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

Michael R. Crusoe | Zendy; C. Titus Brown | Zendy

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

Author(s) -

Michael R. Crusoe,

C. Titus Brown

Publication year - 2016

Publication title -

journal of open research software

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.385

H-Index - 6

ISSN - 2049-9647

DOI - 10.5334/jors.35

Subject(s) - computer science , software , software engineering , software development , data science , programming language

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-fltering 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/.

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