March 2021

Using prototyping to select software for a research software project

Author: Mike Jackson
Posted: 1 Mar 2021 | 14:03

A selection of macaronsChoosing the right software for use in a research software project can be challenging. How do we know which software is both fit for purpose and provides a sound basis for our project for the foreseeable future? And, how do we make such a choice given that the time and effort to explore what could be myriad alternatives may be limited?

This was a challenge we faced in the RiboViz project, a multi-disciplinary team of biologists, bioinformaticians and research software engineers based at EPCC and The Wallace Lab at University of Edinburgh, The Shah Lab at Rutgers University, and The Lareau Lab at University of California, Berkeley. RiboViz is an open source package to help us develop our understanding of protein synthesis via analysis of ribosome profiling data. At the heart of RiboViz is an analysis workflow, implemented in a Python script. To conform to best practices for scientific computing, which recommend the use of build tools to automate workflows and to reuse code instead of rewriting it, we sought to reimplement this workflow within a bioinformatics workflow management system.

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