1. A call for open lab and reusable lab protocols

    About a year ago, I came across a really interesting Science paper entitled "Rapid and inefficient isolation of single cells from soil". In it, the authors -- from a well-known lab at UC Davis -- described how they used low-percentage agarose gels to extract thousands of individual cells from a soil sample …

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  2. Some early experience in teaching using ipython notebook

    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 …

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  3. DRAFT: A community-focused pre-publication data release and sharing policy for sequence data

    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 …

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  4. A simple idea: standard but optional review criteria for bioinformatics papers

    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 …
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  5. The Parable of the Mad Photocopier

    (I came across this fragmentary blog post that I wrote sometime in December. It's a fine example of a failed allegory. To what, I'll let you determine for yourself. Anyway, in case anyone wants to know what dreck doesn't make it out of my computer onto the Intarweb, well, here's …

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