Computing Skills For Reproducible Research: Software Carpentry – Virtual

Overview

Course Overview

Computation is an integral part of today’s research as data has grown too large or too complex to be analysed by hand. An ever-growing fraction of science is performed computationally and many wet-lab biologists spend part of their time on the computer. Many scientists struggle with this aspect of research as they have not been properly trained in the necessary set of skills. The result is that too much time is spent using inefficient tools when progress could be faster. This course provides training in several key tools, with a focus on good development practices that encourage efficient and reproducible research computing.

Audience

This is a course for researchers in the life sciences who are using computers or computing clusters for their analyses, even if not full time. The target student is familiar with some command line/programmatic computer usage, and wants to become more confident using these tools efficiently and reproducibly.

If you have written a for loop in some language before, but do not know what Git is (or at least are not very comfortable using it), you may be the perfect fit for this workshop.

Modules/Resources

• Introduction to scripting and basics of data analysis with Python
• Introduction to the Unix shell and cluster resource management
• Version control with Git and GitHub
• Multi-step analysis and pipeline management
• Literate programming with Jupyter notebooks

Learning Outcomes

After the workshop, participants will be able to:

• write and organise their own scripts for data analysis
• use version control to keep track of, and revert changes to their files
• implement efficient and reproducible pipelines that combine multiple tools and scripts

Speakers and Trainers

Renato Alves

EMBL Heidelberg

Germany

Holger Dinkel

Max Planck Institute for Biological Cybernetics,

Germany

Toby Hodges

The Carpentries,

USA

Melanie Kaeser

EMBL Heidelberg,

Germany

Kimberly Isobel Meechan

EMBL Heidelberg,

Germany

Nikolaos Papadopoulos

EMBL Heidelberg

Germany

Christian Schudoma

EMBL Heidelberg,

Germany

Thomas Schwarzl

EMBL Heidelberg,

Germany

Malvika Sharan

The Alan Turing Institute,

UK

Mike Smith

EMBL Heidelberg,

Germany

Frank Thommen

DKFZ Heidelberg,

Germany

Thea Van Rossum

EMBL Heidelberg,

Germany

Scientific Organisers

Renato Alves

EMBL Heidelberg

Germany

Toby Hodges

The Carpentries,

USA

Course Organisers

Maryann Heck

EMBL Heidelberg

Germany

Raili Pall

EMBL Heidelberg

Germany

Programme