top be sure the samples are pure monocultures. Today I am counting cells on the hemacytometer to compare against the counts that Sebastian obtained from the flow cytometer for my Micromonas sample this morning. Someday soon (next week?!) I will have my bench top set up ready and can perform all of my methods in a single day, then I'll have tons of data to compare. I have to keep reminding myself of the end-goal so I can stay focused and not think of more pieces to add to the puzzle.

I'm in a wedding on Open House weekend, have a blast everyone!

This week I have been manually looking at figures to watch for interesting, or rather peculiar patterns in parameters. I have been recording all of them, and categorizing them to their respective transect so that it wouldn't seem to be all over the place and wouldn't misjudge the results based on the pattern; not knowing they belong to different location on the bay. I should be done with this today, and hopefully start venturing in data concatenation of LRAUV data, also looking at couple of glider data from CenCOOS. I went on the Rachael Carson trip with Ben, and it was great; got to see the 3715th dive of the Ventana and chilled out in the control room. Although I sort of dozed of couple times, not because it was boring but the seats were really comfortable. Dylan, Nettie,Alba, Wilson and I were in the land watch panel today, and to be honest it was a great experience. Those students put so much effort to procure all their resources in 5 hours total and proceeded to advocate their part of the argument. Some of them have never presented in public, and they did an amazing job for first timers. It might be a little selfish of me to volunteer again, but guys>>READ THIS

VOLUNTEER FOR THE LAND WATCH PANEL, it is pretty awesome.

Have a great weekend guys, cheers.

P.S. BOG won't have a booth for the open house, so Alba and I will be available to volunteer wherever we are needed

This week started with lunch on monday with Anela Choy, Kendra and George. We talked about grad school, transition from a masters to PhD, life in Hawaii and all the clichés surrounding it, PhD comics, and life after PhD. The "what are you planning to do after you finish your PhD" question came up, with the typical answer as well (from Anela and myself).

I've met with my mentor several times this week, since he's going to be gone for two weeks starting on sunday. We refined some equations, calculations, and redid graphs. I've decided to park the Atlantic thing for a while, since I'll definitely won't have time for that now. Either I concentrate on the initial stuff or I won't finish anything at all (it's thursday, and I really don't now where the other three days of the week went). I'm putting together the graphs I have for now, and I'm starting to write the materials and methods section of my paper.

The behind the scenes at the Aquarium was amazing!!! I love it there, it's all so well conditioned, organized and explained. I couldn't have imagined that each exhibit needs at least 3 years of work before the actual exhibit becomes a reality. I loved the feeding of the open ocean tank! And I really liked the behind the scenes of the jellys. The YWIS boogie boarding activity was very fun as well, looking out for the little girls out in the ocean enjoying themselves. And today I went to the land watch panel, were I got to hear the talks of some high school kids from Watsonville. I really like this on-the-side activities, they make you reach out into the public to make it a win-win situation: you gain from the people you're teaching or listening to, and you give a little bit of your experiences to the people around you. So cool! Plus, I got two free bags in two days! And breakfast! And pizza! And lunch on monday! Yay!

Oh, and Francisco hasn't said anything about Open House... I guess I'm free?

I have finished programming the microcontroler with PUCK protocol v1.4, and today it has been tested by my mentors and me executing simple command lines. Now it's time to start developing a program capable of executing all this simple command lines, and this way be able to test PUCK compliance with only one software API developed in C programming. I have started working on this development, and I've done a preliminary draft of the flowchart that it should follow in order to test v1.4 compliance. Next week I will start with the main functions described on this flowchart, thereby I would have a base program to follow working on it.

On Wednesday I went to MBA, to "behind the scenes" visit. We were able to see how the aquarium manage the water distribution systems and how they maintain in perfect state, and feed most of the marine animals on there.

I have no current assignment for Open House

Busy week this week. We finally got one of the imaging systems, the LISST-100x off the AUV, so will hopefully start benchtop work with that soon. I've also been looking at some of the past LOPC and SHA data to see if there are any correlations, as this could help a lot with determining how sensitive and accurate the method are. I've also been making a batch of new capture probes for SHA, including some for mussels, barnacles, and a variety of copepod groups. We're also hoping to start using Pseudo-nitzchia australis with zooplankton to test the confounding factor large clumping/chain forming particles will have on the optical and molecular signals from a sample.
Outside the laboratory, the behind the scenes at the aquarium was really cool, between getting to see the open sea anchovies fed and the filter room down below. I also had a lovely lunch with the seminar speaker who threw out some cool ideas that I will probably incorporate into my thesis in the fall.

For open house, I am planning to help with a microscope displaying plankton with one of my mentors.
Another great week, and things are just getting busier.