This week in links #1

In a new style post (for me), some links to things that have caught my eye in the last 2 weeks:

This may become a habit. Though it is likely to be an infrequent one.


  1. Thank you for the link.
    Are you using Kegg pathways for your work? Would you find useful a parser for KGML files?
    Notice that most off the pathways are available in the BioPax format, which can be read by other tools like cytoscape Unfortunately, my pathways are only available in KGML 😦

    Maybe tomorrow I’ll write an update about the KGML parser I am writing.

  2. You’re welcome for the link Giovanni.
    I’m sure a KGML parser will come in handy one day. I’ll keep an eye on the progress of your code.
    By the way, have you tried using cElementTree rather than ElementTree? It is also included in the standard libraries (since 2.5) and it is about an order of magnitude faster.

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