Room 114 IGB
Mar 18-Dec 31, 2015
1:00 pm - 2:00 pm
Instructors: David LeBauer
Helpers:
General Information
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. I am going to be 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.
Who: The course is aimed at graduate students and other researchers.
Where: Institute for Genomic Biology, University of Illinois. 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 dlebauer@gmail.com for more information.
Etherpad: https://etherpad.mozilla.org/2015-01-01-longlab.
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...
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...
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...
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. 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.
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 downloading and running the installer. This will provide you with both Git and Bash in the Git Bash program.
Software Carpentry Windows Installer
It installs and configures nano (Among other things)
This installer requires an active internet connection.
After installing Git Bash:
- Download the Software Carpentry Windows installer.
- Double click on the file to run it.
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 10.8 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.