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


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Keep getting disconnected? This is probably because of inactivity or time limits on network connections (on your computer, at your university, or whatever). See Using ‘screen’ for the best way to deal with this.

0. Start up an EC2 machine.

Work through the instructions here: Getting started with Amazon EC2 for starting up an EC2 machine on AWS.

A brief checklist:

  1. Create an AWS account and log in;
  2. Launch a machine; use m1.xlarge.
  3. Adjust your security rules for the machine and select ‘default’ security profile.
  4. Make sure you can both log into your machine with SSH and with IPython Notebook.
  5. Install Dropbox on your EC2 machine (see Installing Dropbox on your EC2 machine)

There’s a video from last year here that is only slightly out of date.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, 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 Understanding Read Formats and Quality Controlling Data.

If you are interested in what the results mean and don’t want to wait ‘til Wednesday, watch this 12 minute video.