http://www.nd.edu/~gmadey/bioperl/index.htmlClassnotesengmadey@nd.eduCopyright 2007 gmadey2007-11-07T14:12:58-05:00 hourly 1 2000-01-01T12:00+00:00 Wed, 07 Nov 2007 14:16:59 -0500gmadey@nd.eduClassNotes2007-11-07T14:12:58-05:00http://www.nd.edu/~gmadey/bioperl/ClassNotes/files/e4c3a4d2e1f563e6642499ce4001972d-4.html#unique-entry-id-4http://www.nd.edu/~gmadey/bioperl/ClassNotes/files/e4c3a4d2e1f563e6642499ce4001972d-4.html#unique-entry-id-4Lecture

* Discuss Chapter 5: Searching for motifs, more file I/O, more string manipulation, regular expressions, counting nucleotides, and array manipulation
* Exercises at end of Chapter 5

Homework

* For the week of November 12: Read chapter 6 & 8; note, unless there is strong demand for it, we will skip chapter 7
* Try to do as many of the exercises at the end of Chapter 5 as you can; not to be turned in, just to discuss in class; students may be asked for their ideas on each exercise.]]>gmadey@nd.eduClassNotes2007-11-05T14:16:19-05:00http://www.nd.edu/~gmadey/bioperl/ClassNotes/files/2c33fe9ed7b0bfc15b7b56b16375ee82-3.html#unique-entry-id-3http://www.nd.edu/~gmadey/bioperl/ClassNotes/files/2c33fe9ed7b0bfc15b7b56b16375ee82-3.html#unique-entry-id-3Lecture


* Online Perl reference
* Exercises at end of Chapter 4
* Discuss Chapter 5: Searching for motifs, more file I/O, more string manipulation, regular expressions, counting nucleotides, and array manipulation
* Exercises at end of Chapter 5]]>gmadey@nd.eduClassNotes2007-10-31T13:24:08-04:00http://www.nd.edu/~gmadey/bioperl/ClassNotes/files/add273a1aa625a59f1e5b87c98fc28bf-2.html#unique-entry-id-2http://www.nd.edu/~gmadey/bioperl/ClassNotes/files/add273a1aa625a59f1e5b87c98fc28bf-2.html#unique-entry-id-2Lecture

Status report on installing perl on student laptops
Perl documentation:

• http://www.perl.com/
• http://www.cpan.org/
  

Reading from files
Arrays
Printing arrays
Scalar and List context
Exercises at end of Chapter 4

Homework

Read Chapters 1-6 in the textbook
Try to do as many of the exercises at the end of Chapter 4 as you can; not to be turned in, just to discuss in class; students may be asked for their ideas on each exercise.]]>gmadey@nd.eduClassNotes2007-10-29T13:22:05-04:00http://www.nd.edu/~gmadey/bioperl/ClassNotes/files/af1a911a23812d3bddeb643b0bf6fea7-1.html#unique-entry-id-1http://www.nd.edu/~gmadey/bioperl/ClassNotes/files/af1a911a23812d3bddeb643b0bf6fea7-1.html#unique-entry-id-1Lecture

Introductions
Overview
Getting Started with Perl/BioPerl

Homework

Find, install, run a perl program on a computer of your choice
Download and unzip this file ==> begperlbio_all
Read Chapter 1 - 4
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