Can't believe I'm writing another confluence post, it feels as though I wrote the one just a day or two ago... I still have things I need to figure out with the WIND server web pages. The Sample Database is more problematic in comparison to the Expedition DB. Could be because of all the images. Anyways, I'm doing okay.]

Highlight(s) of the Week:

Seeing an otter (almost) everyday of the week.

I got a lot done this week. I solved the oscillation problem that I was having for a week last week and was able to implement it onto the proto board. I did the testing for all 4 electronic load and was able to output constant voltage with no oscillation. I also completed the 4-20mA current loop. I testing the 4-20mA current loop with and without a digital to analog converter (DAC) and was able to get the results I want. I am in the process of proto typing the circuit so I can have it in my instrument simulator. So far, I have been able to complete the tasks asked by Chad. I went surfing two days ago and it was a lot of fun. I really enjoy taking breaks on the beach after completing my tasks.

I am clueless how we are already finishing week three. This week I have been running tests on some of the parts I ordered last week such as CO2 and water permeability. I have also discovered some glitches in the code. When measuring CO2 the ppm are usually around 300-500 range. My sensor will randomly say that the CO2 ppm is 42, I think I have discovered the meaning of life. This weekend off to Yosemite and next week I hope to have my sensor mostly built.

Week 3 almost complete...basically 1/3rd of the way through...why must summer want to leave so quickly. I know I keep repeating it, but gosh darn it time is going by fast and I want to enjoy the summer here as much as possible!

Anyways, onto the project! The code I made for the offline version of the argo_active.txt file works perfectly; however, I made an exact copy of the code so I can use it for the inactive file, but the code doesn't work. The files look exactly the same and I'm a little confused as to why it doesn't work the same.There's also this argo_all.txt file that's a combination of the active and inactive file, but that doesn't work either (I'm guessing it's because the inactive one is in it and he inactive one also gave me a hiccup so the all file will give me some hiccups as well). So that's what I need to work on.

Other than that it's been smooth sailing.

Week 3:

I think I am just as shocked as everyone else that week 3 is almost over. I am still reviewing pulse images for ents. and this morning finally got my hands on a copy of adobe so I can zoom in on images. Some of the animals I am looking for are located in the very back of the camera's field of view and while I can make them out from their distinct pattern of movements I would like to have a higher quality image to look at their lepensspuren. Today and yesterday my computer has been running at a glacial pace which is extremely frustrating since I am working with files that contain ~6000 images. I am hoping to work through the weekend and put a bigger dent in this project prior to the long holiday weekend next week... we will see how that goes!

Week 3:

Trying to pursue several lines of inquiry at the same time is a little difficult to manage. I've been trying to write/interpret code to match sequences of sponge silicateins (proteins needed for silica deposition) to transcriptomes of radiolarians, and it's been really frustrating. In addition to my own lack of programming ability, the database is missing one of the necessary files (even though the online search had it?), and the MBARI scripts are mysteriously malfunctioning (or I'm using it wrong, who knows). Luckily, I don't have to do that all the time, and this week I learned how to use the SEM over at Moss Landing Marine Laboratories. This means I can get more pictures of the structures themselves and spend some quality time with ImageJ. Modeling the spheres has kind of fallen by the wayside, but more data should help move that in the right direction, too. The SEM also lets me look at the structure more dynamically, and just yesterday we noticed some interesting patterns of irregularity that I'll try to investigate more today.

Aside from work...looking forward to Yosemite this weekend!

Week 3:

This week I accessed the BOG database using SQL, through Matlab. People at MBARI have written scripts so that you can type SQL commands in a Matlab function which will return your query into Matlab, which is great.

I also met with Rich Schramm and Mike McCann to access ROV/CTD data that has O2 measurements. There are a lot of data (32 million?). An added little project for me will be to compare the ROV/CTD data (which has never been calibrated with bottle samples & Winkler titration) to the BOG data (~700,000 O2 CTD cast data points there). I using the STOQS database, with the browser UI interface. It is amazing - for the amount of time it can save scientists, for saving me scratching my head writing SQL queries, for the beauty of the UI. People should totally try using it ...

I met with Francisco this week to discuss scientific questions, and prioritized a set of figures to complete first. I joined the CeNCOOS weekly meeting and discussed a final data product I can give them of O2 in the region.

I have signed up for Open House for the Chavez microscope booth and the CeNCOOS booth. I will need to learn/update my plankton classification skills, a nice side learning project, before Open House.

This week I finished measuring (found a protractor btw!) and have been working on our stats. I am finding the statistical analysis to be very stressful. I do not have the strongest stats background so I have definitely been struggling a lot and having to read online/teach myself a lot. Kathy has also been really helpful and great about answering all my questions.
To be honest, I felt a little discouraged during the week because I felt like I was asking her for a lot of help. Even though I know it is not bad to ask questions, I would feel more productive and helpful if I could get a lot more done on my own. As frustrating as it is, I am glad I am struggling through the stats because I think I have learned so much already and hopefully by the time I finish I will feel more confident in my statistical abilities.

This week I finished off testing gas standards and mixtures on the pressure booster system that I'm coupling with laser Raman to examine deep sea gas samples collected at Eel River Canyon. Looking at some of the mixed gas samples, I've been able to see the interesting peak features of methane, ethane, and probably propane. A critical part of my setup will be making sure the system is flushed and evacuated so that I don't have cross-sample contamination. I've been continuing to work with one of my mentors on improving the vacuum and sealing, and I get get the whole system down to a pressure of about 0.12 torr, which is great since after acquiring a spectrum after evacuation I see no residual methane. I got to meet Dr. Brewer on Monday, which was fantastic. He's been giving me papers to read on jellies and Raman spectroscopy of water, because for the lab's next big project he would like to examine how jellies convert liquid water into gel, presumably using very little energy. It's been a lot of fun working with all members of the Brewer Lab this week. Just this morning, I used the laser to look at my first Eel River Canyon sample at a variety of pressures! Looks like there is a complex gas mixture in the sample cylinders. The fact that the sample gas is wet complicates things a little further, but I'll just have to make sure that I clean and flush everything thoroughly between testing samples. I'm really excited to be working with these deep sea samples now!

Progress! On monday I started using ArcGIS to create maps of the section of the Arctic Charlie surveyed while he was doing his methane search dives. Well, to be honest a good amount of the data I needed to make my maps was already there, it took some minor tweak-age to view the sections I wanted to see. Still, it's been really cool learning how to navigate through some new software. As party of the geology team, I have to do make a poster to present at next month's open house. I will likely present my project findings up until this point and will spend the remainder of the day gathering information to put on my poster. If I do a good enough job I can view this as an early head start and rough draft for my final poster project.

Larvacean Log, Week 3:

Lots of progress! I've gotten my Matlab code to successfully trace the boundary of the larvacean as it moves through time. This was a rather monumental step considering where I was last week. However, now the problem has become figuring out orientation and how to stabilize the head of the larvacean for all the frames. Hopefully, this can be figured out early next week... if so, then the kinematic extraction will be done by the time I leave for Alaska.

We leave for Yosemite in just over 2 hours. We will be staying on the northern side of the park, in Tuolumne. I cannot wait to see the "range of light" of the Sierra Nevadas, as John Muir referred to them. I'm sure we will come back with plenty of new stories to share.

Since the last Confluence update, I have been busy taking care of my developing abalone embryos. I worked this weekend to collect samples and preserve them for later analysis. Unfortunately, the amount of 10% formalin we decided to use to fix my samples was too low of a concentration to successfully preserve them and now I have 45 samples of unidentifiable abalone embryos. Since Tuesday, I have been quickly planning for the next step to recover from my loss of data. We are ordering gravid abalone from Davenport today and acclimating our newest members to the Barry team in tubs we rigged for two weeks. Sometime in the middle of July we will start the next iteration of our development experiment and will have a new game plan for fixing our samples so they are able to be identified through the microscope – although, we're still scratching our heads on what to use after many trails.

Nonetheless, I am very excited to start this abalone aquaculture process from the beginning and I just hope I will be able to collect and analyze all the data before intern presentations on August 12th (which I am also very excited for!!)

Still loving MBARI and the people I am working with! This summer has been a blessing and I don't want it to end!

Week Three:

Another week in the books, I agree with Olivia it seems as though time has been flying by. The week started off with George giving a more thorough tour of MBARI for the REU students (Paris and Madison and myself) since we missed the orientation tour; it was amazing to me just how much is really going on here at MBARI, from the lobby you wouldn't have any clue. On Tuesday Sarah and I went out with Brian Kieft, Tom O'Reilly and a few others on the Paragon to deploy the LRAUV Makai and retrieve a waveglider, it was a pretty nice experience and my first boat trip here at MBARI. I was also able to go back out on the Paragon yesterday with Brian and Jordan Stanway using the launch and recovery system to retrieve Makai as it was not diving as it should have been. I had the opportunity to meet with with software engineer Rob McEwen and he set me up with a few documents and spreadsheets to help with my calculations. I have been looking at scales from McMaster-Carr and considering the different setups of the Center of Gravity / Center of Buoyancy tool and the design of the AUV chalks I will need to make. I have some ideas but I have been meaning to meet with Jon Erickson again to get some input on them; it seems as though he has been out of the office for the past few days, I will look into meeting with him on Monday morning after the Intern meeting. Aside from that I feel as though I have a much better view of the first half of my project, I just need to button down some specifics regarding the tool design as I am not sure about the project budget and some of the scales I have seen can be pretty pricey. The most difficult thing so far has been getting in contact with the necessary people and making continuous forward progress without having a lot of guidance, being relatively new to everything it can be difficult to know what the next best step would be and what decisions I can make in the process.

Week 3:

This week was amazing just like the other weeks. However, this week was more interesting because I have identified more species, which makes my work more complicated, but at the same time more wonderful. Prior to the start of the internship I was more knowledgeable about fish, now, because of this work I have substantially increased my knowledge of other taxonomic groups!. Also, I had the opportunity to go to the lab and identify organisms preserved in alcohol. Although I have a lot of work, it is necessary to rest and to enjoy beautiful landscapes. For this reason I am going to close my week in Yosemite!!

Week Three (yikes)

I cannot believe we are already three weeks in! Like all weeks, it has been another great week at MBARI. I got to go on the Paragon again, which was really fun. We launched an LRAUV and retrieved a Wave Glider. Other than my little field trip I have been working on my jellyfish orientation code. I successfully manually found out the orientation of jellies in different video frames and I just (with the help of Prateek) finished the code to retrieve the Centroid, Major Axis Length, and Orientation of jellies from a previous interns code. The next step will probably be to compare the manual data and the code data. Yosemite is only 50 minutes away and I cannot wait. Last weekend was great in the water but spending a weekend on ground has never seemed so nice.

Finally! I have been successful in extracting the acoustic call data of both the fin whales and the blue whales ( both are mysticetes (bandwidth decimated down to 1 to 1.6kHz) from the huge Scripps Dataset, I am currently working on the low frequency data( high frequency is 100kHz-160Hz- dolphins,sperm whale etc). As such a data extraction task was new for me I found it really exciting and it improved my python skills in the process. Currently I have 4977 samples extracted for Blue Whales and around 415 samples for the fin whales.Also recently I was able to  generate acoustic/audio specific features ( MFCC,Spectral Centroid, Entropy of Energy,Spectral Roll-Off , Energy , Zero Crossing Rate etc.) for both the whales , You can read about various audio features at :

http://yaafe.sourceforge.net/features.html

I also started working on the SVM ( Support Vector Machine) classification algorithm . I have tried out the classifier for some basic example( which are already present in the python datasets) , just to get an idea about its working. Next I will be trying out the algorithm on the extracted features for both fin whales and blue whales and to try to design a classifier which can distinguish between the two species. A lot will be revealed once I get the whole system going.

and now off to Yosemite!!!! 

Lisa Ziccarelli's update -
First day in the lab for my project this week. Kris and Kevan helped prepare for and conduct extractions for the Chavez eDNA samples. These samples will be used in addition to the quantitative phytoplankton counts to characterize diversity and I'm looking forward to the comparison. Also, some small successes in MATLAB with Reiko.