Saint Francis Xavier University
March 18-19, 2015
9:00 am - 4:30 pm
Instructors: Gabriel Devenyi, Ross Dickson
Helpers:
General Information
EVENT CANCELLED DUE TO WINTER STORM. VENUE CLOSED.
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.
This workshop is sponsored by ACEnet, a consortium of Atlantic Canadian Universities providing researchers with advanced research computing resources, including training, and support.
Who: The course is aimed at graduate students and other researchers.
Where: Room 342, Coady Institute, Antigonish, Nova Scotia. 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.
Contact: Please mail ross.dickson@ace-net.ca for more information.
Schedule
Day 1
| 09:00 | Automating tasks with the Unix shell |
| 10:30 | Coffee |
| 12:00 | Lunch break |
| 13:00 | Building programs with R |
| 14:30 | Coffee |
| 16:00 | Wrap-up |
Day 2
| 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: https://etherpad.mozilla.org/acenet.
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...
- Sample files
Programming in R
- Working with vectors and data frames
- Reading and plotting data
- Creating and using functions
- Loops and conditionals
- Using R from the command line
- Reference...
- Sample data
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
This page has instructions on testing that you have the right software installed.
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 the editor installed by the Software
Carpentry Installer, it is a basic editor integrated into the
lesson material.
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.
Mac OS X
We recommend
Text Wrangler or
Sublime Text.
In a pinch, you can use nano,
which should be pre-installed.
Linux
Kate is one option for
Linux users. In a pinch, you can use nano, which
should be pre-installed.
The Bash Shell
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Windows
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 Git Bash:
- Download the installer.
- Double click on the file to run it.
Information about the SWC Windows Installer, including the source code, can be found at https://github.com/swcarpentry/windows-installer.
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.
Windows
Git should be installed on your computer as part of your Bash install (described above).
Mac OS X
For OS X 10.8 and higher, install Git for Mac
by downloading and running
the installer.
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 (10.5-10.7) use the
most recent available installer for your
OS available
here. Use the Leopard installer for 10.5 and the Snow
Leopard installer for 10.6-10.7.
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.
R
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
Windows
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE.
Mac OS X
Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.
Linux
You can download the binary files for your distribution
from CRAN. Or
you can use your package manager (e.g. for Debian/Ubuntu
run sudo apt-get install r-base and for Fedora run
sudo yum install R). Also, please install the
RStudio IDE.
SQLite
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.
Windows
Download the sqlite3 program and put it in the directory where you are running examples.
Mac OS X
sqlite3 comes pre-installed on Mac OS X.
Linux
sqlite3 comes pre-installed on Linux.