Software Carpentry: Institute of Molecular Life Sciences, University of Zurich

Institute of Molecular Life Sciences, University of Zurich

Nov 6-7, 2014

9:00 am - 5:00 pm

Instructors: Laurent Gatto, Robert Stojnic

Helpers: Frank Pennekamp, Peter Fields, Jelena Aleksic

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 workshop 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.

Who: This boot camp is an example-driven two-day workshop on advanced R skills. Short tutorials alternate with hands-on practical exercises, and participants are encouraged both to help one another, and to try applying what they have learned to their own research problems during and between sessions. Participants should bring their own laptops to work on.

Where: Winterthurerstrasse 190. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (see course repo for details). They are also required to abide by Software Carpentry's Code of Conduct.

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

Schedule

The aim of the workshop is to provide a set of tools to enable a more structured, efficient and systematic use of programming in computational sciences. We will address the following points throughout the course:

R object-oriented programming: S3 and S4, S4 Reference Classes.
R package development
R documentation and roxygen
Functional programming, vectorisation
Reproducible research and vignettes
Debugging and unit testing
Automating your pipelines with Makefile
Parallelisation: parallel and BiocParallel
Code profiling and strategies for optimisation
Using C/C++ in R and the Rcpp package
Source code versioning using git and github

Some of these topics will be addressed through the development of an R package that applied object oriented programming. The main thread that we will use is the definition and manipulations of generic and biological sequences that will, eventually, materialise into a fully fledged package.

See the course repo for a detailed programme, relevant content and the course material.

Setup

To participate in a Software Carpentry workshop, 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 workshop.

Overview

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.

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).

Windows

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.

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.

R

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE.

Mac OS X

Editor

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

Git

For OS X 10.8 and higher, 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 for your OS available here. Use the Leopard installer for 10.5 and the Snow Leopard installer for 10.6-10.7.

R

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

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 or yum).

Editor

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

R

You can download the binary files for your distribution from CRAN. Or you can use your package manager, e.g. for Debian/Ubuntu run apt-get install r-base or yum install R. Also, please install the RStudio IDE.