hw1.txt

Homework 1 (due Tuesday, Oct 8th, by midnight PST)
##################################################

.. note::

   Need help?  Go to http://angus.askbot.com/ to ask questions and see
   other people's answers!

.. note::

   Keep getting disconnected?  This is probably because of inactivity
   or time limits on network connections (on your computer, at your
   university, or whatever).  See :doc:`amazon/using-screen` for
   the best way to deal with this.

0. Start up an EC2 machine.
---------------------------

Work through the instructions here: :doc:`amazon/index` for starting
up an EC2 machine on AWS.

A brief checklist:

a. Create an AWS account and log in;
b. Launch a machine; use m1.xlarge.
c. Adjust your security rules for the machine and select 'default' security profile.
d. Make sure you can both log into your machine with SSH *and* with IPython Notebook.
e. Install Dropbox on your EC2 machine (see :doc:`amazon/installing-dropbox`)

There's a video from last year `here
<http://www.youtube.com/watch?v=JMedTCa5lec&feature=youtu.be>`__ that
is only slightly out of date.

Two notes:

 * be sure to save your work to Dropbox and shut down your machines when you
   are done working;

 * for now, you will need to pay for your own EC2 machines.  This should be
   less than $2-3/wk.  If you are a BEACON-affiliated graduate student we
   can help you pay.

1. Work through some programming exercises
------------------------------------------

Log in to your EC2 instance via SSH and install ipythonblocks::

   pip install ipythonblocks

download the homework notebook::

   cd /usr/local/notebooks
   curl -O https://raw.github.com/beacon-center/2013-intro-computational-science/master/notebooks/hw1-ipythonblocks.ipynb

Then, go to 'https://' + your EC2 machine name to connect to EC2.  Use
the password 'beacon' to log into the console and then open
hw1-ipythonblocks.  Solve the problems and then download the notebook
(file... save as...) and e-mail it to me as an attachment, with
'cse801 hw1' in the subject line of the e-mail.  Please rename the
attachment so it includes your last name or NetID somewhere.

Note that you can see a static version of the notebook from class
`here
<http://nbviewer.ipython.org/urls/raw.github.com/beacon-center/2013-intro-computational-science/master/notebooks/class1-ipythonblocks.ipynb>`__,
with a download link; if you want to work with it, you can upload this
notebook to your EC2 machine following the instructions below, under
"A few notes."

A few notes:

 - if you aren't going to work on this problem for a while and want to
   shut down your machine, you can download your ipython notebook by
   going to 'File' and 'Save As ipynb'; this downloaded ipython
   notebook can be reuploaded by dragging it from your computer into
   the IPython Notebook console.  This replaces the 'download' command
   above.

 - it is not a failure to use Google to ask questions like "how do I test
   if a number is even in Python?" or "how do I multiply numbers in Python?"

2. Run FastQC on full E. coli data set and trimmed data set
-----------------------------------------------------------

Log in to your m1.xlarge EC2 machine via SSH and follow through all of :doc:`week1/reads_and_qc`.

If you are interested in what the results mean and don't want to
wait 'til Wednesday, watch `this 12 minute video <http://www.youtube.com/watch?v=bz93ReOv87Y>`__.

.. Videos:

.. - spinning up instance;
.. - handing in files via github;
.. - running FastQC

.. next week: run filter-abund trimming, mismatch pos.