General Information

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: Naupaka Zimmerman, Bernhard Konrad, Dav Clark, Andrea Zonca

Who: The course is aimed at graduate students and other researchers.

Where: UCDavis Shields Library. Get directions with Google Maps. Click here for Shield's Second Floor room map.

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

Contact: Please mail admin@software-carpentry.org for more information.

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Monday Schedule

	Lannister Group @ Nelle Branch Instructors: Naupaka and Andrea Helpers: Noam and Ciera Etherpad	Baratheon Group @ LIR Instructors: Dav and Bernhard Helpers: Jonathan and Dave Etherpad
8:30 - 9:00 am	Setup help Intro to the post-doc union and library	Setup help Intro to the post-doc union and library
9:00 - 10:15 am	Basics of the R working environment and language (links: 1 | 2 | 3)	Care and feeding of R objects, Functions
10:15 - 10:45 am	coffee break	coffee break
10:45 am - 12:00 pm	Care and feeding of R objects, Functions	Unit Testing/Code Coverage
12:00 - 1:00 pm	lunch on your own	lunch on your own
1:00 - 2:15 pm	Writing functions, Intro to data munging (links to raw R code: 1 | 2)	Writing functions, Intro to data munging
2:15 - 2:45 pm	light refreshments available	light refreshments available
2:45 - 5:00 pm	Making figures with ggplot2	Making figures with ggplot2
5:30 - 8:00 pm	Dinner/Social, Location: Delta of Venus. Open to all
times approximate, but there will always be two sessions before lunch and two after

Tuesday Schedule

	Lannister Group @ Nelle Branch Instructors: Naupaka and Andrea Helpers: Noam and Ciera	Baratheon Group @ LIR Instructors: Dav and Bernhard Helpers: Jonathan and Dave
8:30 - 9:00 am	Setup help	Setup help
9:00 - 10:15 am	Shell, file manipulation	Shell, file manipulation
10:15 - 10:45 am	coffee break	coffee break
10:45 am - 12:00 pm	Intro to Version Control	Intro to Version Control
12:00 - 1:00 pm	lunch on your own	lunch on your own
1:00 - 2:15 pm	The shell cont'd and Version control, cont'd	The shell cont'd and Version control, cont'd
2:15 - 2:45 pm	light refreshments available	light refreshments available
2:45 - 5:00 pm	Creating workflows and automated pipelines, knitr (Final class exercise)	Creating workflows and automated pipelines, knitr
times approximate, but there will always be two sessions before lunch and two after

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Setup

To participate in a Software Carpentry bootcamp, you will need working copies of the software described below. Please make sure to install everything before the start of your bootcamp.

TL;DR version: make sure you have the Bash shell, Git, R, and RStudio. For detailed instructions, go here.

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.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we will use RStudio, an interactive development environment (IDE).

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