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Software Carpentry workshop at Scripps, Nov 15-16, 2012

NOTE: For real-time help either before or during the workshop, you are welcome to try posting in our chat room:


Workshop materials

.. toctree::
   :maxdepth: 2




Other materials:

The Analyzing Next-Generation Sequencing Data summer course is a good resource for people interested in NGS specifically.

For people interested in learning Python, I got really strong positive recommendations for the MIT OpenCourseware and Khan Academies lectures from a course attendee.

Scripps computational info

  • IT has set up a temporary server for use by class participants. The server name is
  • IT also invites users who want to do more computational work to request accounts on garabaldi
  • To request an account, please send an email to
  • Account will provide access to two nodes for interactive use, and also the potential of using our high-performance computing (HPC) cluster.
  • IT also maintains two general-purpose compute servers:,
  • Both are older machines that currently aren't well supported.
  • We suggest you not use these servers to use/practice the skills learned in this workshop
  • To encourage IT to make these more up-to-date and publicized resources, use it-test7
  • Also, sign up for the mailing list of the Computational Biology and Bioinformatics (CBB) Affinity Group


  • For the moment, we will leave up the hipchat room. If you feel like it, post your questions and/or answer others' questions:
  • Transcripts

Indices and tables

dumb edit