Apr 2-3, 2016
9:00 am - 5:00 pm
Instructors: Devendra Umbrajkar, Kevin Vilbig, Mehdi Eslamieh, Gaurav Kolekar, Daren Card, Anna Williford
Helpers: Nick Long, James Titus-McQuillan, Malini Kotak
Software Carpentry's mission is to help scientists across all disciplines 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.
Who: The course is aimed at anyone who is interested in learning new tools. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
|09:15||Unix Shell 1 Linux lesson; Data; Linux Commands|
|11:00||Unix Shell 2 Data With Scripts And Outputs; Shell History|
|1:30||Programming with Python 1 Python Basics; Python commands|
|3:15||Programming with Python 2 Python lesson II; Data|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
Saved latest version of Etherpad (after the workshop) is here.
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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of Mac OS X is Bash, so no
need to install anything. You access Bash from the Terminal
/Applications/Utilities). 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
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).
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
After installing Git, there will not be anything in your
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"
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.
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.
You can use your favorite text editor. If you do not have one, we recommend
Be aware that you must
add its installation directory to your system path.
To add Notepad++ to the path:
1) Open Git-Bash from the start menu.
2) Type: cd [enter] to make sure you are in your home directory.
3) Type: notepad .bashrc [enter]. This will create .bashrc file in Notepad.
Add the following text to the file:
export PATH=$PATH:"C:\Program Files (x86)\Notepad++"
4) Save the file and exit Notepad. 5) Open a new Git-Bash window. You should now be able to launch Notepad++ by typing: npp [enter]. If you run into trouble please ask your instructor to help you with this.
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).
bash Anaconda-and then press tab. The name of the file you just downloaded should appear.
yesand press enter to approve the license. Press enter to approve the default location for the files. Type
yesand press enter to prepend Anaconda to your
PATH(this makes the Anaconda distribution the default Python).
Once you are done installing the software listed above, please go to this page, which has instructions on how to test that everything was installed correctly.
SQL is a specialized programming language used with databases. We
use a simple database manager called
SQLite in our lessons.
For our lesson you will need Firefox and SQL manager add-on. Follow these steps to complete the set up:
1. Install Firefox
2. Install the SQLite Manager add on:
Menu (the three horizontal lines near the top right corner of Firefox) -> Add-ons -> Search -> SQLite Manager -> Install -> Restart now
3. Add SQLite Manager to the menu:
Menu -> Customize, then drag the SQLite Manager icon to one of the empty menu squares on the right, Exit Customize
4. Open SQLite Manager: Menu -> SQLite Manager