Chantel Johnson's blog

My last week at CMOP was great. Everything went according to plan as far as my paper and presentation go. We did have to make a few last minute changes on the day of presentations, but then again who doesn't? Even though I was the first to present, I wasn't nervous at all. I was completely confident in my work and all the effort I put into it. The past 9 weeks have been full of excitement and discoveries for me and I wouldn't change anything. I'm definitely going to miss all the new friends I made here and I will be sure to keep in touch!!!

Below are some links to my works:

This week I worked on my paper and presentation. Bill and I had a system: I would work on one portion of the paper, email it to him and he would edit it while I worked on the next portion of the paper. It worked out great and Bill's feedback helped a lot.

We finally decided on a stopping point for the application since we ran into that huge problem with the BlastSeq function. We also m et with Dave my senior scientist to discuss the final paper and presentation. He was really helpful in clarifying all the things that need to be covered in the paper. We also divided up the paper in parts and set deadlines as to when I should have each part completed. This was a wonderful idea because I have the tendency to procrastinate!!!

This week we ran into a problem. First we discovered that the function that id supposed to BLAST sequences for the user does not work on my machine. The problem is very deep within one of the packages that were imported into the application. This was a big setback because allowing the user to BLAST on their own machine is one of the main purposes of the application.

Thus week I created a homepage where the user can choose which feature of the application they would like to use. So far we only have four options but hopefully more will come. I also created a schedule of the tasks i need to complete and when I think they will be done. This should give us an idea of a stopping point with the application. I also went home for the weekend!!!

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.

This week we had to present our graphed data of what we have done so far. Bill and I decided to graph the the number of completed and failed requests the Google App Engine could complete. So we wrote a small program that would request our application repeatedly on the Google server. We did this test on two applications: one that held 100 records and another that held 7200 records. The small program we wrote was able to tell the number of failed and completed requests.

This week was very...long lol. Well first we had the visit to the primate center. it was very interesting to hear about the variety of research projects that were being performed this summer. i was a little disappointed because i wanted to see the monkeys but i understand why we couldn't. Then thursday we had the NSF site visit. it was interesting to see the 'administrative side' of CMOP and some of the things that come with it. The site visit also provided us with exposure to some of the NSF representatives, although the two I talked to really just conversated among themselves.

This week we finally moved into the apartment!!! If felt great not be cooped up in a hotel room anymore. And the apartment came equipped with everything we needed and more. Thanks Vanessa! At work, Bill and I finally got my application to work...except it was going extremely slow even after we downsized the file. But at least it worked! This week e also got to visit OHSU's main campus. It was probably one of the biggest campuses I've ever been on. Its funny because I thought thats where we'd be working at but I'm so glad it's not. I am jealous about the beautiful view of Mt. Hood and Mt.

My first week @ CMOP was pretty easy. The first two days or so I didnt exactly know what my project would because some last minute changes had to be made. But the rest of the week I spent learning about the Python programming language and the Google Application Engine. I even wrote a simple program and uploaded it unto the google server. Overall my first week was very progressive.