6. 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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   There are comments.

7. 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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8. 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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9. 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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10. 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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    There are comments.

11. (Some) Principles of Computational Science

    I'm just finishing up my Computational Science for Evolutionary Biologists course, and I'm finding it tricky to come up with a good high-level summary of what I would like them to take away. As you can see from the class notes they've done some reasonably neat stuff with Digital Life …

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12. Open Education, Open Minds, but No Communication?

    PLoS Biology published an article entitled Open Education, Open Minds, in which they solicited ideas for contributions to a series on life sciences education:

    Contributions to the Education Series are encouraged; ideas should be sent to plosbiology@plos.org.

    So I sent in an e-mail and got back

    > This message …

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