This week was a data analysis week. I looked at the density and spatial coverage of Paradiopatra patch over time as well as the patch sizes over time. I am now looking at the association from a statistical point of view. The small number of  patches make the statistic non significant for most of it. My project will help desgin future sampling to investigate Paradiopatra patches ecology over time at Station M.

The benchtop prototype is finally assembled! Gene and I have a couple of things to check before pressurizing it, but I am hoping we can have the system running under full pressure very soon. I haven't been able to work in the test tank as planned because putting the test tank prototype back together took a little bit longer than expected. Hopefully I will have time to get around to it today.

This week I have been reading up on some of the background software that make the STOQS application work. Mainly I've been reading more in depth on how databases are designed and why they are designed certain ways. I've also been looking into django and learning the basic of how it works.

Also I have been working on my paper and presentation and have finished a draft of both of them.

This week I've continued to analyze data and to work on some figures for the final project. I've been thinking a lot about the context in which I want to frame our work, which has involved review of associated literature and chatting with my mentor/other lab members. This has helped me pick out figures and decide how to present them in the paper/presentation. I've been working on a draft of the write-up as well.

Just been plugging away on pieces of the presentation and paper little by little. I'm also still working on my project--it really is never ending. Definitely ran into an issue earlier this week, but I think I've fixed it for the most part, so I can take up where I left off. Still looking at transmissions. I have some more data to look at from the 'AUV guys' on the electric motors MBARI has used in the past. Not much to share this week, but still super busy.

After doing some modifications that my mentor suggested to my project, I've been writing the final paper all week. I'm almost done with it, so I hope to review it this weekend and then send it to my mentors next week. This way they'll have enough time to review it too.
After that I'll start working on the presentation 'cause I think that once the paper is done it will be easier to prepare the ppt with all the figures I've used on the paper, just modifying them a little bit.

This week I have been knee deep in R code! Apparently excel does not like to graph more than 1000 observations. It has been good to refresh my memory of all the R code I learned in school. It has taken a bit of time to get the code done for 13 species and 9 different time periods (that is a lot of graphs!). I think I will be able to finish my length histograms for this this morning. Then I am going to map by biomass points in GIS before I go at R again to get my biomass stuff done. This weekend I need to step it up on my presentation...Well, back to work!

Hey hey! This week has been a bit sluggish. A pressure cell snafu has delayed my project a bit. The pressure cell puts lab samples under high pressure. We are using the cell along with a circulating water bath to simulate pressure and temperature conditions we observed during the ROV dives. We will analyze samples of methane, decane, and methane saturated decane through a small sapphire window in the cell using what else...the laser Raman! These lab samples will serve as references to compare with in situ collected data. Reference data will allow me to isolate the methane signal from the methane saturated decane we observed during the ROV dives. The methane signal will tell me the fraction and rate of release of methane (this is what we're after!).

Aside from my pressure cell problems, I've been starting to put together my presentation for our final talk. I'm hoping to have a completed talk by our practice presentations next week. I'm also working with my mentors on drafting an abstract for a poster session during the AGU Fall Meeting to share some of results of our work beyond MBARI (Yay for sharing science!). 

My main focus for this week was DATA COLLECTION! Meaning, running my urchins in the three Y-mazes (pH 7.2, 7.5 and 7.8) to observe their response towards a flow of either kelp-sensed water vs. plain seawater or if they are indecisive (they don't move). Next week will involve analyzing the results!

I had a big, scary hiccup on Tuesday morning with my urchins!  I came into the seawater room to perform my morning urchin check-up and discovered a tank full of urchins (tank @ pH 7.8) with NO flow of water into their tank (no oxygen input)! To my dismay, they were all in a motionless pile, where normally they are climbing along the tank walls.  I discovered the tube enabling water flow (oxygen flow) had fill out over night!

Good news is that they are slowing recovering, but unfortunately their impairment will have to be taken into consideration in my data analysis.

I have now incorporated an additional step in my experiment to perform an "upside down health test" for each urchin before running them. This simply involves placing the urchin upside down and timing how long it takes for them to flip back over. This will help determine if their health affects their response towards kelp-sensed water flow vs. plain seawater flow within the Y-mazes. As for the impaired urchins (tank @ pH 7.8), the health test determines if any one of those urchins is healthy enough to run.  In other words, if they don't flip back over within about 10 minutes, I will not use them due to the potential impact the accident from Tuesday had on them.

Nevertheless, data collection is proceeding, and as of right now going smoothly!

This week has been great for progress on my project. It started with the wonderful realization that we still have another full week before presentations and turning in our papers. I revived some of my cultures--I had let some of them get past their max growth (at which point their fluorescence values plummet and bacteria begin to take over the happy growth conditions), so I moved some into new happy growth media before that happened. This is good because it means I can run healthy cultures on my two instruments - the ECO Puck and the LISST-100, which both saw improvements in bench top set up this week. Denis helped with my ECO Puck design by creating a new, more optically-black (we think) design that I ran dark counts and two of my four cultures on this week. I am going to plot out the data for comparison between my older and newer set up. I had help from John Ryan and Denis on setting up the LISST-100 with the software package that Heather shared from a previous meeting with John. Shoot that reminds me, I wonder if I will have time to access and run some Pseudo-nitzschia samples...that would be cool. It may not happen in the next week and a half. I also helped with my mentor's project proposal for next year, in that I helped Thomas put together a budget by way of telling him what I need for this project to sustain beyond this summer. I probably should have told him to include salary for a research tech in the proposal...
This place is so cool, if you want to test something you can easily order the parts you need and build it, or start a new project with really cool instruments and make it happen.

Goals for the next day and a half: put together my presentation, work on my paper, analyze data! Maybe run another set of samples tomorrow if I can verify that everything is copacetic with my LISST-100 set up. Oh and run calibration beads on the two instruments. And run a sample with flow cytometry data as well. Order sea salts..oh the shopping list, how it grows.

This week has been a lot of writing and organizing to make sure all the page content flows smoothly.  I've spent a little time in the video lab listening to and watching parts of the dives.  I've also been piecing together my paper and presentation.  Things are coming along slowly, so I'll probably come here this weekend to make sure things keep progressing. 

Oh no, it happened again. I plan to post around 11 and then too much happens around here to remember to do so, like whales feeding right outside and meeting a former fascinating intern, and talking to my fabulous mentor about our upcoming weeklong expediton out to sea with the Peter Brewer sea floor chemistry crew! Yipeeeee!

This week I have been very busy creating the methane mounds illustration. It would be nice to have it completed today but it is looking like it will be tomorrow.

I emailed what I have so far to the sea floor chemistry crew but haven't received feedback yet due to this being a very busy for them with their 2014 proposals and all. I hope I will only have to make minor changes and nothing major at this point.

I will make my presentation this weekend and next week finish up my iceberg illustration.

I have been working to finalize a testing protocol using the newly attached diffusion cell on my instrument. We had planned on deploying it last Thursday but we had to postpone it to Monday, which got postponed to Tuesday, which got postponed one more time to next Tuesday.  I was having issues with getting the sensitivity dialed in, getting the sample into the flow cell and a few plumbing issues.  Yesterday was my mentors last day at MBARI and a few of us had planned on taking him out for a beer after work, but he left before we could surprise him so that was a bit disappointing.  After I got the testing protocol finalized I began catching up on data processing and outlining my paper. I'm also catching up on the many journal articles I  want to cite. My last goal is to have my python scripts polished into a fully deployable beta stage that I can use on Tuesdays session.  Seeing the humpbacks this morning was pretty cool and is just one more thing I'll miss after the internship. This time has gone too fast.

I have been finishing graphs and doing some statistics for my data. Just when I think I'm done, I look back at the plots and notice that something's missing, so I have to re-plot them, or re-do statistics to check if I'm doing it right. They're done so far, and description is almost finished. Introduction is done as well, and I'm still working on mat & methods, because as there's so much equations involved, I'm trying to make it as less boring as possible. I have a meeting with Francisco at 15h, to discuss some results and I think the rest of the paper. I'll propose a title for the presentation and if he's ok with it, then I'll e-mail it to Linda. I think I'll start working on the powerpoint on the weekend, or between Monday and Tuesday. Busy week, I can't believe we have only two weeks left

Lots of writing. Very slow going. Everything is taking longer than I thought it would, so ill be here this weekend probably. I'm hoping consistency will pay off because I can't quite see the light at the end of the tunnel yet. I think this confluence update would have been a lot more optimistic had I written it this morning. It was nice to see some engineering projects yesterday afternoon!

I'm finally running experiments! But they are taking forever, but I'm hoping to finish up this weekend, then run the molecular analysis next week, then data analysis over the weekend just in time for the presentation.
I've got drafts of my paper and presentation, but the results section is just going to have to wait.
Some late nights ahead, but it'll come together

This week was good. I finally got my project together and now I am doing runs under the water by simply putting the whole module on the test tank. I am still working on some functionality issues and the radio communications are not done. I have been also working on  my paper which is almost ready, I need to work a little bit more on it.  Next step is to finish up the radio communications, finish my paper and start working on the presentation.

Took my break, and now back to Matlab! Got 2/3 of what I need to defend my argument, and the more statistical work I do the better (but that's if time permits). A sneak preview, When backscatter sensor data are plotted against fluorescence you can observe what are lithogenic, non-living material and what are living material. Within the living, you can vaguely distinguish between diatom communities from other planktonic organisms. I've got a, pretty simple power point frame for my presentation and it will take shape into something good; I hope. The paper is on the same boat as well. I've been given the privilege to be independent and explore on my own, and it definitely has its ups and downs. I think I've spent the bulk of time chasing so many things that were interesting and intriguing to me, but couldn't find something to grasp on for this project; but hey, finally got something for the presentation =)