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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">
<!-- For syntax highlighting -->
<link rel="stylesheet" href="lib/css/zenburn.css">
<!-- If the query includes 'print-pdf', use the PDF print sheet -->
<script>
document.write( '<link rel="stylesheet" href="css/print/' + ( window.location.search.match( /print-pdf/gi ) ? 'pdf' : 'paper' ) + '.css" type="text/css" media="print">' );
</script>
<!--[if lt IE 9]>
<script src="lib/js/html5shiv.js"></script>
<![endif]-->
</head>
<body>
<div class="reveal">
<!-- Any section element inside of this container is displayed as a slide -->
<div class="slides">
<section>
<h1>BIOF 309</h1>
<h3>Class 1: Introduction and Installation</h3>
<h3>Christopher Coletta</h3>
</section>
<section data-markdown id="talk_outline">
<script type="text/template">
## Class 1 Outline
1. About Me <!-- .element: class="fragment" -->
2. Goals for the course<!-- .element: class="fragment" -->
2. About the course<!-- .element: class="fragment" -->
2. How to get help<!-- .element: class="fragment" -->
3. Discussion of programming language ecosystem and where Python fits in<!-- .element: class="fragment" -->
4. What makes Python distinctive<!-- .element: class="fragment" -->
5. The Python data analysis stack: core Python + essential 3rd party modules<!-- .element: class="fragment" -->
6. Setup of Environment<!-- .element: class="fragment" -->
7. Using Python interactively via IPython notebook<!-- .element: class="fragment" -->
8. Running a program<!-- .element: class="fragment" -->
9. Homework: Email me the magic number.<!-- .element: class="fragment" -->
</script>
</section>
<section data-markdown id="aboutme">
<script type="text/template">
## About Me
* Computer Scientist
* NIH FTE
* National Institute on Aging, JHU Bayview Campus
* Laboratory of Genetics, David Schlessinger, Chief
* Image Informatics and Computational Biology Unit, Ilya Goldberg, Head
* Specialize in computer vision, machine learning
* Project: [WND-CHARM](https://github.com/wnd-charm/wnd-charm)
* Software Engineer writing software professionally since 2006
</script>
</section>
<section data-markdown id="goals">
<script type="text/template">
## Goals for BIOF309
- To teach you how to write programs that provide insight into your data <!-- .element: class="fragment" -->
- To teach you how to think like a computer <!-- .element: class="fragment" -->
- Teach you HOW to learn other programming languages in the future. <!-- .element: class="fragment" -->
</script>
</section>
<section data-markdown id="about">
<script type="text/template">
## About the course
* Target audience: Research professionals who have not programmed before <!-- .element: class="fragment" -->
* Style of course is linear: one concept builds on the next <!-- .element: class="fragment" -->
* Screencast lectures <!-- .element: class="fragment" -->
* No required textbook <!-- .element: class="fragment" -->
* Final grade: 80% homework, 20% final project <!-- .element: class="fragment" -->
* Use Test-Driven Development paradigm for homework <!-- .element: class="fragment" -->
* I provide the homework test, so you'll know if your program works or not before you pass it in <!-- .element: class="fragment" -->
* All questions related to material and logistics: use google groups email list <!-- .element: class="fragment" -->
* Any file submission: follow naming convention lastname_firstinitial_hw99_STUFF.py <!-- .element: class="fragment" -->
</script>
</section>
<section>
<section>
<h2>How to get help</h2>
<p>
<figure>
<img src="stress_reduction_kit.png">
</figure>
</p>
</section>
<section data-markdown id="help">
<script type="text/template">
## How to get help
* If you get an error message, READ THE ERROR MESSAGE <!-- .element: class="fragment" -->
* Google error message, or google your question "How do I ..." <!-- .element: class="fragment" -->
* Trial and error <!-- .element: class="fragment" -->
* "Worst thing that can happen is that it won't work" - Coglianti <!-- .element: class="fragment" -->
* help() in the console <!-- .element: class="fragment" -->
* Email the group<!-- .element: class="fragment" -->
* BTW, links: <!-- .element: class="fragment" -->
* [Instructional Videos](http://showmedo.com) <!-- .element: class="fragment" -->
* [Beginner's Guide for non-programmers](http://wiki.python.org/moin/BeginnersGuide/NonProgrammers) <!-- .element: class="fragment" -->
* [How to think like a computer scientist](http://interactivepython.org/courselib/static/thinkcspy/index.html) <!-- .element: class="fragment" -->
* [Online Python Tutor](http://www.pythontutor.com/) <!-- .element: class="fragment" -->
* [Learn Python The Hard Way](http://learnpythonthehardway.org) <!-- .element: class="fragment" -->
</script>
</section>
</section>
<section> <!-- outer -->
<section>
<h2>Programming Languages</h2>
</section>
<section data-markdown id="expressiveness">
<script type="text/template">
##Expressiveness
Figure from *"Comparison of programming languages"* [wiki article](http://en.wikipedia.org/wiki/Comparison_of_programming_languages#Expressiveness)
</script>
</section>
<section data-markdown id="static">
<script type="text/template">
##Static Programming Languages
* Examples: C, C++, Java
* FAST to run, slow to develop, difficult to "try things outs"
* Compiled into machine code before you run the program
</script>
</section>
<section>
<h2>Compiling xkcd Comic</h2>
<p>
<figure>
<a class="image" href="http://xkcd.com/303/"><img src="http://imgs.xkcd.com/comics/compiling.png"></a>
</figure>
</p>
</section>
<section data-markdown id="dynamic">
<script type="text/template">
## Dynamic Programming Languages
### a.k.a "scripting languages"
* [Dynamic programming language Wiki article](http://en.wikipedia.org/wiki/Dynamic_programming_language)
* Often used as "glue" to piece together different programs into one program
* Code not compiled ahead of time but interpreted at run time
* Slower than compiled languages
* Dynamic concept has strong overlap with "high-level programming language" concept
* Pros: Easier to use interactively (type statements in one-at-a-time, examine outputs, try things out)
* Cons: Abstraction penalty
</script>
</section>
<section data-markdown >
<script type="text/template">
## Best of Both Worlds (Advanced)
1. Write the code C and wrap it in Python
* E.g., Python packages Numpy & Scipy (and R, I think)
2. [LLVM](http://en.wikipedia.org/wiki/Low_Level_Virtual_Machine) - Compiler infrastructure that does language-agnostic program optimization
* Python package Numba does this
</script>
</section>
<section data-markdown>
<script type="text/template">
## TIOBE Index
* Measures how widely used programming languages are
* [website](http://www.tiobe.com/index.php/content/paperinfo/tpci/index.html)
</script>
</section>
</section><!-- end outer -->
<section> <!-- begin python sect -->
<section>
<h2>Python</h2>
<p>
<figure>
<img src="python-logo-master-v3-TM.png">
</figure>
</p>
</section>
<section>
<h2>Python xkcd Comic</h2>
<p>
<figure>
<a class="image" href="http://xkcd.com/353/"><img height="441" width="389" src="http://imgs.xkcd.com/comics/python.png"></a>
</figure>
<figcaption>Randall Munroe's caption: <q>I wrote 20 short programs in Python yesterday. It was wonderful. Perl, I'm leaving you.</q></figcaption>
</p>
</section>
<section>
<p>
<figure>
<img src="200px-Guido_van_Rossum_OSCON_2006.jpg">
</figure>
<figcaption>Guido van Rossum - Python Inventor and B.D.F.L.</figcaption>
</p>
</section>
<section data-markdown >
<script type="text/template">
## Brief History of Python
* Not named after the snake, but Monty Python -> FUN!
* Published in 1991, 1.0 in 1994
* Explicitly created as a teaching language
* "low-brow language," low barriers to entry, natural language syntax
* A person who programs in Python is a "Pythonista"
* The collective noun of a group of Pythonistas is [an "indentation."](https://gist.github.com/mariusGundersen/6925246)
</script>
</section>
<section data-markdown >
<script type="text/template">
## What makes python "Pythonic"
* indentation style
```python
def perm(l):
"""Compute the list of all permutations"""
if len(l) <= 1:
return [l]
r = []
for i in range(len(l)):
s = l[:i] + l[i+1:]
p = perm(s)
for x in p:
r.append(l[i:i+1] + x)
return r
```
</script>
</section>
<section data-markdown>
<script type="text/template">
## Moar "Pythonic"
* <code>import this</code>
* List comprehension
* Lambda functions
* Large core library with great types sets, dicts, etc
* Everything is an object
* Exceptions
* Built to be interactive
* Read-Evaluate-Print - one command at a time
</script>
</section>
<section>
<h2>Python Data Analysis Stack</h2>
<p>
<figure>
<img width="573" height="381" src="python_data_analysis_stack.png">
</figure>
<figcaption>Figure: Karissa McKelvey</figcaption>
</p>
</section>
<section>
<h2>Python Essential 3rd Party Modules</h2>
<p>
<figure>
<img class="stretch" src="core_3rd_party_modules.png">
</figure>
<figcaption>Figure: Karissa McKelvey</figcaption>
</p>
</section>
</section> <!-- end python sect -->
<section><!-- begin interactive-->
<section data-markdown>
<script type="text/template">
## Interactive Python
* You talking directly to the computer! <!-- .element: class="fragment" -->
* The computer talks back! <!-- .element: class="fragment" -->
* Scotty from Star Trek IV Video: <!-- .element: class="fragment" -->
* Crew of the Starship Enterprise travels back in time from the 23rd-century to the mid-1980's because blah blah blah... <!-- .element: class="fragment" -->
* Scotty, the engineer of the Enterprise, is posing as a professor with Dr. McCoy because blah blah blah... <!-- .element: class="fragment" -->
</script>
</section>
<section>
<iframe class="stretch" data-autoplay src="http://www.youtube.com/embed/v9kTVZiJ3Uc" frameborder="0" allowfullscreen></iframe>
</section>
<section data-markdown>
<script type="text/template">
## IPython Notebook
* Ideal for trying stuff out <!-- .element: class="fragment" -->
* One command at a time, one statement per line <!-- .element: class="fragment" -->
* The "kernel" - Python "engine" running in the backgorund <!-- .element: class="fragment" -->
* That what the open terminal is, just leave it be <!-- .element: class="fragment" -->
* The function and purpose of Ctrl-C <!-- .element: class="fragment" -->
* Exceptions <!-- .element: class="fragment" -->
* <code>%quickref</code> <!-- .element: class="fragment" -->
* Output cache: Out[4] or _4 for example <!-- .element: class="fragment" -->
</script>
</section>
</section><!-- end interactive -->
<section><!-- begin choice of editor -->
<section data-markdown>
<script type="text/template">
## Code Editor
* IPython Notebook
* Spyder - comes with Anaconda
* [Mac only: Sublime Text](http://www.sublimetext.com/)
* Notebook/TextEdit (for n00bs)
</script>
</section>
<section>
<p>
<figure>
<img class="stretch" src="Angelina_Jolie_hackers.jpg">
</figure>
<figcaption>vim/emacs: hax0rz only!</figcaption>
</p>
</section>
</section> <!-- end choice of editor -->
<section data-markdown>
<script type="text/template">
## In-class Exercise
* Fire up IPython Notebook
* Run [Magic Number](homework/hw1/biof309_hw1.py) program
</script>
</section>
</div>
</div>
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