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UC San Diego

July 18-22, 2016

9:00am - 12:30pm

Instructors: Juliane Schneider, Matt Critchlow, Reid Otsuji, Tim Dennis

Helpers: Tim Dennis, Ryan Johnson

General Information - Library Carpentry Workshop

**This is a Library Carpentry Workshop**.

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at librarians and library staff. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: 9500 Gilman Dr, La Jolla, CA 92093, Seuss Room. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers have checked that:

  • The room is wheelchair / scooter accessible.
  • Accessible restrooms are available.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch and we will attempt to provide them.

Contact: Please mail for more information.

  • REGISTER FOR DAY 1 - Jargon Busting and Regular Expressions (7/18)
  • REGISTER FOR DAY 2 - Basics of Using Bash with Data (7/19)
  • REGISTER FOR DAY 3 - Git and GitHub for Version Control (7/20)
  • REGISTER FOR DAY 4 - Open Refine and Data Cleaning (7/21)

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.



Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Day 1

09:00 Coffee
09:30 Intro and Jargon Busting
10:15 Foundations
11:00 Break
11:15 Regular Expressions
12:00 Wrap-up

Day 2

09:00 Coffee and file/tool download troubleshooting
09:30 Basics of Shell
10:10 Counting and mining
11:05 Break
11:20 Cleaning and Transforming
12:05 Wrap-up and Shell Reference Sheet

Day 3

09:00 Coffee and file/tool download troubleshooting
09:30 Git and Github
09:55 Github pages and Markdown
10:50 Break
11:05 Practice and/or discussion
12:00 Wrap-up

Day 4

09:00 Coffee and file/tool download troubleshooting
09:30 Introduction to OpenRefine
09:40 Importing data
09:50 Basic Functions I
10:50 Break
11:05 Basic Functions II and Advanced Functions
12:05 Wrap-up

Day 5

09:00 Office hours, questions, discussion


Unix Shell



To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.


Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Click on "Next".
    4. Click on "Next".
    5. Click on "Next".
    6. Select "Use Git from the Windows Command Prompt" and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
    8. Select "Use Windows' default console window" and click on "Next".
    9. Click on "Next".
    10. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

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). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.


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 is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

You will need an account at for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.


Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.


If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo yum install git.

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


Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.


nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.


OpenRefine (previously Google Refine) is a tool for data cleaning that runs through a web browser, and any browser - Safari, Firefox, Chrome, Explorer - should work fine. You will need to download Google Refine and install it, and when you open it, it will run through the browser, but you don't need an internet connection, and the data will all be stored on your computer.

  • Go to the OpenRefine download page
  • Click on Windows kit to download the install file
  • To use it, unzip, and double-click on google-refine.exe (if you're having issues with google-refine.exe try refine.bat instead)
  • Google Refine will then open in your web browser.
  • If it doesn't open automatically, open a web broswer after you've started the program and go to the URL http://localhost:3333 and you should see OpenRefine.