From: Milad Fatenejad <milad@flash.uchicago.edu>
Date: Sun, 1 Apr 2012 02:46:01 +0000 (-0500)
Subject: More updates to the shell section
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=b8915d0d5788dbb14e6a7ea3cef933ff6e5ffe4c;p=swc-workshop.git

More updates to the shell section
---

diff --git a/1-Shell/Readme.md b/1-Shell/Readme.md
index 3141a52..ff25032 100644
--- a/1-Shell/Readme.md
+++ b/1-Shell/Readme.md
@@ -7,7 +7,7 @@
 
 **Presented By : Milad Fatenejad**
 
-**Based on a presentation By: ??????**
+**Most of this material came from a presentation by: ??????**
 
 # What is the shell how do I access the shell?
 
@@ -34,3 +34,53 @@ most important reasons are that:
     your computer. You will also be able to perform many tasks more
     efficiently.
 
+The shell is just a program and there are many different shell
+programs that have been developed. The most common shell (and the one
+we will use) is called the Bourne-Again SHell (bash). Even if bash is
+not the default shell, it usually installed on most systems and can be
+started by typing "bash" in the terminal. Many commands, especially a
+lot of the basic ones, work across the various shells but many things
+are different. I recommend sticking with bash and learning it well.
+
+# The Example: Manipulating Experimental Data Files
+
+We will spend most of our time learning about the basics of the shell
+by manipulating some experimental data from a hearing tests. 
+
+**Cochlear Implants**
+
+A cochlear implant is a small electronic device that is surgically
+implanted in the inner ear to give deaf people a sense of
+hearing. More than a quarter of a million people have them, but there
+is still no widely-accepted benchmark to measure their effectiveness.
+In order to establish a baseline for such a benchmark, our supervisor
+got teenagers with CIs to listen to audio files on their computer and
+report:
+
+1.  the quietest sound they could hear
+2.  the lowest and highest tones they could hear
+3.  the narrowest range of frequencies they could discriminate
+
+To participate, subjects attended our laboratory and one of our lab
+techs played an audio sample, and recorded their data - when they
+first heard the sound, or first heard a difference in the sound.  Each
+set of test results were written out to a text file, one set per file.
+Each participant has a unique subject ID, and a made-up subject name.
+Each experiment has a unique experiment ID. The experiment has
+collected 351 files so far.
+
+The data is a bit of a mess! There are inconsistent file names, there
+are extraneous "NOTES" files that we'd like to get rid of, and the
+data is spread across many directories. We are going to use shell
+commands to get this data into shape. By the end we would like to:
+
+1.  Put all of the data into one directory called "alldata"
+
+2.  Have all of the data files in there, and ensure that every file
+    has a ".txt" extension
+
+3.  Get rid of the extraneous "NOTES" files
+
+If we can get through this example in the available time, we will move
+onto more advanced shell topics...
+