During the last week, I watched ROV videos! I will be done tonight!!! So Monday Linda and I will retrieve the data from VARS (the annotation software) and I will start playing with data,. I also had several discussions with Linda on how we can deal with fauna associated with my tube mats, I also have been introduced to old camera sled pictures and I am going to look at some of these pictures to enlarge my time-series data set. We also had two meetings about the Open House, We will be in Ken lab tent (Climate change tet) with mini ROV, plane with camera, data and pictures from the cold and Sta. M video transect (Larissa is doing a poster on megafauna and I am doing a poster on infauna).

This week progress is definitely being made! I have finished the data collection of holothuroids from the 2012 transects. Now I am going back to older dives to obtain a little more data over the breadth of the study. I am starting to get excited about the analysis and conversions that I am going to start next week. I think having biomass estimates of these populations will add a compelling part of the story of deep sea populations. There is just so much we just don't know about the deep sea organisms! I have definitely come up with hundreds of questions that I want to know about...about their larval cycles, nutrient uptake, morphology, and even their associations...but their is definitely a gap in knowledge when it comes to the deep sea.

On another note, Claire and I have attended several meetings with the Smith Lab about Open House. It is very funny to see just how competitive this lab is when it comes to open house...I would tell you what we are doing, but I think it is akin to classified information at this point.

Cheers to another week!

I've been inching closer to actually running experiments this week, finally! We've gotten the LISST-HOLO off of the Dorado AUV, and I am in the process of learning the software for it, though am still awaiting the arrival of the ethernet cord that will complete the picture. I've also been setting up my copepod and Pseudonitzschia cultures so I can start running experiments as soon as possible. Thankfully a test run of the probes for both these groups found very similar signal strength and variation, so hopefully I won't have to correct for that. I also determined that isolating the nauplii from my cultures is uselessly time consuming at the moment, and can hopefully be abandoned in favor of working with the more easily isolated adults.
I'm also still slowly chipping away at the five years of data from the LOPC and corresponding SHA analyses to look at any correlation between the data sets.

Looking forward to the bbq at Hopkins tonight!

Hey Fellow Interns! I've had a great week (I think I say that every week, I love it here!). The majority of the week has been spent analyzing spectral data gathered on last week's cruises. I am using a software program to make baseline corrections because the intensity of the Raman laser can fluctuate during data acquisition. From there, I'm using the same software to do integrations of spectral peaks of the compounds of interest. This process is somewhat time consuming because the two chemical species of interest, decane and methane, have overlapping characteristic spectral peaks. Separating the two involves a deconvolution process in the GRAMS software. I'll learning a similar deconvolution process in MATLAB today. I'm excited to learn some basics about MATLAB. I know it is skill that will come in handy in the future.

Hey guys! I have to agree with Wilson on this one... I sure love it here. Only problem is it goes by too fast! I have almost finished collecting my data for the part of my project that deals with the juvenile Chiroteuthis calyx and Nanomia bijuga behavioral comparison and now I am back to looking at the juvenile's behaviors. My list of behaviors is getting more complete and I am trying to figure out how I will quantify their behaviors and reveal novel information about this species. The three things that I have on my list for my project will be to examine the aforementioned comparison (almost done), compare adult and juvenile behaviors (getting there), and determine the typical threat response of most juveniles and offer some insight as to why they do what they do (getting there). Most of my lab is out of town and the post doc, Henk-Jan, just left, so it's just me and my lab mate for now!    

Its pretty crazy to think that we are almost finished with week 5. I pretty much finished with calculations at this point for this part of design, but have just been spending the week manipulating numbers to try and determine the flight envelope for the air flight portion.With a series of graphs I have been looking at the climb/takeoff performance and the steady flight performance and have been focusing on determining the impact that small changes in the overall weight will have as well as the affect of velocities on required power. This was going smoothly until I realized that values weren't matching up. I tend to not use xcel very often, but for the amount/type of data and numbers I'm looking at its the most useful, but right now it is being very temperamental, so I've being trying to fix those problems.

Bill hasn't been here this week, so I'm looking forward to Monday to discuss some of the information we are looking at. Before he left for the week, we discussed some potential ideas for the motor and based upon the specs for power, we thing we can used just a go kart motor for propulsion and have thrown the idea around of designing a hybrid motor for the AUV, which I think is pretty cool! So we'll see when I talk to him again! 

 Looking forward to the BBQ tonight, as well as, Arreyo seco on saturday!

Week 5 holy cow!

Well, sadly Ken Johnson's C-SOBOM collaborative float project with Princeton lost its NSF funding. Just like that-Poof its gone. So my opportunity to have Princeton publish my illustration also went Poof! Sad, but Hello real world. I will still do Ken's illustration I just don't know the details at this point.

OK so moving on, I completed a second draft of Ken Smith's Iceberg illustration and I have received good feedback and recommended changes. They have also requested to use what I have so far as a poster in their Open House booth. That will be fun.

And this week has also been full of Intern T-shirt madness! (madness in a good way).

We have all come together to make a decision on the design. It will be a colaborative effort between myself, Nick, and Ben. So hopefully it will be amazing and make everyone happy.

Hello guys let me just tell you something to release some pressure 50% done, it is going so fast :'(

This week has not been the greatest so far, I start the week by getting my sensor wet, so I had to change he sensors and recalibrating using some Serial communication commands. That process took me around day and half. On Wednesday I could finally restart  the experiments in equilibration of the Teflon AF tubing in water. So far, what Patrick Ken and I have discovered is that the Teflon AF tubing is not equilibrating pretty well on low CO2 concentrations.  it takes too long to equilibrate and it does not quite get to the point we want. Nevertheless, for high concentrations of CO2 it does a pretty good job. More experimenting needs to be done in order to get to a point where we can equilibrate the Teflon AF tubing with any CO2 concentration.

Changing topics, I am almost done with the radio communications for the node (sensor with micro controller) and the base station. After doing that in my free time I will try to work on the user interface so it will be easy for an user to program the sensor. I have to learn a little bit of Lab View to do that but I know it is a powerful tool that will become handy in the future, so I probably should learn it pretty well.

Week 5! * Begins humming favorite Bon Jovi song to sing along with during marathons... *

This week has been productive but not as stressful as the past couple. I think this is a good sign that things are coming together to begin running my experiments with calibration beads and the actual organisms. I am awaiting one piece of my project (black out material) before I can make definitive statements about size distributions of my monocultures. I have also worked a bit more on my paper, which I've been neglecting thoroughly for the past week and a half. Must stay on top of writing and taking notes so my final paper comes together nicely.

I also met with 2/3 of my thesis committee earlier this week and we chiseled away at my 4 questions and have focused things a bit, which is thrilling. I have to re-write some of my proposal because of that conversation, mostly background and methods, but the good news is that this internship project will still be a large part of my thesis work. I'm happy about that.

Upcoming: Local marine science interns social BBQ, kickin it with the interns in Arroyo this weekend, intern BBQ on Wed, and my first Rachel Carson cruise on Thursday. I'll be helping with what I can set up for open house before I leave after work next Thursday. If you guys know of anyone needing help before open house then let me know, I'd like to do what I can since I will be in Virginia as a bridesmaid that weekend. I'm bummed to miss the open house this year, but will be thinking of you guys.

Early this week, I spent time on working with the "old" sea urchins and observing their response when used in the Y-maze experiment. The Y-maze contains two inlets (cues) for the urchin to decide between, 1) inlet with flowing kelp water and 2) inlet with ambient pH water. We expected the urchins to crawl-up the kelp inlet, in search for food. Our expectations were proven correct!

 This week my mentors and I also officially set-up the Y-mazes in sea-water room A! Set-up involved placing the large Y-mazes safely on the ground, insuring equal water flow and accurate pH concentrations to each inlet, LOTS of tubing organization allowing water to flow to the mazes, camera set-up to view urchin progression, and set-up of kelp buckets for each Y-maze.  We have three Y-mazes set-up for three pH levels (7.2, 7.5, and 7.8).   Acclimated urchins in their specific pH levels (prepared from last week) will be tested in these Y-mazes to observe if there will be a difference in their response to food when exposed to lower pH waters.

The goal for next week: Collect a WHOLE BUNCH more urchins on the Rachel Carson cruise on Wednesday! This means a lot more experimentations, hence data collections! The more the better.

It's good to see everyone else's projects progressing.

I've spent the past week or so trying to get reproducible results with varying degrees of success. Late Monday morning my mentor brought up the possibility of tagging along another CTD cruise with Tim and Marguerite to M2. Shortly after we got confirmation with them my instrument stopped co-operating. As it turns out affter days of trouble shooting and banging my head on the desk my lack of reproducible results stems from an improper dilution I made on day 1 that I have been using since and just recently ran out of. This required me to make a new standard that was diluted properly, only I didn't realize the old one had been made wrong. So I thought I was going insane for a short while.  After realizing my busch league error  and quintuple checking all of my subsequent dilutions things have been going great. It's looking like I will be able to get the results close to what we were hoping for, and after Monday I will have blue water field data to analyze .

    My quest to automate the data processing has been fruitful as well. I have gotten python to graph most of the things I need and am no focusing on formatting and otherwise beautifying the graphs. I also had a short discussion with Josh Plant(another of my mentors, who works in the background) today that gave me some hints to help handle the data easier. I will be furiously working on finalizing testing protocols and preparing supplies for our cruise Monday. It looks like it will be a +5 day week for me, but the work is fun now that things are going well again. 

Keep an eye out for me on the video feed Monday.

Here's my confluence update, I would like to point out for Andrew that I have not shanked myself yet. (I spent about half an hour removing high strength tubing from the bench top pressure testing system so I can rework the hydraulics). Besides from that, today has been pretty productive. I built a new simulink model for estimating the added mass of the test tank prototype profiling float, and I've put together some equations for estimating the drag coefficient. Wayne is working with the test tank model right now, so I probably have about a week before I can perform those tests. I also rewired the MTS position sensor that we use to measure the external bellows extension and I have verified that it works.

This week I have also started writing up my report and worked with Gene and Ginger on a particle counter based on the Coulter principle. We've run into some small problems with getting consistent detections. Hopefully we can make progress on that soon!

It's hard to believe we're finishing week 5! This week I've been working on an animation about methane hydrates, which I'll be adding audio for soon.  I've been looking at videos and images that will be good to use on the site, and scripting/labeling for those as well. The VARS annotations have been extremely helpful for pinpointing certain indicators of the chemical activity specific for this expedition leg.  I also hope to speak with Edward Peltzer today to get his input about the expedition and my ideas for the site.   

Also, I'm headed to Hawaii next week!!! I'm super excited about the EARTH Conference, and the opportunity to learn from all the people that will be there. Also, I hear it's beautiful and warm which I'm really looking forward to .  This week I've been getting prepared for Open House next Saturday (the day we fly back!).  The children's booth is going to be a ton of fun....I can already tell by the boxes that are invading my office space!   Next week if going to be a whirlwind of activity, but I'm definitely looking forward to it!

This week I could finish all the compliance tool test, and now I'm working on the device auto discovering on the network. This means that I have to apply Apple zeroconf browser to my app. developed in c language and be able to integrate it in only one running program. This way when a user executes the test tool, doesn't need to search for its IP and port, he only needs to know what is the instrument functionality or its name. This way it won't be necessary any knowledge of networking in order to execute and understand this PUCK v1.4 appplication

Also, today we have the bbq with MBA, Hopkins and NASA interns, which I'm sure it will be a good opportunity to know more about their projects and to have a REALLY REALLY GOOD TIME...

This week I've worked on trying to figure out what setting changes would shift when the TPS was dropping off in a graph I produced. The first settings that I thought would cause the desired change, failed to produce any noticeable difference. Then after doing some more reading I found a different setting to change, which so far has produced the desired change. Along with this I've been working on learning what iostat and vmstat outputs can tell me about were, if any, bottleneck is happening.

The seminar this week was very interesting to me, since I'm thinking about going into the field of AI in the future. Projects like the one Michael Benjamin describe

I found the seminar this week very interesting, mainly because I'm planning on going to the field of AI in the future. Working on AI in the realm of uuvs is something I have been thinking about more since coming to MBARI and getting to see a project in that area was very informative.

Also tonight is the BBQ with the other interns and I'm really looking forward to finding out what other projects people are working on. This will also be a great change to do some networking, which is always a great thing.

Ok. So you've got to be kidding me. Half way through? Uh-oh... Seriously, this is like we're in some kind of time capsule, were time is going way faster here than anywhere else.

Anyway... On Monday, I was doing graphs for the paper and I ran into some results I didn't understand. I had already included denitrification values into our model, but there were some constants I didn't get. So I had to talk to Monique about that. And also, I was redoing some calculations that didn't match Reiko's (another researcher that works in Francisco's group). Monday ended up with neither of us knowing where we had got those results from, and having to look at Matlab scripts to work it out. On Tuesday we got a clue, and on Wednesday we realized no more calculations had to me redone; we were just mixing things up. So graphs are already made and I put together a paper outline for Francisco to see what we have and what we're missing. I have to read papers to put together an intro for next week.

In other matters, I'll be working with Nettie, Bailey and VG in the children's booth for open house. I'll have to dig up my drawing skills!

And I am also looking forward for tonight's BBQ; it'll be fun. And I am also very excited for our weekend's adventure to Arroyo Seco!!! Iujuuu!!!

I have done quite some reading about topography influence on physical and biological properties of shelf and deep waters. My focus has been all over the place, because it's the coast and there are a myriad of interesting relationships going on. I had a meeting with my advisor from Moss Landing, and we spoke about things I should focus on, things to pay attention to and what not. There are some backscatter that did not have correlation with chlorophyll fluorescence, and this either meant it was cross-shore, on shore transport of dead plankton, lithogenic material or resuspension of benthic sediment. With trends that seem to change cross-shelf, I would be looking on excursions of these mass of material and try to figure out their origin, and estimate the hot spots. Like I mentioned there are a lot of interesting patterns that I was able to note down and plot, but with the half-way mark already passed I am going to pick one and focus on it.

The cruise has been a great experience so far, and also has really allowed me to connect the dots between my project at MBARI and the actual organisms we're studying. The last few days, between the ROV footage and samples , have allowed me to gain a better conception of what these data actually describe - what does it mean for an animal to appear in our database as an observation? Seeing exactly how this data is collected, along with some time behind the annotation station myself, has given me a new perspective on the data that one can only get in the field. We've seen all kinds of cool bioluminescence, ctenos, jellies, and cephalopods out here - having a blast! Also really fun are the trawls I've been doing - a sort of grab bag of interesting mesopelagic gelatinous zooplankton, crustaceans, and fish.