Stanford University

Li Ka Shing Center room 120, 291 Campus Drive, Stanford, CA 94305
Aug 14-15, 2014
9:00 am - 5:00 pm

General Information

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: Azalee Bostroem, Chris Lonnen (Lonnen)

Helpers: Matar Haller, Chris Beitel, Ian Korf, Dani Traphagen

Who: The course is aimed at graduate students and other researchers.

Where: Li Ka Shing Center room 120, 291 Campus Drive, Stanford, CA 94305. Get directions with OpenStreetMap or Google Maps.

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

Contact: Please mail for more information.


Day 1

Time Subject Instructor
8:30 - 9:00 Set Up Everyone
9:00 - 9:15 Welcome from Host Amy
9:15 - 9:30 Welcome Azalee
9:30 - 10:30 Shell Lonnen
10:45 - 11:00 Break -
11:00 - 12:15 Local Git Azalee/ Dani
12:15 - 1:15 Lunch -
1:15 - 2:00 Local Git Azalee
2:00 - 2:05 Stretch -
2:05 - 3:00 Python Lonnen
3:00 - 3:15 Break -
3:15 - 4:30 Python Lonnen
4:30 - 5:00 Flextime -

Day 2

Time Subject Instructor
9:00 - 10:00 Python Lonnen
10:00 - 10:15 Taste of Testing Chris
10:15 - 10:30 Break -
10:30 - 12:15 Remote Git Azalee
12:15 - 1:15 Lunch -
1:15 - 2:15 Data Visualization Azalee
2:15 - 2:20 Stretch -
2:20 - 3:15 Code Review Lonnen
3:15 - 3:30 Break -
3:30 - 4:00 Code Review Lonnen
4:00 - 4:15 Closing Azalee
4:15 - 5:00 Questions Everyone


The Unix Shell

  • Files and directories: pwd, cd, ls, mkdir, ...
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things: grep, find, ...

Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals: for, if, else, ...
  • Defensive programming
  • Using Python from the command line

Version Control with Git

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why

Code Review

  • what is code review
  • basic techniques for review
  • review excercise


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.



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, try typing the escape key, followed by ':q!' (colon, lower-case 'q', exclamation mark), then hitting Return 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 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


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.



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

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.

Software Carpentry Installer

This installer requires an active internet connection

After installing Python and Git Bash:

  • 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.


nano is the editor installed by the Software Carpentry Installer, it is a basic editor integrated into the lesson material.

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.


We recommend Text Wrangler or In a pinch, you can use nano, which should be pre-installed.


Install Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.


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



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.


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 or yum).


Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.


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).


Virtual Machine

If you cannot install one or more of the items listed above, please download the virtual machine. This will allow you to participate in the lesson. During the break or at the end of the day and instructor or helper will assist you in setting up your machine.

  1. Install VirtualBox.
  2. Download our VM image. Warning: this file is 1.7 GByte, so please download it before coming to your bootcamp.
  3. Load the VM into VirtualBox by selecting "Import Appliance" and loading the .ova file.