Educators:
Toby Hodges (Zeller Team, EMBL)
Malvika Sharan (Gibson Team, EMBL)
Luis Pedro Coelho (Bork Group, EMBL)
Frank Thommen (HD-HuB, DKFZ)
Thomas Schwarzl (Hentze Group & Huber Group, EMBL)
Mike Smith (HD-HuB, Zeller Team, Huber Group, Korbel Group, EMBL)
Georg Zeller (HD-HuB, EMBL)
Date:
19-09-2016 - 21-09-2016
13:00-18:00 (Day 1)
09:00-18:00 (Days 2 & 3)
Location:
ATC Computer Training Lab, EMBL Heidelberg
Contents:
The aim of Software Carpentry is to enable researchers to be more productive while producing work of higher quality. This 2.5 day workshop will teach the key skills required to practise robust computational science effectively and efficiently, and provide an overview of some of the tools and resources available for modern computational biology.
Topics covered include:
• An introduction to scripting in Python, and using the language for scientific applications and biological data handling
• Effective use of the Unix command line, and compute cluster job submission
• Version control with git and GitHub
• Analysis pipeline management with SnakeMake
Learning goals:
This course aims to teach software writing skills and best practices to researchers in biology who wish to analyse data, and to introduce a toolset that can help them in their work. The goal is to enable them to be more productive and to make their science better and more reproducible.
Prerequisites:
This is a course for researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will know a little bit of command line/programmatic computer usage, but not consider themselves an expert. A target student will have written a for loop in some language before, but will not know what git is (or at least not be very comfortable with advanced git usage).
Keywords:
Programming; Command Line; Version Control; Bioinformatics; Data Analysis; Cluster Computing
Tools:
Python; Bash; Unix/Linux; Git; GitHub; SnakeMake; Biopython; Pandas; Numpy; SciPy; Matplotlib
Contact:
Toby Hodges
Event URLs:
Course Homepage: http://tobyhodges.github.io/2016-09-19-heidelberg/
Registration & Venue Info: http://www.embl.de/training/events/2016/SWC16-01/index.html