George Washington University

Virginia Science and Technology Campus, Ashburn, VA
Apr 29-30, 2014
9:00 am - 4:30 pm

General Information

George Washington University, Virginia Science and Technology Campus, Ashburn, VA
Hosted by the IMPACT project and sponsored by Professors Tarek El-Ghazawi & Lorena Barba
April 29th-30th, 2014
9:00 am - 4:30 pm
Room 101 Exploration Hall

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: Aron Ahmadia, Joshua R. Herr, William Rowell

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. 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.

Content: The syllabus for this bootcamp 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.
Documentation and debugging.

Where: Virginia Science and Technology Campus, Ashburn, VA. Get directions with OpenStreetMap or Google Maps.

Registration: Registration information is found on IMPACT's (Institute for Massively Parallel Applications and Computing Applications) Website.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Contact: Please email Josh Herr or Aron Ahmadia for more information.

Etherpad Link

We will use an Etherpad page to communicate and share notes together throughout the bootcamp.

Schedule

Tuesday	09:00	Overview
	09:30	Introduction to task automation with the Unix shell
	12:00	Lunch break
	13:00	Building programs with Python
	16:00	Wrap-up
Wednesday	09:00	Version control with Git
	12:00	Lunch break
	13:00	TBD
	15:00	TBD
	16:00	Wrap-up

Setup

To participate in this Software Carpentry bootcamp, you will need working copies of:

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.

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.

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.

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.

The instructions for installing each of these components is organized below by operating system.

MacOSX

Mac OS X / Bash

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.

Mac OS X / Editor

We recommend Text Wrangler or Sublime Text.

Mac OS X / Git

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.

For Mac OS X 10.7 and higher:

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.

For Mac OS X 10.6

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 .dmg file. Finally, install just git.

Mac OS X / Python

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.)

Download the installer that matches your operating system and save it in your home folder.
Open a terminal window.
Type
```
bash Anaconda-
```
and then press tab. The name of the file you just downloaded should appear.
Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).

Windows

Windows / Git Bash

Install Git for Windows by downloading and running the installer. This will provide you with both Git as well as Bash in the Git Bash program.

Windows / Editor

Notepad++ is a popular free code editor for Windows.

Windows / Anaconda Python

We recommend the all-in-one scientific Python installer Anaconda.
Use all of the defaults for installation.

Windows / Software Carpentry Installer

Finally, there is an optional script for installing the nano editor. Please install this after Anaconda and Git Bash

Download the installer.
If the file opens directly in the browser select File→Save Page As to download it to your computer.
(You may need to restart Windows first if this doesn't work). Double click on the file to run it.

Linux

Linux / Bash

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.

Linux / Git

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,yum, etc.).

Linux / Editor

Some options for Linux users include Sublime Text, Kate, or Geany.

Linux / Python

Download the installer that matches your operating system and save it in your home folder.
Open a terminal window..
Type
```
bash Anaconda-
```
and then press tab. The name of the file you just downloaded should appear.
Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).

Miscellaneous

Virtual Machine

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:

Install VirtualBox.
Download our VM image. Warning: this file is 1.7 GByte, so please download it before coming to your bootcamp.
Load the VM into VirtualBox by selecting "Import Appliance" and loading the .ova file.

Reference

Instructors

Aron Ahmadia works at the intersection of applied mathematics, software engineering, and application domains as diverse as adaptive optics, semiconductor lithography, and ice-sheet modeling. His focus is in the collaborative development of robust, reproducible, and scalable software tools for computational science.

Josh Herr is a post-doctoral researcher at Michigan State University in the Department of Microbiology & Molecular Genetics. He holds a B.S. in Biochemistry, M.S. in Plant Biology, and a Ph.D. in Integrative Biology. His research interests introduced him to phylogenetics at the command line and he has transitioned from the lab bench (almost entirely) to the computational analysis of microbial genomes and metagenomes. Josh blogs about his research interests at Cyme & Cystidium and is an editor at the bioinformatics help forum Biostar.

Billy Rowell is a Research Specialist for the Howard Hughes Medical Institute at the Janelia Farm Research Campus. Trained primarily as a geneticist and molecular biologist, he has studied plant disease resistance, fruit fly development, and gene expression. Currently he works in behavioral neuroscience, where he develops tools to process large sets of behavioral data.