Wed, Oct 2, 2013 - ipythonblocks; read QC
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`Google doc for machine names <https://docs.google.com/spreadsheet/ccc?key=0ArcOEBWnXSBidEVPSll3VXhyQVZjRXZLT25Fb0VVX1E#gid=0>`__

Outline of day:

0. Survey.
----------

(until ~20 minutes after)

You should all have received a survey e-mail from Claudia Vergara.
Please fill out survey; I will leave room and return at 20 after.

1. Introduction; office hours; grading and hand-in policy.
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I've already done the introduction at the workshops, but basically
we're going to show you three things in this class: (1) some basic
programming, (2) how to run and think about sequence data analysis,
and (3) how to do some simple evolutionary modeling.

Lectures
~~~~~~~~

There will be some online lectures, especially about technical stuff
like starting up machines, handing in homework, and various aspects
of programming and running NGS programs.

Homework and grading
~~~~~~~~~~~~~~~~~~~~

If you're auditing you're expected to hand in the homeworks until
you stop auditing, and vice versa.

Grading will be P/F each week, with each week representing 10% of the
final grade.

Homework handed in after the official due date/time may not be graded.

If I do not send you comments on your homework by the end of the
weekend following hand-in, (Sunday evening), you get a PASS garde.

I would suggest that you get together in study groups to do the
homework.

Office hours
~~~~~~~~~~~~

Primary support will be via e-mail.  I can schedule a Google Hangout
with you if you need one-on-one or one-on-group time.  I propose to
specify one or two times a week where I will be available, decided on
by Doodle polls.  Pushback?

2. ipythonblocks introduction; in-class exercises.
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Pick one of the machines randomly (see 
`Google doc for machine names <https://docs.google.com/spreadsheet/ccc?key=0ArcOEBWnXSBidEVPSll3VXhyQVZjRXZLT25Fb0VVX1E#gid=0>`__) and open up a new IPython
Notebook link.  (Password: 'beacon'.)

Select the notebook 'class1-ipythonblocks' & make a copy!

See a static copy of the notebook `here <http://nbviewer.ipython.org/urls/raw.github.com/beacon-center/2013-intro-computational-science/master/notebooks/class1-ipythonblocks.ipynb>`__.

3. Read trimming and QC; FastQC reports.
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A short introduction to NGS sequencing, and what can go wrong; a
FastQC report.  (Lecture whiteboard: `go to JotWithMe/titus801-1
<http://jotwithme.com/view?session=titus801-1>`__.)

To see a FastQC report, pick one of the machines randomly (see `Google
doc for machine names
<https://docs.google.com/spreadsheet/ccc?key=0ArcOEBWnXSBidEVPSll3VXhyQVZjRXZLT25Fb0VVX1E#gid=0>`__)
and open up the associated FastQC link.  To generate this, I did ::

   cd /usr/local/share
   curl -O http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip
   unzip fastqc_v0.10.1.zip
   chmod +x FastQC/fastqc

   cd /root
   curl -O http://athyra.idyll.org/~t/100k_1.fq
   curl -O http://athyra.idyll.org/~t/100k_2.fq

   mkdir /var/www/fastqc
   /usr/local/share/FastQC/fastqc 100k_1.fq 100k_2.fq -o /var/www/fastqc