Software Carpentry: University of Delaware

University of Delaware

Newark, DE, USA
Sep 11-12, 2014
9:00 am - 4:30 pm

General Information

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:

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: Newark, DE, USA. Get directions with OpenStreetMap or Google Maps.

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 joshua.r.herr@gmail.com for more information.

Etherpad Link

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

Schedule

Day 1

08:30	Intructors Availble for Setup Troubleshooting
09:00	Introduction to Software Carpentry
09:15	Introduction to the Shell
10:45	Coffee break
11:00	More Shell and Automating Tasks
12:00	Lunch break
13:00	Building programs with Python
14:45	Coffee break
15:00	More Programming using Python
16:00	Wrap-up

Day 2

08:30	Intructors Availble for Questions During Setup
09:00	Introduction to Version Control and Using Git
10:45	Coffee break
11:00	Using Git Collaboratively In-House and with Github
12:00	Lunch break
13:00	More Python
14:45	Coffee break
15:00	More Python
16:00	Wrap-up

Syllabus

The Unix Shell

Files and directories: pwd, cd, ls, mkdir, ...
History and tab completion
Pipes and redirection
Looping over files
Creating and running shell scripts
Finding things: grep, find, ...
Reference...

Programming in Python

Using libraries
Working with arrays
Reading and plotting data
Creating and using functions
Loops and conditionals: for, if, else, ...
Defensive programming
Using Python from the command line
Reference...

Version Control with Git

Creating a repository
Recording changes to files: add, commit, ...
Viewing changes: status, diff, ...
Ignoring files
Working on the web: clone, pull, push, ...
Resolving conflicts
Open licenses
Where to host work, and why
Reference...

Setup

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.

Overview

Text 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. 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.

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. 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

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.

Windows

Python

Download and install the free Anaconda Python distribution from Continuum Analytics. You should select the Python 2.7 installer.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Git Bash

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

Software Carpentry Installer

This installer requires an active internet connection

After installing Python 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.
Double click on the file to run it.

Text Editor

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.

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.

Editor

We recommend Text Wrangler or Sublime Text. In a pinch, you can use nano, which should be pre-installed.

Git

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.

Python

Download and install the free Anaconda Python distribution from Continuum Analytics. Please select the Python 2.7 installer.
Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

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.

Git

If Git is not already available on your machine you can try to install it via your specific distro's package manager (e.g. apt-get or yum).

Text Editor

Kate is one option for Linux users. In a pinch, you can use nano, which should be pre-installed.

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 bootcamp.)

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).

Reference

Instructors

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.

Joshua Adelman is a computational biophysicist who uses modeling and simulation to understand how small molecules and ions move across the cell membrane. He is one of the core developers of the open source, Weighted Ensemble Simulation Toolkit (WESTPA) and spends most of his days building computational tools and crunching data for the good of science. He received his Ph.D. in Biophysics at the University of California, Berkeley and is currently a Research Assistant Professor in the Department of Biological Sciences at the University of Pittsburgh.