University of Chicago

BSLC 115, 924 East 57th Street
Sept 19-20, 2013
8:30 am - 4:30 pm

Instructors: John Blischak, Will Trimble, Emily Davenport

What: More and more fields of biology are using computational methods for research. However, most undergraduate programs in biology do not provide the foundations of computer programming and software development in their curriculum, leaving graduate students to inefficiently struggle to self-teach themselves skills throughout their dissertation research. This is why Software Carpentry exists. Our goal is to help scientists and engineers become more productive by teaching them basic computing skills. In this two-day boot camp, attendees will learn basic programming, as well as best practices for writing correct and reproducible code, through short tutorials interspersed with hands-on practical exercises.

Who: This particular boot camp is aimed at graduate students in the life sciences with minimal programming skills.

Requirements: Participants must bring a laptop with a few specific software packages installed.

Content: The syllabus for this boot camp will include:

using the shell to do more in less time
basic Python programming
basic R programming
using version control to manage and share information

Contact: Please mail jdblischak@uchicago.edu for more information.

Schedule

Subject to Change

Day 1

8:30 - 8:45	Setup Help
8:45 - 9:00	Introduction
9:00 - 10:30	The Shell
10:30 - 12:00	Python Variables
12:00 - 1:00	Lunch
1:00 - 2:30	Python Data Structures
2:30 - 4:30	Python Flow Control

Day 2

9:00 - 10:30	Python Functions and Modules
10:30 - 12:00	Data processing example with the shell and Python
12:00 - 1:00	Lunch
1:00 - 4:30	Introduction to R

Chatroom

Link to etherpad chatroom

Lessons

Link to lesson material

Setup

The Bash Shell

Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.

Windows

Install Git Bash following these instructions. This gives you Git as well as Bash.

Mac OS X

The default shell in all versions of Mac OS X is bash, so no need to install anything. You access bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

GNU/Linux

The default shell is usually bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words.

Windows

Notepad++ is a popular free code editor for Windows.

Mac OS X

We recommend Text Wrangler or Sublime Text.

GNU/Linux

Kate is one option.

R

R is a programming language that specializes in statistical computing. It is a powerful tool for exploratory data analysis. To interact with R, we will use RStudio, an interactive development environment (IDE).

Windows

Install R by downloading and running this .exe file from The Comprehensive R Archive Network (CRAN). Also, please install the RStudio IDE.

Mac OS X

Install R by downloading and running this .pkg file from The Comprehensive R Archive Network (CRAN). Also, please install the RStudio IDE.

GNU/Linux

You can download the binary files for your distribution from The Comprehensive R Archive Network (CRAN). Or you can use your package manager, e.g. for Debian/Ubuntu run apt-get install r-base. Also, please install the RStudio IDE.

Git

Git is a state-of-the-art version control system. It lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com.

Windows

Install Git Bash following the instructions here. This gives you Bash as well as Git.

Mac OS X

Installing Git may require you to first install XCode. This is a very large download (several gigabytes), so please do it before arriving at the bootcamp.

For Mac OS X 10.7 and 10.8:

Go to the Xcode website. Get XCode from the App Store making certain to install the command line tools (from the Download preferences pane). Git is included in the command line tools.

For Mac OS X 10.6

If you have Mac OS X 10.6, first get XCode by going to the Apple developer site. You have to sign in with an Apple ID linked to a Developer account. If you don't have one, you can register and create one. Once you log in, go to page 8 and find "XCode 3.2.6 and iOS SDK 4.3 for Snow Leopard". Click to open that section, and then download the .dmg file. Finally, install just git.

GNU/Linux

If Git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get).

Python

Python is becoming more and more popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We will be using Python version 2.7. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend using an all-in-one installer.

Canopy

Installing everything you need on your own can be a bit difficult so we recommend just installing Enthought Canopy, which comes in free and academic versions for Mac, Windows, and GNU/Linux.

Virtual Machine

Installation issues can and do happen. To ensure that you can continue to participate in a lesson even if one of your software programs fails, we provide a Linux virtual machine that contains all the necessary software pre-installed. Please install VirtualBox and download this virtual machine image. Load the VM into VirtualBox by doing Import Appliance and loading the .ova file.