Software Carpentry: SIB @ University of Lausanne

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General Information

This workshop is hosted by the SIB Swiss Institute of Bioinformatics, at the University of Lausanne (UNIL) with support from SIB, Library Information Switzerland (BIS), the swissbib project and the Scientific Information School.

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: Université de Lausanne, room 2020 (2nd floor, same floor as main entrance), Bâtiment Génopode, UNIL Sorge, 1015 Lausanne. Find the room on Planète UNIL, get directions on 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 French as well.

Instructors:
Julia Gustavsen is a PhD student at the University of British Columbia in Biological Oceanography. Her thesis work focuses on the changes in marine viral communities over time and space.
Diana Marek works at the SIB Swiss Institute of Bioinformatics, where she is involved in scientific collaborations, teaching bioinformatics for postgraduates, as well as in coordinating training and outreach activities, such as scientific fairs, conferences, seminars and workshops for the layperson as well as for scientists.
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, another Software Carpentry workshop will also be held in Basel.
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 - June 20

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
17:00	Apéro/Social

Day 2 - June 21

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

Etherpad: http://pad.software-carpentry.org/2016-06-20-lausanne.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Syllabus

The Unix Shell

Files and directories
History and tab completion
Pipes and redirection
Looping over files
Creating and running shell scripts
Finding things
Reference...

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 Data with SQL

Reading and sorting data
Filtering with where
Calculating new values on the fly
Handling missing values
Combining values using aggregation
Combining information from multiple tables using join
Creating, modifying, and deleting data
Programming with databases
Reference...

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

Download the Git for Windows installer.
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

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

Mac OS X

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

Linux

Open http://continuum.io/downloads with your web browser.
Download the Python 3 installer for Linux.
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.)
Open a terminal window.
Type
```
bash Anaconda-
```
and then press tab. The name of the file you just downloaded should appear.
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).

SQLite

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.

Windows

The Software Carpentry Windows Installer installs SQLite for Windows. If you used the installer to configure nano, you don't need to run it again.

Mac OS X

SQLite comes pre-installed on Mac OS X.

Linux

SQLite comes pre-installed on Linux.

If you installed Anaconda, it also has a copy of SQLite without support to readline. Instructors will provide a workaround for it if needed.