University of Southern California
Sept 16-17, 2013
8:30 am - 4:30 pm
Instructors: Ariel Rokem, Matt Terry, John Mehringer, Karan Vahi
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 boot camp, 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. Attendants are offered online office hours: regular events to get one-on-one help from Software Carpentry instructors, online.
Who: The course is aimed at 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. Basic knowledge of programming and data structures is presumed.
Enrolment in this bootcamp is restricted to USC Faculty, Staff and Students. Please use our Eventbrite site for registration.
Requirements: Participants must bring a laptop with a few specific software packages installed. (The list will be sent to participants a week before the boot camp.)
Content: The syllabus for this boot camp will include:
- using the shell to do more in less time
- using version control to manage and share information
- basic Python programming
- how (and how much) to test programs
- introduction to workflows and Pegasus WMS
- RNASeq bioninformatics pipeline through Pegasus WMS
In addition, there is a custom USC module on
- HPCC computing resources
Contact: Please mail admin@software-carpentry.org for more information.
Parking: Attendees can park in 'Structure D' which is closest to the Davidson Center . The daily rate is $10.00.
Alternatively people from the Health Science Campus can take the shuttle to the main campus. Look at the schedule for Intercampus Service from HSC to UPC here. We recommend taking the 7AM shuttle on the first day, especially if you have not been to Davidson Center before.
Note: Attendees are responsible for paying for parking. Registration fees don't include parking.
Setup
The Bash Shell
Bash is a commonly-used shell. Using a shell gives you more power to do more tasks more quickly with your computer.
Mac
The default shell in Mac OS X is bash.
Windows
Install Git Bash following the instructions here.
Linux
The default shell is usually bash but if not you can get to bash by opening a terminal and typing bash.
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.
Mac
We recommend Text Wrangler, Sublime Text, or Text Mate 2.
Windows
Notepad++ is a popular free code editor for Windows.
Linux
Git
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.
Mac
Download and install the most recent version from hereWindows
Install Git Bash following the instructions here.
Linux
If git is not already available on your machine you can try to install it via your distro's package manager (e.g. apt-get git).
Python
Python is becoming more and more popular in scientific computing, and it's a great language for teaching general programming concepts due to its easy-to-read syntax. We will be using Python version 2.7. Installing all the scientific packages for Python individually can be a bit difficult, so we recommend using an all-in-one installer.
Please install Enthought Canopy .
Virtual Machine
Installation issues can and do happen. To ensure that you can continue to participate in a lesson even if one of your software programs fails, we provide a Linux virtual machine that contains most of the necessary software pre-installed.
Please download and install Virtual Box for your OS from here . Please download the SWC VM file from here. On the first day we will do a walkthrough of how to setup and launch the bootcamp VM through Virtual Box.
The Workflows module and the RNASeq Module on the second day will be done using the Pegasus VM.
Note: The Pegasus VM does not have a GUI. The IPython notebook and the plotting exercises with matplotlib need X environment and cannot be done in the Pegasus VM, which is why you also need to download the SWC VM.We will use the following Etherpad page to communicate and make notes.
| 8:30 - 9:00 | Introduction and Setup Help | - |
| 9:00 - 10:00 | The Unix Shell | Video |
| 10:00 - 10:15 | Coffee | - |
| 10:15 - 11:00 | The Unix Shell | - |
| 11:00 - 12:00 | Version control with git | Video |
| 12:00 - 1:00 | Lunch | - |
| 1:00 - 2:30 | More git | - |
| 2:30 - 2:45 | Coffee | - |
| 2:45 - 4:30 | Programming in Python | Video |
| 8:30 - 9:30 | Scientific computing in Python ( Plotting, Arrays ) | Video |
| 9:30 - 9:45 | Coffee | - |
| 9:45 - 12:00 | Software validation and testing | Video |
| 12:00 - 1:00 | Lunch | - |
| 1:00 - 1:45 | Introduction to HPCC | Video |
| 1:45 - 3:15 | Introduction to Workflows and Pegasus | Video |
| 3:15 - 3:30 | Coffee | - |
| 3:30 - 4:00 | Pegasus and Workflows continued. | - |
| 4:00 - 4:30 | RNASeq Workflows | Video |
| 4:00 - 4:30 | Wrap-up and feedback | - |