Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation. This two-day hands-on bootcamp will cover basic concepts and tools; 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 female postgraduate students and other scientists who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate this knowledge into practical tools to help them work more productively.
Where: Lawrence Berkeley National Laboratory, Berkeley, California. To get close, you can get directions with OpenStreetMap or Google Maps. Once you're in Berkeley, take the Blue Uphill Shuttle from Berkeley to Lawrence Berkeley National Laboratory. Then, navigate to the room dedicated for your track. There are Novice, Intermediate, and Advanced tracks.
Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).
Contact: Please mail firstname.lastname@example.org for more information.
Register: Seats are limited, but registration is free and open to anyone who identifies as female. To register, please go to the Eventbrite Page. Once you have registered, please fill out the skills survey so that you can be placed in a room that targets your skillset.
|Novice||Bldg. 54 Room 130||Schedule||Etherpad|
|Intermediate||Bldg. 15 Room 253||Schedule||Etherpad|
|Advanced||Bldg. 50A Room 5132||Schedule||Etherpad|
To participate in a Software Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything (or at least to download the installers) before the start of your bootcamp.
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.
Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.
Git is a state-of-the-art version control system. It 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.
Python is becoming very popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We teach with Python version 2.7, since it is still the most widely used. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.
SQL is a specialized programming language used with databases. We use a simple database manager called SQLite, either directly or through a browser plugin.
For an all-in-one installer:
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.
Install Git for Windows by download and running the installer. 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 (found
/Applications/Utilities). You may want
to keep Terminal in your dock for this workshop.
Installing Git may require you to first install XCode. This is a very large download (several gigabytes), so please do it before arriving at the bootcamp.
Go to the Xcode website. Get XCode from the App Store making certain to install the command line tools (from the Download preferences pane). Git is included in the command line tools.
If you have Mac OS X 10.6,
first get XCode by going to
the Apple developer site.
You have to sign in with an Apple ID linked to a Developer account.
If you don't have one,
you can register and create one.
Once you log in,
go to page 8 and find "XCode 3.2.6 and iOS SDK 4.3 for Snow Leopard".
Click to open that section,
and then download the
install just git.
Or, if you prefer a GUI, install Git for Mac by download and running the installer.
The default shell is usually
but if your machine is set up differently
you can run it by opening a terminal and typing
There is no need to install anything.
If Git is not already available on your machine you can try
to install it via your distro's package manager
Kate is one option for Linux users.
In a pinch, you can use
which should be pre-installed.
sqlite3 comes pre-installed on Linux.
you may install the Firefox SQLite browser plugin described below.
We recommend the all-in-one scientific Python installer Anaconda. (Installation requires using the shell and if you aren't comfortable doing the installation yourself just download the installer and we'll help you at the boot camp.)
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).
Instead of using
sqlite3 from the command line,
you may use this plugin
for Firefox instead.
To install it:
Some instructors prefer to have learners use a virtual machine (VM) rather than install software on their own computers. If your instructors have chosen to do this, please:
Many thanks to our generous sponsors who made this bootcamp possible:
And a special thank you to Lawrence Berkeley National Lab for providing a space for this workshop.