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going with the flow

Today is Saturday/Sabato!  In a non-grad school world it might involve sleeping late (oh wait, I already did) and enjoying a leisurely day at the market (oh wait, I will do that on my walk to the lab) and then sitting in front of a computer for the rest of the day (yes, that is true).  However, somehow it seems that despite my efforts to avoid enjoyment, it is still possible! The transition to living abroad for my doctoral program has been a welcome change of pace from my previous life.  It is truly satisfying to wake up every day and just walk out the door without having to drive somewhere.  I will never miss that aspect of my former routine. Read More…


2010 recap

It’s a new year, and what better way to begin the week of a new year with a Monday post? Let’s see, a recap from 2010 might be a great way to shed the previous year and begin fresh.  Here are some highlights or milestones if you will from the world of phytography.

This summer was a welcome hiatus from academia while I worked and lived on Appledore, Island at the Shoals Marine Laboratory. I enjoyed interacting with students, faculty and public visitors to the island while maintaining my role in providing a functional laboratory space.

While on the island, I collaborated with a colleague to utilize a FLOWCM particle analyzer to investigate the effects of increased nutrient amendments on coastal phytoplankton community composition.  For more information on this project, please visit the Fluid Imaging press release.

The fall brought a period of time to begin data analysis of the images from this project.  While contemplating the next step in my career, I awaited the news from an international PhD program.  In late November I received an acceptance letter and by December 1st, I was en route to Europe. All in all, it’s been a pretty fruitful year.  I won’t share any more lists of goals with you, suffice to say it will be a well-blogged year.  Happy 2011!

ripple effect

ripple effect

It’s a new year! This marks the second year of research blogging. I began my efforts mid-way through my master’s degree at the height of my experimental work. One might think that would be the worst time in the world to begin a blog and dedicate one’s time and efforts to writing.  In fact, that was the best thing I could have done at the time to stimulate my creative writing efforts.  I’ve enjoyed being here on wordpress and I think that the ripple effect is an apt way to describe your small impact on the world.  At times (especially as a graduate student) one could feel as though their contributions were trivial.  This couldn’t be further from the truth.  Each day we wake up, we have another chance to set an example, change things, and reflect on how to improve ourselves.  As a scientist, I am constantly testing the waters, looking for opportunities that will challenge me to think and take action to solve problems.  This is a dynamic time to be a scientist! Here’s to a great new year.

Thesis presentation

It seems as though I’ve reached the end of my  tenure as a Master’s candidate in this program.  Thus, I will be defending the research I’ve done over the past 2 years in an upcoming thesis seminar entitled:

“Picoplankton distribution patterns across the Patagonian shelf break region”

Monday, May 3rd at 1:30pm

to be held: Science #7 conference room

Please email me or leave a comment if you need more information.

exploratory data analysis

I’m in the exploratory data analysis phase of my project at the moment. Before I move on and start processing some incubation samples from the cruise, I’m working with the data set I have now and trying to find trends in the results. As our biostats professor went over the exploratory data analysis section in our last chapter, I concluded that this was what I was doing.

Here’s a couple of plots from the work so far:

copas08_stations_temp_scatterThis is a very obvious plot – temperature versus depth of the stations that we sampled across the latitude.  In fact, Lisa and I spent a bit of time discussing the region in between the group of stations on the far right side of the plot and those on the left. It appears to both of us that there is an intermediate water mass between the two – either as a result of something like the Brazil current or another water feature.  As the latitude increases, the temp. decreases.

I also have nutrient  data from the cruise which I have to sort through and plot against my different populations. That will also be helpful  in identifying different water properties.  Now I will have to turn my attention on the literature and read up a bit about the circulation patterns in that area so I can correlate that with the different nutrient regimes that we might see.

So the next step is to run the samples flow cytometrically from the CO2 incubation experiment. These will be interesting. I’ll have to get my reagents up and running again to do work on the flow. I’ll have to spend some time in the lab next week and figure that out. Once I’m set up it doesn’t take that much time to run them.

– that’s all for now from the land of data analysis…

general news

Sample processing has become somewhat routine as I embark upon finishing the last 5 sets of stations from the cruise. Seems as though I should had these finished by now, but I guess that is part of the whole scientific process. I’m much more patient with the process than I used to be – as well as with myself. It takes time to learn something and master it well enough such that you feel completely comfortable. For instance, operating a piece of equipment.

The next phase of my summer project should be working with isolates to regenerate them and hopefully bring them into laboratory culture. These will no doubt have viral contamination, but I’m interested to see if I can apply the HTC method. While I wind down with flow cytometer sampling, the isolates would give me a good opportunity to work with my data in anticipation of my biostats ccourse this fall. Good tiiming all the way around.

I was starting to think that I didn’t have enough credits to finish the MS requirement, but that is quite wrong, by at least 6 more. I’m not worried about that. I’m not sure how many extra courses this might mean for the first year of a doctoral program.

In personal news, I’ve made a commitment to biking in from further and further away each day. The ultimate goal would be to split my car ride substantially. I’m not sure if I can do it in half, there are some bad road choices, but I’m starting out with more mileage to get used to it. I’m making a big effort to cut back on driving this summer because I’m piling up the miles back and forth to Portland, and I generally dislike driving. The ocean breezes feel great and so does the satisfaction of having made the trek into school for the day.

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