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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>BIOF309 Course website</title>
<meta name="description" content="Course website for the Introduction to Python Class given at FAES">
<meta name="author" content="Christopher Coletta">
<meta name="apple-mobile-web-app-capable" content="yes" />
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<link rel="stylesheet" href="css/reveal.min.css">
<link rel="stylesheet" href="css/theme/default.css" id="theme">
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<link rel="stylesheet" href="lib/css/zenburn.css">
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document.write( '<link rel="stylesheet" href="css/print/' + ( window.location.search.match( /print-pdf/gi ) ? 'pdf' : 'paper' ) + '.css" type="text/css" media="print">' );
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</head>
<body>
<div class="reveal">
<!-- Any section element inside of this container is displayed as a slide -->
<div class="slides">
<section id="main">
<h1>BIOF 309</h1>
<h3>Introduction to Python</h3>
<p>
<small><a href="http://www.chriscoletta.com">Chris Coletta</a> / <a href="mailto:christopher.coletta@gmail.com">christopher.coletta@gmail.com</a></small><br/>
<small><a href="http://www.mattshirley.com">Matt Shirley</a> / <a href="http://twitter.com/mdshw5">@mdshw5</a></small><br/>
<small>Anatoly Dryga / <a href="mailto:anatoly.dryga@nih.gov">anatoly.dryga@nih.gov</a></small><br/>
<small>Ben Busby / <a href="mailto:ben.busby@gmail.com">ben.busby@gmail.com</a></small>
</p>
<p>
<a href="#/handouts">Handouts</a> /
<a href="#/homework">Homework Assignments</a> /
<a href="#/slides">Lecture slides</a> /
<a href="#/screencasts">Screencasts</a> /
<a href="#/notebooks">IPython Notebooks</a>
</p>
</section>
<section data-markdown id="handouts">
<script type="text/template">
## Handouts
- [Course Syllabus](syllabus/BIOF309_Spring2014_Syllabus.pdf) - updated Mon, Jan. 27, 2014
[Back to main](#/main)
</script>
</section>
<section data-markdown id="homework">
<script type="text/template">
## Homework Assignments
1. The Magic Number - [code](homework/hw1/biof309_hw1.py)
2. Number Guessing Game - [zipfile](homework/hw2/biof309_hw2_files.tar.gz)
3. Answer the Riddle - [directions](homework/hw3/biof309_hw3_directions.pdf), [zipfile](homework/hw3/biof309_hw3_files.tar.gz), [template](homework/hw3/biof309_hw3_template.py)
4. Nucleotide to Amino Acid Translator [template](homework/hw4/biof309_hw4_template.py), [zscan4_dna.fasta](homework/hw4/zscan4_dna.fasta), [zscan4_dna_invalid_nt.fasta](homework/hw4/zscan4_dna_invalid_nt.fasta), [autograder](homework/hw4/biof309_test_hw4.py)
[Back to main](#/main)
</script>
</section>
<section data-markdown id="slides">
<script type="text/template">
## Lecture Slides
1. [Introduction and Installation](class1.html)
2. [Functions](slides/functions_anatoly_dryga_slides.pdf)
3. March 6: Gene expression case study - [slides](slides/biof309_gene_expression_case_study.pdf), [files](biof309_gene_expression_case_study.tar.gz)
4. March 13: Pattern Matching - [slides](slides/biof309_lecture5_slides.pdf), [regexp crossword](slides/regular_expression_xword.pdf)
[Back to main](#/main)
</script>
</section>
<section data-markdown id="screencasts">
<script type="text/template">
## Screencasts
1. [Class 2: Python Primatives, part 1](https://vimeo.com/59039770)
2. [Class 2: Python Primatives, part 2](https://vimeo.com/59039771)
[Back to main](#/main)
</script>
</section>
<section data-markdown id="notebooks">
<script type="text/template">
## IPython notebooks
You can right click on the notebook link and Save Link As, or just browse the HTML version.
1. Lesson 3: Iterables - [notebook](notebooks/BIOF309_Iterables.ipynb), [HTML](notebooks/BIOF309_Iterables.html)
2. Lesson 4: Control Flow - [notebook](notebooks/BIOF309_ControlFlow.ipynb), [HTML](notebooks/BIOF309_ControlFlow.html)
3. Project Ideas - [notebook](notebooks/BIOF309_ProjectIdeas.ipynb), [HTML](notebooks/BIOF309_ProjectIdeas.html)
4. Class notes from Feb 27: Functions [notebook](notebooks/BIOF309_class_notes_20140227.ipynb), [HTML](notebooks/BIOF309_class_notes_20140227.html)
5. Class notes from Mar 6: Files [notebook](notebooks/BIOF309_class_notes_20140306_gene_expr_case_study.ipynb), [HTML](notebooks/BIOF309_class_notes_20140306_gene_expr_case_study.html)
6. Class notes from Mar 13: Regexps [notebook](notebooks/BIOF309_class_notes_20140313_regexp.ipynb), [HTML](notebooks/BIOF309_class_notes_20140313_regexp.html)
7. Object Oriented Programming, Part 1 [notebook](notebooks/BIOF309_OOP_Part1.ipynb), [HTML](notebooks/BIOF309_OOP_Part1.html)
8. Object Oriented Programming, Part 2 [notebook](notebooks/BIOF309_OOP_Part2.ipynb), [HTML](notebooks/BIOF309_OOP_Part2.html)
9. Intro to Machine Learning w/ Scikit-learn (lecture by Parsa Hosseini) [notebook](notebooks/sklearn-notebook-parsah.ipynb)
10. Calculating Google Group email statistics [notebook](notebooks/BIOF309_using_gmail_api.ipynb), [HTML](notebooks/BIOF309_using_gmail_api.html)
[Back to main](#/main)
</script>
</section>
</div>
</div>
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