Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab
By: Michael R. Crusoe and C. Titus Brown
References
-
Brown
C T
BIGDATA: Small: DA: DCM: Low-memory streaming prefilters for biological sequencing data
2012
http://www.ged.msu.edu/downloads/2012-bigdata-nsf.pdf -
Brown
C T
Howe
A
Zhang
Q
Pyrkosz
A
Brom
T H
A reference-free algorithm for computational normalization of shotgun sequencing data
review at PLoS One
2012
July
Preprint at
http://arxiv.org/abs/1203.4802 -
Chacon
S
Github flow
2011
http://scottchacon.com/2011/08/31/github-flow.html - Crusoe M R Criteria-based assessment of the khmer suite figshare 2013 10.6084/m9.figshare.1558321.v1
- Crusoe M R Criteria-based assessment of the khmer suite v1.0 figshare 2014 10.6084/m9.figshare.1558322.v2
- Howe A C Jansson J K Malfatti S A Tringe S G Tiedje J M Brown C T Tackling soil diversity with the assembly of large, complex metagenomes Proceedings of the National Academy of Sciences 2014
-
Jackson
M
Crouch
S
Baxter
R
Software evaluation guide
2013
http://www.software.ac.uk/resources/guides-everything/software-evaluation-guide - Pell J Hintze A Canino-Koning R Howe A Tiedje J M Brown C T Scaling metagenome sequence assembly with probabilistic de bruijn graphs Proc Natl Acad Sci U S A 2012 Aug 109 33 13272 7 10.1073/pnas.1121464109 22847406
-
Preston-Werner
T
“semantic versioning 2.0.0”
2013
http://semver.org/ - Zhang Q Pell J Canino-Koning R Howe A C Brown C T These are not the k-mers you are looking for: Efficient online k-mer counting using a probabilistic data structure PLoS ONE 2014 Jul 9 7 e101271 10.1371/journal.pone.0101271
DOI: https://doi.org/10.5334/jors.35 | Journal eISSN: 2049-9647
Language: English
Submitted on: Apr 7, 2014
Accepted on: Oct 18, 2016
Published on: Nov 29, 2016
Published by: Ubiquity Press
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year
© 2016 Michael R. Crusoe, C. Titus Brown, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.