I had two main goals this week: doing more literature research on 1) Paradiopatra species. The idea is to better understand the ecology of these species in perviously described ecosystems and see how we can apply this knowledge to this study or help us better define the hypotheses of this study 2) on deep-sea sponges that are often found within these patches. In particular, one of our hypothesis is that sponges may favor the apparition of Paradiopatra patch or be linked to one of its functions. The second part of my work has been to decide how to annotate my Paradiopatra patch (what features would be interesting for further analyses) and what other specimens may be interesting to annotate along side to better understand Paradiopatra ecology. I have seen 15 hours so far and I have started measurement of the patch size.

I started out the week with one of my favorite things in the world...going out on the boat! I went for a day trip on the R/V Rachel Carson. I have worked with ROVs before, but it was amazing to see the Ventana in action. The sheer size of this rov is something to behold. Then, add all the mechanical arms and functions to the equation and you have an amazing feet of engineering. I was able to sit in the control box while the rov was being used. Kendra and I were even able to help when the Ventana collected samples of Allocentrotus fragilis urchins. We remained in the control box while we brought those samples back to the deployed Benthic Sampler where they will undergo carbon dioxide experiments.

Tuesday made for a pretty exciting day with the Day of Engineering, Science, and Technology events. I watched quite a few of the talks. It was a great way to get a sample of everything going on at MBARI. I like the fact that the scientists at MBARI are very interested in making their research and ingenuity available for a larger audience. Thus making their research address large-scale, global issues rather than just the Monterey region.

As for my project, I have already started collecting size data from video transects at Station M. I am hoping to have my data collected by the end of next week. This is perhaps too ambitious given the amount of dives I need to go through, but I want to have more time for my analysis. I am going to be converting the length data to biomass. The goal is to determine the biomass and in turn the food consumption rates. Eventually, we want to be able to make some predictions on what may happen to deep sea communities as carbon levels (and in turn, primary productivity) changes since the deep ocean is fueled by organic matter coming from the surface of the ocean.

Cheers to another week!

This week saw continued fine-tuning of our VARS database retrieval scripts and continued familiarization with the resources and species associated with our proposed midwater ecology/population dynamics study. More exciting though, was the collection of an actual ROV dataset, with about 900 midwater dives from Doc Ricketts, Ventana, and Tiburon combined. This dataset contains over two million annotations and spans over 20 years in time - so we've got plenty to work with! Most of this week so far has involved cleaning up this dataset, filtering it for particularly interesting taxa, and beginning to work on some basic data visualizations so that we can identify interesting midwater taxa to focus our attention on. I've been working a lot with R to generate plots that allow examination of taxonomic trends over spatial and temporal axes. A productive and exciting week 2, and not without a few computer crashes along the way!

My main goal for this week was/is to read up on how to use pgbench and learn how to use the results from pgbench to make configuration changes. Since the pgbench tool uses a few other tools, like pg_buffercache, within its execution I also had to read up on those tools. I did have a minor setback yesterday when I broke the virtual machine I was using and had to spend some time getting the new one to the same point the old one was at. I think this was a good thing to happen now though, since it's early in the internship and it made me start taking snapshots of my VM, so I will be ready if it happens again.

Aside from my project, getting to partack in the DOEST event was great. I enjoyed seeing some of the research that is currently going on at MBARI and talking to some of the MBARI board members and staff is always fun. Although I know I need to work on my networking skills since I'm not that social of a person.

I got to start the week with Miguel, Larissa, Kendra, and Nettie out on the Rachel Carson, and it was a beautiful day on the bay. The Barry lab was deploying the benthic respirometer system (BRS) at 200m, adding urchins to the chambers, and bringing a few urchins up to the surface for further analysis. The dexterity of the arm is amazing to see, from picking up urchins to shooing off a particularly sessile rock fish to closing the BRS chambers. It's easy to forget how much life is on the seafloor even in the absence of light, and the abundance and diversity of macrofauna is fascinating.
Besides enjoying the ship time, I also collected whole water samples by bucket and several surface zooplankton tows with an 3m, 80 um net. These samples are for some possible work with the sandwich hybridization assay (SHA) that I've been learning.

Tuesday's DOEST talks and reception were an interesting way to get an overview of some of the research currently being done at MBARI. I attended quite a few talks during the day, and also enjoyed hearing the board's questions. The reception was a great way to practice meeting people, and while I did have some good conversations with both MBARI researchers and Packard representatives, I feel like networking is a skill I still need to work on.

Yesterday, I spent the morning running an SHA protocol from start to finish on two samples of Harpacticoid copepods that I isolated from culture last week. I feel that I am getting to the point where I could run the entire assay with only a few questions to confirm the protocol or best way to do a step, which is great as I suspect I'll be spending a lot of time on it this summer.
I also filtered the whole seawater from Monday's cruise to make filtered seawater, which is very useful in working with live organisms, as well as using for creating a control against which to test environmental background.

Going forward, I plan to look at the net tow samples from Monday's cruise. Julio Harvey has developed probes for annelid worms as well as the larvae of some crabs, so I will hopefully be able to isolate some of these from the net tows to test the probes on. These probes have been tested on laboratory cultures, not natural samples, so I'm hoping to find enough to work with.
In terms of the AUVs, we're waiting for the L-OPC or the LISST-100 to be made available independent of the AUV body so that we can start running known quantities of copepods through both the in situ system as well as the SHA molecular technique. Hopefully we'll be able to do that soon, as I'm becoming more confident with the SHA technique and I'm looking forward working with the in situ sensing systems.

So far this week has been pretty productive, but definitely not without its frustrating moments. My goal this week was to 1)continue reading literature based upon WIG (wing in ground effect) crafts and 2) get through my calculations for power needed for both modes of the craft. I've had some fun trying to determine the affect of ground effect on lift and drag in comparison to 'regular' flight. The AUV is designed to fly only about half its wingspan above the surface of the water, so about 2 meters--this creates an air cushion that reduces drag and increases lift.  This step is incredibly important for determining the potential propulsion configurations and whether or not the same propulsion system will be sufficient for both air and water.

I'll hopefully start looking at efficiencies of different propellers tomorrow and the start of next week.. As I begin to add components, I'll add to a weight and balance spreadsheet for the entire vehicle. It's been really nice having Bill back this week so we can discuss potential ideas. These have included such things as having the aircraft flip over for when its in the water and looking at ways for the AUV to take off from the water on its return flight.

On a lighter note, I really enjoyed the DOEST!! I feel like I've been so focused just on what I've been working on and its awesome to hear about some of the other MBARI projects. The scope of what MBARI is doing really is inspiring. This was also a great chance to meet some very interesting people and work on networking. Bill was a great wingman who took me around to meet a lot of the board members.

This week has been mainly a literature search for background information on my (and related) study organism. I am mostly trying to get all of the sources/info I need for my introduction, methods, discussion, and data analysis. Since my mentor has been busy this week with the conferences, I will find out later today if my topic will be approved by meeting with the members of my lab and my mentor and discussing the aspects of my project. There will most likely be some adjustments made to it, but hopefully the work I have put into it this week will not go to waste. This week I have been in contact with some of the other people doing research in this field and I don't think that I will be stepping on anyone's toes as a behavioral ethogram for this species has never been done before!

It was great to go to DOEST and see some of the research going on here at MBARI and have it explained to me in a manner that I can understand! I also enjoyed meeting some of the board members and attending Anela's seminar. I am really looking forward to going out to sea again next week!

I started this week looking at some Matlab scripts from last year, and remembering what we had done. There is a potential other project which is to replicate what we're doing in the Pacific, for the Atlantic. So I have been modifying last years scripts with some improvements and some setbacks, most of which are due to the fact that Matlab keeps on doing strange things and won't select the data I'm asking him to . I'm meeting this afternoon with Monique Messié, who works with Francisco too, and knows her way around Matlab wayyyyyyyy better than I do. I'll show her what I've done, what I think the problems are, and see if we can solve this together. So hopefully, by tomorrow (finger's crossed), I'll have at least being able to creat a mask for the Atlantic and select the pixel nearest to the eastern coast, which is were I'll select the data from in later steps.

In other more exciting news... I went to some of the conferences of DOEST on tuesday. I really liked the ROV videos showing what they do on the sea floor: collecting invertebrates and putting them in the benthic chambers. It looked very interesting! Hopefully I can go on another cruise that does something similar... I would really want to be in the control room and do what Larissa and Kendra did on monday!

Back to the project: for next week I have to get together with my mentor and other members from the BOG group, discuss the results that we have so far, and see if we need to do some recalculations (or not) so that I can start describing these results and try to figure out what they mean and how I can explain them. Francisco also wants to get together with VG and me to review/discuss a paper; this will be an interesting and useful tool, just in case we get a paper to review someday.

No more (for now)... new reports on monday!

I started off week 2 participating on the R/V Rachel Carson Cruise early Monday morning! While on the cruise, a Benthic Respirator System (BRS) was deployed! The BRS is a magnificent AUV capable of testing on marine organisms in response to different pH levels (CO2 injection from an air tight bag, attached to the BRS. Using the Ventana ROV, the crew was able to explore the benthic seafloor in search of Strongylocentrotus (or Allocentrotus) fragilis to be used in the BRS. The urchins were initially difficult to find, but thanks to Jim Barry and the crew, soon hundreds were found at 220m.  It was extremely interesting to see how many there were and their mass aggregations. 

                Furthermore, Tuesday was DOEST! It was an opportune day to meet the faces of MBARI, including the Board of Directors, researchers and staff.  Once again, MBARI blew my mind with the amazing scientific work that is and will be performed! All speakers were extremely intriguing in their work. Personally, I took a great interest in the XFOCE project and Jim Barry's Benthic and midwater respiration studies.

Speaking of benthic respiration studies, this week I was able to progress in the design and steps needed for my project.  I will be looking at behavioral and physiological responses from S. fragilis (urchins collected from Monday) when prompted by kelp stipes (giant seaweed they feed on) and/or affinity to each other, while exposed to different pH levels. Next week, I will be working on building the Y-flumes that will be used to perform my experiments.

While working in the Benthic and Ecology lab this week, I have spent much time familiarizing and researching scientific papers in relation to my project. Also, I have been trained on the pH spectrophotometer, Alkalinity analyzer (TitroLine 7000) and the CO2/H2O Analyzer (by this Friday).

After several meetings, lots of reseach: reading journal articles and expedition logs, looking at all the framegrab images available for each expedition, Google searches, and video lab visits; my main goal for the week was to complete not one but two sketches, one for each of my first two projects, and to send them off for feedback. So far, I have emailed off the first sketch to the Iceberg AUV team, Ken Smith's crew. And next will be to complete the Seafloor chemistry sketch which will be sent out tomorrow morning.

The DOEST seminars were very interesting, and due to Ken Johnson's talk on his upcoming global float project it is now imparitive that I do the third illustration. I met Ken after his talk and he said there was a lot of interest in an illustration for this project, specifically from Princeton. With all of the international attention on this project I would be foolish to turn this opportunity down just because I wanted to get some sleep at some point during this internship. So Nancy Barr, my mentor, and I have a meeting with Ken on Friday.

 This week has been very busy for me as developing sketches is, a lot of times, the most difficult part of the process. But next week is going to be a whole lot of fun. I am going out on the Rachel Carson on Monday, and then we go to the aquarium Wednesday. Oh, I just realized I will miss our fabulous cookie break-how sad-but I will be at sea with Ben looking for mid-water critters!

This week I continued my work growing up my algal monocultures to ultimately run on the ECO puck and LISST-100 sensors. I was trained on the Accuri flow cytometer by Jian, which I will also use to determine size distributions and fluorescence of my five strains of phytoplankton. I have made a lot of progress in the biological side of my experiment, but am still working on my experimental bench-top set up, which was the original plan for this week. Today I've run a crash course in optics and reflective properties of seawater and particles of various sizes by way of literature searches. I feel like I'm learning a ton but still need to track down a couple equations to properly set up the experiment and get some preliminary results. I feel behind schedule in this respect, so hopefully I can make up some of the time by reading and working on my paper on my flights to/from Washington. My plan next week is to dive right into DAPI staining and quantify the fluorescence values I've been taking (converting to cells/mL), and begin running the filtered artificial sea water (ASW), glass beads and ultimately the algal cultures on the bath-stlye (ECO puck) and flow-through (LISST) systems.

Oh I got my webpage set up! I promise I will get you guys the blog info soon. Maybe that will be my Fri morning flight plan - write the welcome blog post.

Fun stuff I did this week...the Surfing Squirrels won our first game, that was rad. I went surfing yesterday with some of the interns too, it was windy but a lot of fun.

Interns host the cookie break next Monday! I can't wait.

This week is going well thus far.  Going out on the R/V Rachel Carson was a great experience! It was interesting to see the ROV in flight, and to hear the communication amongst the pilot, scientists, and members of the crew during navigation.  The DOEST presentations were fantastic.  It was nice to get details on the different projects I've been hearing about since I arrived.  Listening to the questions from the board members, and speaking with a few of them during the reception was another highlight of the week!

I've narrowed my project focus, and am now investigating the Gulf of California (GOC) 2012 Expedition.  Specifically, I will be designing a web page for the fourth leg of the expedition which investigated deep-sea chemistry.  I reviewed the MBARI Style Guides which outline the standards used to convey information both internally and externally. I'll be practicing incorporating that format into my writing.  For now, I am drafting an outline of the webpage and a summary of the content.  I'll review those with Connor when she returns next week.  An additional component of my project is to seek out educators and learn their perspectives on the use of scientific media in classrooms, which educational tools they view as most effective, and what resource developments would they like to see in the future.  I've come up with a set of questions, and hopefully the answers I receive will help guide my project!

This week I've been reading all the programming code used to implement PUCK protocol on Luminary micro controller that my mentor gave to me. I've detected which parts have to be modified, in order to make this code PUCK protocol v.1.4 compliance, and I've started working on it.

After a couple of days without being able to solve functionality bugs, I've just solved them. So I have made a lot of progress with the micro controller program, and I'm close to have it working properly with the CTD.

Furthermore I went to some DOEST seminars on Tuesday, which I found really interesting, although I would like to assist to the wave glider demonstrations on building B. I look forward to go on a glider mission to the sea and be able to sea how it works.

Now it's time to start reading information about how was made the previous test tool for PUCK v.1.3, in order to port this tool to TCP/IP stack, and this way be able to develop the PUCK protocol system and its testing tool which is the goal of my internship.

I've managed to sort all the data (well AUV/CTD data for now) that I needed to run some of the visualization I wanted, and I successfully did not mess it up. With some of the sensor data on the AUV I plotted a 3-D plot of one variable (say temperature) that contain long-lat and depth properties on the bathymetry of Monterey bay. Since this worked, and I am content with myself compared to last week I am going to set a threshold for depth so that I can study boundary layers close to bottom. Once Matlab cooperates with me, I should have a visual comparison on how with bathymetry, that variable behaves;but we already know that with changing depth it gets colder, higher nitrate levels etc. However for future study it will help show within the mission transect which particular area has an interesting pattern even within a scale of 24 hours.

We had the DOEST event on Tuesday, and I tried to attend most of the talks and they were excellent; inclusive of how to present their science to an audience that not necessarily have their field of expertise pertaining to the speakers'. At 4 o'clock when the social event took place, some of the interns and I gathered contemplating on who to start the conversation with, and with much surprise Julie Packard came up and initiated a conversation with us. I am not sure about the rest, but I was trembling with humility and to an extent fear. It was great to have the homebrew share their elixir of courage, some amazing stout, wheat beer and pale ales.

In my first few days at MBARI, I've become better acquainted with my mentor's collaborators: Ed Peltzer and Peter Walz. I feel like I've gotten a lot done this week alone. I've been introduced with the experiments I'll be helping conduct. I have a better idea of scientific questions my project seeks to answer. The scientific questions are interesting and important! I'm looking forward to sharing more during the next weekly intern meeting.

Additionally I've been reading related scientific literature papers and set up an Endnote folder for my references (something I suggest for others to do!). I started the methods and introduction section of my paper. I've been documenting the fabrication process of the ROV attachment arm that will be used to conduct the experiments with pictures and video to share in the presentation, paper and possibly the blog that Diane is working on.

This week has been very good. The co2 snesor is running and working. In addition I was able to attach the clock and memory to it. So  basically what I have right now is a sensing device of Co2, temperature, and RH which allows me to do real time measuring and store all the data on a 256kBytes memory.

The next step of the project is to program the module to work in ultra low consumption mode (sleep mode)  for a controlled period of time; until it has to turn on and start doing measurements. Also program the module in a way that when it finds the base station, which will be connected in a computer, to send all the data stored into memory via wireless.

We had a lot of activities this week. Somehow, I did manage to squeeze in some work in between. After many hours wrestling with solidwork's FEA analysis tools I have nearly finished a design for reinforcing the pressure housing on the benchtop ballast engine. I just received some quotes for steel bar stock. All I have left for this portion of the project is to order raw materials, and send drawings to the lovely people over in the shop! Hopefully I can send over the drawings tomorrow morning. Tomorrow I'm going to switch gears and start wiring up the RS-232 connected DC motor as well as force and pressure transducers which run through a Ni-DAQ. My goal is to have the motor and transducers up and running by the middle of next week!

This week I was able to plumb a 6-way injection valve onto the fluorometer as well as hook up a peristaltic pump and heater  block  to the sample and carrier. lines. I was also able to get timings down so I could get repeatable sample volumes in order to create a standard curve. This curve will ultimately enable us to calculate the concentration of ammonia in the sample. While DOEST was going on I went to a variety of talks in the morning that I found really interesting. At the reception I was able to talk to a few of the board members  and representatives from the Packard Foundation. Everyone was very nice and interested in how I found out about the internship. The amount of knowledge contained in the area outside of Pacific forum was staggering. In between talks and meeting board members I began working with lower concentration standards and changing the emission wavelength we were observing. Since the ammonia levels we are trying to detect should be very small we are able to look at emission wavelengths closer to the ideal emission peak of ammonia. Bubbles within the instrument created noisy data but after they cleared I was able to get usable data and get the instrument zeroed for lower concentration samples.  Wednesday was spent troubleshooting  issues within the instrument and oversights by me. I began having issues with flow going the wrong direction after I changed tubing diameters and then a minor catastrophe when a line ruptured at the pump. I also realized after Patrick brought up some doubts to me that I had miss-typed a formula in excel that I was basing my calculations off of. The error was corrected and to assure ourselves that the numbers were good we collected empirical data on flow rates for the different tubing we were using.  Today Patrick and  I went out with Tim and Margarit on their monthly CTD cruise on the  Rachel Carson. We assisted them and another researcher Mia with their work and then collected some low-nutrient sea water to use as standards in the chemical sensors lab. In addition to aiding with sample collection and processing from the rosette  we made an attempt to locate a BEDS sensor that had lost communication with the monitoring network. The Carson made a single pass over the last known location but the acoustic boom was unable to get a signal lock during this I helped communicate between the bridge and the ROV control room.  The weather was a little rough on the way out the M2  and got us a bit uncomfortable but all in all the cruise was a success.  Tomorrow I aim to add more tubing to the Fluorometer setup so that we get the required residence time in the heater block for each sample. This will allow for rapid sample injection and processing.