Simon Fraser University

8888 University Drive, Burnaby
Feb 22 and Mar 1, 2014
9:00 am - 4:30 pm


Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on bootcamp will cover basic concepts and tools; participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Instructors: Bernhard Konrad, Scott Chamberlain, Christina Koch, Lynne Williams

Who: The course is aimed at postgraduate students and other scientists who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate this knowledge into practical tools to help them work more productively.

Where: Simon Fraser University Burnaby campus. Map here. The room for the R event on Day 2 (notice the room change) is ASB 9896 E in the Applied Sciences Building, and for Python is K9509 in Shrum Kinesiology. You can look at this map on the Simon Fraser University website to find the building that you need to go to.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Contact: Please mail admin@software-carpentry.org for more information.


February 22nd
Room SCK 9509 TASC-I 9204 E
8:30 - 9:00 Setup help Setup help
9:00 - 9:15 Overview and introduction (Christina) Overview and introduction (Bernhard)
9:15 - 10:30 Navigating in the shell (Lynne) Intro to R and RStudio (Bernhard)
10:50 - 12:00 Local version control (Christina) Care and feeding of R objects (Scott)
12:00 - 1:00 Lunch break (no lunch provided) Lunch break (no lunch provided)
1:00 - 2:30 Intro to remote version control + shell scripts and automation (Christina and Lynne) Local version control (Bernhard)
2:50 - 4:30 Introduction to python, and ipython blocks (Lynne) Data aggregation using plyr (Scott)
March 1st
Room SCK 9509 ASB 9896 E
9:00 - 10:00 Day 1 review, more shell, Python intro (Lynne) Day 1 review. Project organization (Bernhard)
Overview of knitr, RPubs (Scott)
10:20 - 12:00 Python flow control, functions, plotting (Lynne) Version control in shell and Github (Bernhard)
12:00 - 1:00 Lunch break (no lunch provided) Lunch break (no lunch provided)
1:00 - 2:30 Resolving conflicts (git) and fixing bugs (python) (Christina) Making figures using ggplot2 (Scott)
2:50 - 4:30 Python from the command line (Christina) Functions and debugging (Bernhard)
The R workflow in action (Scott)

Chat rooms during the bootcamp


Setup

To participate in a Software Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp.

Overview

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. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, type the escape key, followed by ':q!' (colon, lower-case 'q', exclamation mark) to return to the shell.

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.

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.

Python

Depending on the programming language that you signed up for you need to install Python or R, but not both.
Python is becoming very popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We teach with Python version 2.7, since it is still the most widely used. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.

R

Depending on the programming language that you signed up for you need to install Python or R, but not both.
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

Software Carpentry Installer

For an all-in-one installer:

  • Download the installer.
  • If the file opens directly in the browser select File→Save Page As to download it to your computer.
  • Double click on the file to run it.

Editor

Notepad++ is a popular free code editor for Windows. Be aware that you must add its installation directory to your system path in order to launch it from the command line (or have other tools like Git launch it for you). Please ask your instructor to help you do this. If you are in the R section, RStudio will be sufficient.

Git Bash

Install Git for Windows by download and running the installer This will provide you with both Git and Bash in the Git Bash program.

Python

  • Download and install Anaconda CE.
  • Use all of the defaults for installation except before pressing Finish make sure to check Make Anaconda the default Python.

R

Please follow our R install instructions.

Mac OS X

Bash

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.

Editor

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed. If you are in the R section, RStudio will be sufficient.

Git

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 higher:

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.

Python

We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the bootcamp.)

  1. Download the installer that matches your operating system and save it in your home folder.
  2. Open a terminal window.
  3. Type
    bash Anaconda-
    and then press tab. The name of the file you just downloaded should appear.
  4. Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).

R

Please follow our R install instructions.

Linux

Bash

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.

Git

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).

Editor

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed. If you are in the R section, RStudio will be sufficient.

R

Please follow our R install instructions.

Python

We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the boot camp.)

  1. Download the installer that matches your operating system and save it in your home folder.
  2. Open a terminal window..
  3. Type
    bash Anaconda-
    and then press tab. The name of the file you just downloaded should appear.
  4. Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).