(Or, "A better way to publish bioinformatics.")
We just got word that our paper, "Scaling metagenome assembly with probabilistic de Bruijn graphs" [ arXiv ] [ github ] has been accepted for publication in PNAS. (Yay!) I just posted the final version to github, and the arXiv PDF should be updated to the third …
read moreThere are comments.
At our 2012 course on Analyzing Next-Generation Sequencing Data, we talked quite a bit about future sequencing technologies, as well as about what analyses are reasonably cookbook (and which ones aren't).
Here are my thoughts -- yours welcome!
The basic conclusions about sequencing tech were these:
There are comments.
As part of the 2012 Analyzing Next-Generation Sequencing Data course, I've been trying out ipython notebook for the tutorials.
In previous years, our tutorials all looked like this: Short read assembly with Velvet -- basically, reStructuredText files integrated with Sphinx. This had a lot of advantages, including Googleability and simplicity; but …
read moreThere are comments.
I just returned from a NESCent Catalysis meeting on Cephalopod Genomics. I was invited as a bioinformatics and genomics guy, and so I spent four days in North Carolina talking about the opportunities and challenges of sequencing cephalopods.
Cephalopods are a class of the molluscs, and include squid and octopus …
read moreThere are comments.
This is a draft proposal of a policy to encourage pre-publication data release and data sharing within a community. This policy is based on discussions at the Cephalopod Genomics Workshop (a Catalysis workshop sponsored by NESCent).
Note, this is made available under a CC-BY-SA license permitting use and re-use with …
read moreThere are comments.
Greg Wilson, Ethan White and I have been talking a bit about what Responsible Conduct of Research (RCR) standards would look like for computational science. I'm having trouble coming up with more than the below standards, which are largely related to publication.
Note, if you regard these as obvious, that's …
read moreThere are comments.
Brad Chapman (@chapmanb on twitter) wrote and signed a nice review of my submission to the Bioinformatics Open Source Conference. In his review, he said
My only small suggestion is to include some discussion about your reproducibility work during the talk: the Amazon AMI, documentation and reproducible ipython workflows. This …read more
There are comments.