This is the webpage for the Software Carpentry Bootcamp that was held at the University of Delaware, Newark, DE on September 11th-12th, 2014. This bootcamp was being sponsored by the Delaware Biotechnology Institute and the University of Delaware Bioinformatics Student Association (BiSA).
When: The bootcamp took place on September 11th-12th, 2014.
Location: Delaware Biotechnology Institute (DBI), 15 Innovation Way, Newark, DE. The bootcamp will be in Room 102.
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.
Instructors: Joshua R. Herr, Joshua L. Adelman
Helpers: Erin Crowgey, Reza Hammond, Modupe Adetunji, Liang Sun, Matthew Ralston
What: Our goal is to help scientists and engineers become more productive by teaching them basic computing skills like program design, version control, testing, and task automation. In this two-day bootcamp, short tutorials will alternate with hands-on practical exercises. Participants will be encouraged both to help one another, and to apply what they have learned to their own research problems during and between sessions.
Who: The course is aimed at postgraduate students and other scientists who may be familiar with basic programming but need help to translate this knowledge into practical tools to help them work more productively.
Content: The syllabus for this bootcamp will include:
Registration: Sorry, Registration is closed as of September 9th, 2014. All the seats for the bootcamp have been filled and there is a large waitlist.
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.
|08:30||Intructors Availble for Setup Troubleshooting|
|09:00||Introduction to Software Carpentry|
|09:15||Introduction to the Shell|
|11:00||More Shell and Automating Tasks|
|13:00||Building programs with Python|
|15:00||More Programming using Python|
|08:30||Intructors Availble for Questions During Setup|
|09:00||Introduction to Version Control and Using Git|
|11:00||Using Git Collaboratively In-House and with Github|
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. Git lets you track who made changes to what file when. Git also can be used in the cloud with third-party code resources such as 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 version of Python. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend an all-in-one installer.
Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program.
This installer requires an active internet connection
After installing Python and Git Bash:
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.
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.
Install Git for Mac by downloading and running the installer. For older versions of OS X (10.5-10.7) use the most recent available installer available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.
The default shell is usually
bash, 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 specific distro's package manager (e.g.
Kate is one option for Linux users. In a pinch, you can use
nano, which should be pre-installed.
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 bootcamp.)
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).