Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab

Abstract

The khmer software project provides both research and production functionality for largescale nucleic-acid sequence analysis. The software implements several novel data structures and algorithms that perform data pre-filtering for common bioinformatics tasks, including sequence mapping and de novo assembly. Development is driven by a small lab with one full-time developer (MRC), as well as several graduate students and a professor (CTB) who contribute regularly to research features. Here we describe our efforts to bring better design, testing, and more open development to the khmer software project as of version 1.1. The khmer software is developed openly at http://github.com/dib-lab/khmer/.