I desperately need something to run and test things at the command line, both for course documentation (think "doctest" but with shell prompts) and for script testing (as part of scientific pipelines). At the 2011 testing-in-python BoF, Augie showed us cram, which is the mercurial project's internal test code ripped …
read moreThere are comments.
First, I write a recipe file, 'metagenome.recipe', laying out my job description for, say, sequence trimming and assembly with Velvet:
fasta_file soil-data.fa qc_filter min_length=50 remove_Ns=true graph_filter min_length=400 velvet_assemble k=33 min_length=1000 scaffolding=True
Then I specify machine parameters, e.g. 'bigmem.conf':
[defaults] n_threads …read more
There are comments.
I just parachuted in on (and heli'd out of?) the Beyond the Genome conference in Boston. I gave a very brief workshop on using EC2 for sequence analysis, which seemed well received. (Mind you, virtually everything possible went wrong, from lack of good network access to lack of attendee computers …
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.
Laurie Dillon just posted the SIGPLAN eduction board article on Why Undergraduates Should Learn the Principles of Programming Languages to our faculty mailing list at the MSU Computer Science department. One question that came up in the ensuing conversation was: what functional programming language(s) would/should we teach?
I …
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.