Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab
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 a...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Ubiquity Press
2016-11-01
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| Series: | Journal of Open Research Software |
| Subjects: | |
| Online Access: | http://openresearchsoftware.metajnl.com/articles/35 |
| _version_ | 1818972114943737856 |
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| author | Michael R. Crusoe C. Titus Brown |
| author_facet | Michael R. Crusoe C. Titus Brown |
| author_sort | Michael R. Crusoe |
| collection | DOAJ |
| description | 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 <a href="http://github.com/dib-lab/khmer/">http://github.com/dib-lab/khmer/</a>. |
| first_indexed | 2024-12-20T15:03:08Z |
| format | Article |
| id | doaj.art-108f6df0acdf4ab0b7ad2473548d3018 |
| institution | Directory Open Access Journal |
| issn | 2049-9647 |
| language | English |
| last_indexed | 2024-12-20T15:03:08Z |
| publishDate | 2016-11-01 |
| publisher | Ubiquity Press |
| record_format | Article |
| series | Journal of Open Research Software |
| spelling | doaj.art-108f6df0acdf4ab0b7ad2473548d30182022-12-21T19:36:36ZengUbiquity PressJournal of Open Research Software2049-96472016-11-0141e44e4410.5334/jors.35105Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology LabMichael R. Crusoe0C. Titus Brown1Michigan State UniversityMichigan State UniversityThe 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 <a href="http://github.com/dib-lab/khmer/">http://github.com/dib-lab/khmer/</a>.http://openresearchsoftware.metajnl.com/articles/35WSSSPEk-mer |
| spellingShingle | Michael R. Crusoe C. Titus Brown Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab Journal of Open Research Software WSSSPE k-mer |
| title | Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab |
| title_full | Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab |
| title_fullStr | Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab |
| title_full_unstemmed | Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab |
| title_short | Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab |
| title_sort | walking the talk adopting and adapting sustainable scientific software development processes in a small biology lab |
| topic | WSSSPE k-mer |
| url | http://openresearchsoftware.metajnl.com/articles/35 |
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