Laughter to God’s Jokes

I dislike thinking about this week, because it ended up being that week the cause me to continue on the project until november. Here is what happened.

As I mentioned the previous post, I had met with the biochemists and Dr. Shatkay, to sort out what they thought about the work to date. They had made several suggestions, some of which I would not have the time to implement. The time constraint came from the fact that I was start my graduate studies at UBC in about two weeks. Also I still needed to write the final report.

I had spent most of the week thinking about the changes that were required of me and I figured, with the report, I could maybe need an extra week to be done everything. While wroking on the report, I was carefully checking and commenting the scripts on the server, organizing them in a neat way for people to work with them. I also tested them for functionality. As I was doing this, I took some scripts off the server (ooh the folly of my ways!!!) to comment them and read over them. I got through what I call my phase one scripts okay. It was friday and I was going through my phase 2 scripts when in the middle of it all my hard drive died.

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This week was certainly not as slow as the previous weeks in terms of waiting for Dr. Shatkay to get back to me, but it was still a very easy going week. Since I wasn’t terrible sure how Dr. Shatkay felt about the repot that I was planning to make here, I didn’t want to step too out of bounds. It may have been more pretitent to focous on some aspect of the documentation or to continue to scrutinize my code. Howevee, seeing as I really wanted to build a nice flex interface I thought that this would be my chance to prototype my baby. SO naturally, I didn’t mind to get cracking.

This week was another week filled with learned because I decided to fully tackel XML::SIMPLE. the Perl module was showcased to me first my by mate Rob who was also working with Dr. Shatkay in the lab and is doing stuff with Swiss prot. I asked him to borrow some code for reference to see how the parsing strcture of the XML Swiss Prot Uniprot Flatfiles work. And let me tell you, it was messy.

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So, this week was a very slow week. Dr. Shatkay was away the whole week, so there weren’t too many tasks comming my way at all. Having finished the report and needed to wait for her thoughts on it, I was even more of a loss at what I should do until she gets back later this (July 21 onwards) week. I continued my documentation spree and reading on interface things in flex. Things seem to work okay, but for certain I wouldn’t be able to do the kind of interface I wanted by the the time the project finished. But I thought to myself that I have this protein information, but what is a decent way to present the information?

I decided to figure out how to write an automated report generator. I wanted it to be efficient and practical and herein I found the necessary task to bring a greater sense of completeness to the project. The way that the report is going to be set up is similar to my idea of using the Flex interface, expect I am stripping it of all it’s interface beauty. I decided instead to create an HTML report, with in page anchors and links to information.

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This week will contain the shortest journal post ever. This week I started and finished the report on the results which Dr. Shatkay had asked me to comprise. I took my time with it, because she mentioned that it should be thoughtfully written and that I should try be brief but very concise. The report is here!

I feel like I was much a better writer in high school. I think that taking AP English was a bonus to that, plus I had more time to read so that my vocabulary was not as shunted as it now is. My spelling and grammar have never been fantastic but at least the context of what I wrote was properly organized an meaningful. With science though, I seem to have lost the talent even for contextual writing. This could be because I like writing about what I see more in metaphor’s, similes and tones of a piece of writing. Scientific writing has always been dull and bland, and as I have found variable depending on the T.A. that is marking it. I thought that I finally got the hang of it from my biochemistry class, but what the biochem T.A.’s liked, the computing profs did not. I throw up my hands in frustration and vexation!

So this report is very short, a lot of space is taken up by charts and stats, and things that are not my own writing. But it took me a long time to write, because I kept rambling, and explaining things.In the end I cut many things out, rewrote, condensed…made many drafts. I kept reviewing my vocabulary. It was alright, but as always I was unsure with the end result. Hopefully I get a hang of this stuff later on. My final report may be a little bit of a pain to write.

Half the summer is over!! So was half the week thanks to Canada Day being on the the Tuesday. I came back with scripts already to go on paper, it was just a matter of testing it out now. I sat down and started to code the line by line scripts and pattern matching which would break down the XML document and extract the good statistics for me. The work could be done quickly on my own laptop, I didn’t even need the computing power of the server. This made me pretty happy.

I should add an aside here: for the first time in my coding life, I realized the importance of complexity of an algorithm in my fourth year of University. Before, it probably didn’t matter if you had loops embedded within loops because your input was so small. But in a project we were given, the input was rather large, and if you weren’t clever about how you wrote you code, it could make the difference between a two minute computation and a longer one. In another class, Medical Informatics, we had to reconstruct a 3D image from about 200 smaller x-ray slices (we were to imitate the behavior of a CT scanner). So, I decided the best way to approach this problem would be to use interpolation. With that, on my laptop (which has only 512 mb of RAM, it’s not a pretty machine) it took 20 minutes for the image to be reconstructed. However, most of my other classmates had to run the code over night. So you see, thinking about how you do things, can make a very large difference in when the answer is coming to you, but there are always catches.

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