I'm on my way back from the Terabase Metagenomics meeting in Snowbird, UT, and I'm buzzing with ideas about how to move forward in metagenomics and bioinformatics research. Metagenomics, the use of genomics approaches to study microbial communities, has been opening up as sequencing drops in price. With sequencing becoming …
read moreThere are comments.
I've spent the last few weeks working on a simple solution to a challenging problem in DNA sequence assembly, and I think we've got a nice simple theoretical solution with an actual implementation. I'd be interested in comments!
Briefly, the algorithmic challenge is this:
We have a bunch of …
There are comments.
After my recent next-gen sequencing course, which was supposed to tie into the whole software carpentry (SWC) effort but didn't really succeed in doing so the first time through, I started thinking about the Right Way to tie in the SWC material. In particular, how do you both motivate scientists …
read moreThere are comments.
Our sequencing analysis course ended last Friday, with an overwhelmingly positive response from the students. The few negative comments that I got were largely about organizational issues, and could be reshaped as suggestions for next time rather than as condemnations of this year's course.
The 23 students -- most with no …
read moreThere are comments.
So, I've been teaching a course on next-generation sequence analysis for the last week, and one of the issues I had to deal with before I proposed the course was how to deal with the volume of data and the required computation.
You see, next-generation sequence analysis involves analyzing not …
read moreThere are comments.
So, I'm running this summer course and I am trying to figure out how to organize the notes for students. I'd like to mix curriculum-specific notes ("here's what we're doing today, and here are some problems to work on") with tutorials (material independent of a single course, like "here's how …
read moreThere are comments.
In conversation with a colleague the other day, I found myself making a surprising prediction: the age of the big sequencing centers (Broad Institute, WUSTL, Baylor, DOE JGI, etc.) is coming to an end. In 5 years they will no longer exist.
This prediction is obvious in hindsight.
That is …
read moreThere are comments.