Ten Simple Rules for Developing Usable Software in Computational Biology

PLoS Computational Biology

Volumn 13, Issue 1, 2017, Pages

  List, Markus ^a   Ebert, Peter ^a,b   Albrecht, Felipe ^a,b  

^a MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^b Graduate School for Computer Science   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS;

COMPUTATIONAL BIOLOGY; SIMPLE++;

BIOLOGY;

DATA ANALYSIS; DATA GROWTH; EDITORIAL; HUMAN COMPUTER INTERACTION; INFORMATION PROCESSING; MOLECULAR BIOLOGY; SOFTWARE; SOFTWARE USABILITY; BIOLOGY; PRACTICE GUIDELINE;

COMPUTATIONAL BIOLOGY; GUIDELINES AS TOPIC; SOFTWARE;

EID: 85011340485     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1005265     Document Type: Editorial

References (19)

1. Sandve GK, Nekrutenko A, Taylor J, Hovig E, Ten simple rules for reproducible computational research. PLoS Comp Biol. 2013;. doi: 10.1371/journal.pcbi.100328524204232
2. Osborne JM, Bernabeu MO, Bruna M, Calderhead B, Cooper J, Dalchau N, et al. Ten simple rules for effective computational research. PLoS Comput Biol. 2014;10(3):e1003506. doi: 10.1371/journal.pcbi.100350624675742
3. Prlić A, Procter JB, Ten simple rules for the open development of scientific software. PLoS Comput Biol. 2012;8(12):e1002802. doi: 10.1371/journal.pcbi.100280223236269
4. Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost FdV, et al. Ten Simple Rules for Taking Advantage of Git and GitHub. PLOS Computational Biology. 2016jul;12(7):e1004947. doi: 10.1371/journal.pcbi.100494727415786
5. Dillon A, Encyclopedia of Human Factors and Ergonomic. Ed. London: Taylor and Francis, ch. User Acceptance of Information Technology; 2001.
6. Thielsch MT, Engel R, Hirschfeld G, Expected usability is not a valid indicator of experienced usability. PeerJ Computer Science. 2015;1:e19. doi: 10.7717/peerj-cs.19
7. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome research. 2005;15(10):1451–1455. doi: 10.1101/gr.408650516169926
8. Wolstencroft K, Haines R, Fellows D, Williams A, Withers D, Owen S, et al. The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic acids research. 2013;p. gkt328. doi: 10.1093/nar/gkt32823640334
9. Goodstadt L, Ruffus: a lightweight Python library for computational pipelines. Bioinformatics. 2010;26(21):2778–2779. doi: 10.1093/bioinformatics/btq52420847218
10. Köster J, Rahmann S, Snakemake—a scalable bioinformatics workflow engine. Bioinformatics. 2012;28(19):2520–2522. doi: 10.1093/bioinformatics/bts48022908215
11. Morgenthaler JD, Gridnev M, Sauciuc R, Bhansali S. Searching for build debt: Experiences managing technical debt at Google. In: Proceedings of the Third International Workshop on Managing Technical Debt. IEEE Press; 2012. p. 1–6.
12. Sculley D, Holt G, Golovin D, Davydov E, Phillips T, Ebner D, et al. Machine Learning: The High Interest Credit Card of Technical Debt. In: SE4ML: Software Engineering for Machine Learning (NIPS 2014 Workshop); 2014.
13. Nichols D, Twidale M, The Usability of Open Source Software. First Monday. 2003;8(1). Available from: http://firstmonday.org/ojs/index.php/fm/article/view/1018.
14. Seffah A, Metzker E, The obstacles and myths of usability and software engineering. Communications of the ACM. 2004;47(12):71–76. doi: 10.1145/1035134.1035136
15. Macaulay C, Sloan D, Jiang X, Forbes P, Loynton S, Swedlow JR, et al. Usability and User-Centered Design in Scientific Software Development. IEEE Software. 2009Jan;26(1):96–102. Copyright—Copyright IEEE Computer Society Jan/Feb 2009; Document feature—; Last updated—2012-07-19; CODEN—IESOEG. Available from: http://search.proquest.com/docview/215838611?accountid=104681. doi: 10.1109/MS.2009.27
16. Sloan D, Macaulay C, Forbes P, Loynton S. User research in a scientific software development project. In: Proceedings of the 23rd British HCI Group Annual Conference on People and Computers: Celebrating People and Technology. British Computer Society; 2009. p. 423–429.
17. Baxter SM, Day SW, Fetrow JS, Reisinger SJ, Scientific software development is not an oxymoron. PLoS Comput Biol. 2006;2(9):e87. doi: 10.1371/journal.pcbi.002008716965174
18. Borchardt JC. Usability in free software;. Last access: 2016-09-30. Available from: http://jancborchardt.net/usability-in-free-software.
19. Nielsen J. Why you only need to test with 5 users;. Last access: 2016-09-30. Available from: https://www.nngroup.com/articles/why-you-only-need-to-test-with-5-users/.