Computing skills for reproducible research: software carpentry

Overview

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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 but 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 doing steps manually or 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 course is aimed at researchers in the life sciences who wish to use or design analysis pipelines on individual or clusters of computers. The target learner 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 or Nextflow is (or at least are not very comfortable using them), you may be the perfect fit for this workshop.

Modules/resources

• Introduction to the Unix shell
• Version control and history tracking with Git
• Introduction to scripting and basics of data analysis with Python
• Multi-step analysis and pipeline management with Nextflow
• Best practices for reproducible analysis in high performance computing environments

Learning outcomes

After the course, participants will be able to:

• interact with a command-line shell for local and remote computing needs
• 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
• execute and troubleshoot command line tools and pipelines on a high performance computing cluster

What past participants say about the course

“I highly recommend the Software Carpentry course, as it covers all the necessary basics, and by the end of the week you are able to write your own little program for your own purposes.” – Erzsebet Baka, Department of Molecular Ecology, Hungarian University of Agriculture and Life Sciences, Hungary

“An excellent course with excellent and very nice mentors who are always willing to help. The organization is fantastic and they help you with any questions you may have.” — William Zamora, University of Costa Rica, Costa Rica

Sponsors

Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information.

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