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University Library Basel

Vortragssaal (1. Floor)

June 23-24, 2015

9:00 - 17:00

Instructors: Geoff Fucile, Stefan Pfenninger, Thomas Guignard

Helpers: Silvia Witzig, Lionel Walter, Martin Reisacher, Paul Coray, Sebastian Schuepbach, Thomas Julou

Register

The workshops have filled up very quickly ! Please register on the waiting list, we are evaluating the various possibilities and will keep you updated before the end of May.

General Information

This workshop is hosted by the University Library Basel. It is organized in collaboration with the SIB Swiss Institute of Bioinformatics and with support from SIB and the Swissbib project.

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 could be applied to libarians as well. 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 graduate students, researchers and librarians. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: UB Hauptbibliothek, Vortragssaal (1. Floor), Schönbeinstrasse 18-20, CH-4056 Basel. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Language: The class will be taught in English, but the instructors do speak German and French as well.

Instructors:
Geoffrey Fucile works at the SIB Swiss Institute of Bioinformatics and sciCORE - the center for high performance computing at the University of Basel. He is involved in training and research activities in life sciences, with a focus on genomics and structural biology.
Stefan Pfenninger is a postdoc in the Climate Policy Group at ETH Zürich’s Department of Environmental Systems Science.
Thomas Guignard is a Swiss engineer turned librarian now based in Toronto, Canada. He's also a maker and hobby programmer, and strongly believes in empowering kids and adults through a better understanding of technology.

Contact: Please mail thomas.guignard@gmail.com for more information.

During the same week, Software Carpentry will also be held in Lausanne.
If you are interested in open data, skills learned at this workshop are a perfect introduction to the 2nd Swiss Open Cultural Data Hackathon to be held in Basel on the 1st and 2nd of July 2016.


Schedule

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Day 1

09:00 Automating tasks with the Unix shell
10:30 Coffee
12:00 Lunch break
13:00 Building programs with Python
14:30 Coffee
16:00 Wrap-up
16:30 Have a drink together (at unternehmen mitte)

Day 2

09:00 Version control with Git
10:30 Coffee
12:00 Lunch break
13:00 Managing & cleaning up data with OpenRefine
14:30 Coffee
16:00 Wrap-up

Etherpad: http://pad.software-carpentry.org/2016-06-23-basel.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


Syllabus

The Unix Shell

Programming in Python

  • Using libraries
  • Working with arrays
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Defensive programming
  • Using Python from the command line
  • Reference...

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
  • Reference...

Managing & Cleaning Up Data with OpenRefine

  • Creating a project & importing data
  • Exploring data through filtering and faceting
  • Cleaning up data: split, merge, cluster, remove whitespaces, etc.
  • Use GREL to perform more complex operations
  • Save and reuse workflows
  • Exporting data
  • Reconciliation and APIs
  • GREL Reference
  • GREL and Regular expression cheat sheet

Setup

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.

Windows

  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".

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). You may want to keep Terminal in your dock for this workshop.

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.

Git

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 github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

Windows

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

Mac OS X

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.

Linux

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.

Windows

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. It should be pre-installed.

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

Linux

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.

Python

Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.4 is fine).

We will teach Python using the IPython notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows

  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for Windows.
  3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.

Linux

  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for Linux.
  3. Install Python 3 using all of the defaults for installation. (Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  4. Open a terminal window.
  5. Type
    bash Anaconda-
    and then press tab. The name of the file you just downloaded should appear.
  6. 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).

OpenRefine

OpenRefine (formerly Google Refine) is a powerful tool for working with messy data: cleaning it; transforming it from one format into another; and extending it with web services and external data. Please look at the Installation Instructions from the OpenRefine project for more details on how to run OpenRefine on your machine. The instructions below are adapted from this link. We will be using version 2.6-rc2 during the workshop. A Java Runtime Environment (JRE) is required to run OpenRefine. If the installation procedure below fails, make sure you have a working JRE installed on your computer.

Windows

  1. Download OpenRefine v. 2.6-rc2 for Windows
  2. Once you have downloaded the .zip file, uncompress it into a folder wherever you want (such as in C:\Open-Refine).
  3. To launch OpenRefine, run the .exe file in that folder. You should see the Command window in which OpenRefine runs.
  4. To shut down OpenRefine, press Ctrl-C in the command window that is running OpenRefine. Wait until there's a message that says the shutdown is complete. That window might close automatically, or you can close it yourself. If you get asked, "Terminate all batch processes? Y/N", just press Y.

Mac OS X

  1. Download OpenRefine v. 2.6-rc2 for Mac
  2. Once you have downloaded the .dmg file, open it, and drag the OpenRefine icon into the Applications folder.
  3. To launch OpenRefine, double-click the OpenRefine app. You'll see the OpenRefine app appear in your dock.
  4. If you get an error message preventing you from opening the app because it's from an unidentified developer, do the following (you only have to do it once when you open the app for the first time):
    1. Press the ctrl (Control) key and click on the app icon
    2. Choose Open from the shortcut menu
    3. There should now be an Open button under the "unidentified developer" error message. Click that button to open the app.
  5. To shut down OpenRefine, right-click on its icon in the Dock and choose the Quit option.

Linux

  1. Download OpenRefine v. 2.6-rc2 for Linux
  2. Once you have downloaded the .tar.gz file, uncompress it into a folder wherever you want.
  3. To launch OpenRefine, open a shell, navigate to that folder and type ./refine
  4. To shut down OpenRefine, press Ctrl-C in the shell that is running OpenRefine.

Running OpenRefine

OpenRefine is operated from within a web browser (such as Chrome or Firefox). If your browser doesn't open automatically when you start OpenRefine (see above), navigate to http://127.0.0.1:3333/ in your favourite browser to open the OpenRefine window. Please note that even though you use a browser to operate OpenRefine, it is still run locally on your machine, and not on the web.