6. PyCon sprints - playing with named pipes and streaming and khmer

   I'm at the PyCon 2015 sprints (day 2), and I took the opportunity to play around with named pipes.

   I was reminded of named pipes by Vince Buffalo in this great blog post, and since we at the khmer project are very interested in streaming, and named pipes fit well …

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7. Taking grad students to PyCon

   I am still up at PyCon 2015 in Montreal, and most of my lab is here with me.

   On Saturday, I told Terry Peppers and some others that PyCon had been one of my (limited) lifelines to (limited) sanity during my early tenure-track years. Whenever I was in danger of …

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8. PyCon 2015 talk notes for "How to interpret your own genome"

   Here are talk notes and links for my PyCon 2015 talk.

   The talk slides are up on SlideShare.

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   General background

   You should definitely check out Mike Lin's great blog posts on "Blogging my genome".

   I found SNPedia through this wonderful blog post on how to use 23andMe irresponsibly, on Slate …

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9. Towards a bioinformatics middle class

   Note: Turns out Nick Loman is a C programmer. Well, that's what happens when I make assumptions, folks ;).

   Jared Simpson just posted a great blog entry on nanopolish, an HMM-based consensus caller for Oxford Nanopore data. In it he describes how he moved from a Python prototype to a standalone …

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10. OpenCon webcast: "How to get tenure (while being open)"

    This is a stub blog post for the talk notes for my OpenCon talk on how to get tenure as an open scientist.

    A few links --

    • Link to webcast
    • My blog post on gaining tenure as an open scientist
    • My slides
    • Summary stats from my annual reports at MSU

    More …

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11. Cultural confusions about data - the intertidal zone between two styles of biology

    A few weeks back, a journalist contacted me about my old blog post comparing physics and biology, and amidst other conversation, I pointed them at my latest blog post on data and said that I thought a lot of (molecular) biologists were "culturally confused about data". The next question was …

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12. Some ideas for workshops and unconference models for data-intensive biology

    Here at the Lab for Data-Intensive Biology (TM) we are constantly trying to explore new ideas for advancing the practice of biological data sciences. Below are some ideas that originated with or were sharpened by conversations with Greg Wilson (Executive Director, Software Carpentry) and Tracy Teal (Project Lead, Data Carpentry …

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