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A Practical Introduction to Programming for Biologists


poster marchGARNet’s 2014 workshop is a collaboration with Software Carpentry - a bootcamp at the University of Warwick on 9th and 10th April 2014, which will give biologists a tailor-made practical introduction to programming.

Software Carpentry teaches principles of good programming applicable to any coding language or application, whether sequencing data, phenotypic trait analysis or biochemical assays. Tutorials will start from first principles and cover Python programming, managing data in Excel and Python; and scientific plotting using BioPython and R. Teaching will be a combination of live coding guided by the trainer and independent practical exercises.

Although the content is suitable for complete beginners, researchers who know what a command-line is will also benefit from being taught good practice like version control and test-driven development. These practices will make your programs more sustainable, vastly reducing replication in your code over time, and make them easier to share with team members, collaborators and even in publications.

Attendees must be familar with the Unix shell before the bootcamp. Don't worry - there are easy to follow tutorials on the Software Carpentry website. To follow the instructions in the tutorial on a Mac, you need to use Terminal, an application found in Utilities. On a PC use Command Prompt, which is found in Accessories. There is an explanation of the differences in commands for the two operating systems at the end of the second tutorial.


PROGRAMME

The draft programme is here.

We’re pleased to confirm our instructors, Aleksandra Pawlik and Christina Koch. Local helpers will be: Leonor Garcia-Gutierrez, Krzysztof Polanski and Jason Piper, all PhD students from the University of Warwick.

LOCATION

The bootcamp will be in the School of Life Sciences on Gibbet Hill Campus. Parking is very limited, please use public transport where at all possible.


ACCOMODATION

A limited number of double en-suite rooms are available on in the Radcliffe House Hotel for the night of 9th April. If you wish to stay in this on-campus hotel, you must select this option during registration by 1 March 2014.

SPONSORS

We are grateful to the Company of Biologists and the Software Sustainability Institute/Elixir UK for support of the workshop.

 CoB SSI