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Week 5- Calm And Quiet........

This week was slow one. I succeeded in fixing the experiment which I mentioned last week and it only took me three trials and a new secondary stock solution. I have only been using the cuvettes lately because I wanted to see low of a concentration could be measured. I also started using Instant Ocean so see if it gave me a similar concentration to distilled water. My lab was very active up until Wednesday because they were preparing for the cruises. Now, it is so quiet; there is actually walking space.

13 July 2008 R/V Wecoma cruise

We casted the CTD at stations along the coast up to CM-10 off Cape Meares, OR, and then went directly to station CR-4 off the Columbia River to start an offshore transect. We cast the CTD at nine stations (CR-4, 7, 10, 15, 20, 25, 30, 35, 40), and collected water samples a four (CR-7, 15, 30, 40). We also measured primary production at station CR-7, and collected sediment cores at CR-7 and CR-40. This was a full day of work and we had no major setbacks. Spirits are up, seasickness is memory, and everyone is in a smooth routine.

Week 4: July 13-18

Monday: Grant gave me three things to do:
1) Predict the time difference between the maximum change in salinity and maximum turbidity during each change in tide
2) Find the correlation between tidal range and the magnitude of turbidity
3) Do all analyses with regard to all classes of turbidity spikes

I made progress with the first goal. I got some results, but will need to revise and improve them. I made a small amount of progress on the second goal, although not enough to make any conclusions.

12 July 2008 R/V Wecoma cruise

When the sun came up we cast the CTD at NH-55 to collect our fourth and final set of NH water samples. This site is 2880m deep, so several in the science team decided to see what that kind of water pressure does to styrofoam cups...

We then motored to Newport to drop off a seasick student before heading up the coast to do CTD casts along the 100m isobath.

cups

WEEK FIVE - RNA and high horses

This week I've completed more RNA isolations, read two more articles, re-stocked needed materials and ran the autoclave, went to the bioanalyzer to record the quality of previous RNA samples, and prepared for the upcoming research cruise. It turns out that the RNA that I've isolated is not degraded, and looks good! I was complimented by Mariya and Holly which was exciting :)

Then I accidentally left sterile tubes out overnight, so the high horse I was riding was dismounted... Overall it was a successful week, and I'm very excited for next week's cruise!

WEEK 5 7/14/08-7/18/08

Sooo, you all may have noticed there were no h.s. interns in the building last Friday...that is because we were all donw at OSU for the ASE Midsummer Conference. So, most of us took the bus down there Friday morning and we all stayed in the dorms at Weatherford Hall.
Overall, it was not bad, except for some boring sessions like Life as a Chemical Oceanographer and going down to CORE Labs to look at tubes of mud -_-. The best presentation by far was Pathways to Civil and Structural Engineering by a civil/structural from CH2M HILL.

WEEK 4 7/7/08-7/11/08

On Monday, we gave a presentation to Antonio and that went well. Then after that, I spoke to Lydie Herfort about the data from her cruise last August where they took samples during an ETM. Then, I imported the data into Excel with minor difficulties since it was in a weird format. Then on Wednesday we had to give a presentation to our parents in the evening of what we've been working on all this time and our long term and short term goals. Then Grant wanted to put the cruise data into Excel, so I started formatting the data by hand which was taking like 5 years.

WEEK FIVE - Phytoplankton

So, this week I actually got my phytoplankton to move! Which isn't all that exciting I bet, but I've never used MATLAB before this summer so getting the animation to work was pretty exciting.

I also met with Karen, my senior mentor, this week to update her on my progress and get her feedback. This week, I'll be adding some more information to the program and hopefully by next week or the one after, I should be able to run some experiments.

Week 5

This week, I worked on a feature of the program that would allow users to upload their FASTA files through a ZIP folder and BLAST each sequence. But, we discovered that the Google App Engine would time out before all the files were uploaded. We discovered yet another limitation but we will work around it...once again.

Week 5-Half Way Point

This week I feel like I have made some progress toward my final project. Things are starting to piece together which is great since we are at the half way point already! I can't believe how quick those 5 weeks have gone by.

I spent a lot of time working with Sergey's Matlab code. When I first saw it, I must admit it looked a bit foreign. I took an introductory course on Matlab winter term, but this was a bit beyond that class. Grant helped explain some of the stuff but I mostly manipulated it so I could use it for my own data.

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