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   sphinx-quickstart on Sun Nov  4 10:10:29 2012.
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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: http://j.mp/SWCchat

:doc:`instructors`

Workshop materials
------------------

.. toctree::
   :maxdepth: 2

   install

   day1

   day2

Other materials:

  The `Analyzing Next-Generation Sequencing Data summer course
  <http://ged.msu.edu/angus/>`__ 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 <http://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-00sc-introduction-to-computer-science-and-programming-spring-2011/>`__ and `Khan Academies <http://www.khanacademy.org/science/computer-science/v/introduction-to-programs-data-types-and-variables>`__ 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-test7.lj.ad.scripps.edu
 * iPython Notebook is available at http://it-test7.lj.ad.scripps.edu:8888/ (NOTE: only available from the Scripps network)
 * This server is also available for interactive shell use -- SSH to username@it-test7.lj.ad.scripps.edu (replacing 'username' with your Scripps username)
* 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 hpc_ca@scripps.edu
 * 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: home.scripps.edu, app.scripps.edu
 * 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
 * Web sign up: http://lists.scripps.edu/majorcool.cgi
 * Or, send email to majordomo@scripps.edu with 'subscribe cbb' (no quotes) in the message body

Hipchat
-------
* For the moment, we will leave up the hipchat room.  If you feel like it, post your questions and/or answer others' questions: http://j.mp/SWCchat
* Transcripts
 * `Wednesday 14th <./_static/14.html>`__
 * `Thursday 15th <./_static/15.html>`__
 * `Friday 16th <./_static/16.html>`__



Indices and tables
==================

* :ref:`genindex`
* :ref:`search`

.. * :ref:`Instructors`


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