>Updates

>It has been a VERY busy week since I last wrote. Mainly, that was due to my committee meeting on Friday, where I had to present my thesis proposal. I admit, there were a few things left hanging going into the presentation, but none of them will be hard to correct. As far as topics go for my comprehensive exams, it sounds like the majority of the work I need to do is to shore up my understanding of cancer. With a field that big, though, I have a lot of work to do.

Still, it was encouraging. There’s a very good chance I could be wrapping up my PhD in 18-24 months. (=

Things have also been busy at home – we’re still working on selling a condo in Vancouver, and had two showings and two open houses over the weekend, and considering the open houses were well attended,that is an encouraging sign.

FindPeaks has also had a busy weekend, even though I wasn’t doing any coding, myself. A system upgrade took FindPeaks 3.1.9.2 off the web for a while and required a manual intervention to bring that back up. (Yay for the Systems Dept!) A bug was also found in all versions of 3.1 and 3.2, which could be fairly significant -and I’m still investigating. At this point, I’ve confirmed the bug, but haven’t had a chance to identify if it’s just for this one file, or for all files…

Several other findpeaks projects are also going to be coming to the forefront this week. Controls and automated file builds. Despite the bug I mentioned, FindPeaks would do well with an automated trunk build. More users would help me get more feedback, which would help me figure out what things people are using, so I can focus more on them. At least that’s the idea. It might also recruit more developers, which would be a good thing.

And, of course, several new things that have appeared that I would like to get going on: Bowtie is the first one. If it does multiple alignments (as it claims to), I’ll be giving it a whirl as the new basis of some of my work on transcriptomes. At a rough glance, the predicted 35x speedup compared to Maq is a nifty enticement for me. Then there’s the opportunity to do some clean up code on the whole Vancouver package for command line parameter processing. A little work there could unify and clean up several thousand lines of code, and make new development Much easier.

First things first, though, I need to figure out the source and the effects of that bug in findpeaks!