>At the end of my committee meeting, last month, my advisors suggested I spend less time on engineering questions, and more time on the biology of the research I’m working on. Since that means spending more time on the cancer biology project, and less on FindPeaks, I’ve been spending some time thinking about how I want to proceed forward – and I think the answer is to work smarter on FindPeaks. (No, I’m not dropping FindPeaks development. It’s just too much fun.)
For me, the amusing part of it is that FindPeaks is already on it’s 4th major structural iteration. Matthew Bainbridge wrote the first, I duplicated it by re-writing it’s code for the second version, then came the first round of major upgrades in version 3.1, and then I did the massive cleanup that resulted in the 3.2 branch. After all that, why would I want to write another version?
Somewhere along the line, I’ve realized that there are several major engineering things that could be done that would make FindPeaks faster, more versatile and able to provide more insight into the biology of ChIP-Seq and similar experiments. Most of the changes are a reflection of the fact that the underlying aligners that are being used have changed. When I first got involved we were using Eland 0.3 (?), which was simple compared to the tools we now have available. It just aligned each fragment individually and spit out the results, which left the filtering and sorting up to FindPeaks. Thus, early versions of FindPeaks were centred on those basic operations. As we moved to sorted formats like .map and _sorted.txt files, those issues have mostly dissapeared, allowing more emphasis to be placed on the statistics and functionality.
At this point, I think we’re coming to the next generation of biology problems – integrating FindPeaks into the wider toolset – and generating real knowledge about what’s going on in the genome, and I think it’s time for FindPeaks to evolve to fill that role, growing out to better use the information available in the sorted aligner results.
Ever since the end of my exam, I haven’t been able to stop thinking of neat applications for FindPeaks and the rest of my tool kit – so, even if I end up focussing on the cancer biology that I’ve got in front of me, I’m still going to find the time to work on FindPeaks, to better take advantage of the information that FindPeaks isn’t currently using.
I guess that desire to do things well, and to get at the answers that are hidden in the data is what drives us all to do science. And probably what drives grad students to work late into the night on their projects…. I think I see a few more late nights in the near future. (-;