6. The Molgula again -- attending the Int'l Tunicate Meeting

   I just flew back from Montreal, where I gave a talk at the International Tunicate Meeting on the Molgula project. This is a project wherein we are doing quantitative mRNA sequencing on two species of ascidians, or sea squirts -- specifically, on M. oculata (tailed), M. occulta (tailless) -- and their hybrids …

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7. Course: Analyzing Next-Generation Sequencing Data (2011 version)

   The second iteration of our bioinformatics summer course, Analyzing Next-Generation Sequencing Data, just finished. It was a great success, at least judging from the comments that people made to us personally; the evaluations aren't yet complete.

   The what: a two week course on analyzing next-gen sequencing data, using the Amazon …

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8. Laundry zero - the new manifesto that's sweeping the nation

   Like a lot of the best fresh starts, this one's a total psych-out; also, like many of the best ones, you won't believe how well it works until you actually try it for yourself.

   1. Go to your laundry room.

   2. Pick up your laundry hamper.

      (If you have more than one …

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9. Trying out 'cram'

   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 …

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10. My new data analysis pipeline code

    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 …

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11. The last five years

    Looking back, the last 5 years have, collectively, been rather overwhelming.

    Five years ago, I was a big-mouthed 7th year graduate student. The biggest change in my recent life was getting a cat (first) and getting married (second).

    Now, I'm the father of two (adorable) daughters. I have a minivan …

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12. What's in it for me? Thoughts on open science.

    If you've been under a rock (or indulging in arsenic yourself), you've heard about NASA's "arsenic" article, claiming the discovery of a microbial species that can substitute arsenate for phosphate. The paper was pre-announced via a press conference that then announced the results.

    Immediate blogtastrophe! The paper was critically reviewed …

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