Scientific software development is not an oxymoron

PLoS Computational Biology

Volumn 2, Issue 9, 2006, Pages 0975-0978

  Baxter, Susan M ^a   Day, Steven W ^a   Fetrow, Jacquelyn S ^b   Reisinger, Stephanie J ^c  

^a NATIONAL CENTER FOR GENOME RESOURCES   (United States)

^b WAKE FOREST UNIVERSITY   (United States)

^c ProSanos Corporation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OXYMORONS; SCIENTIFIC SOFTWARE DEVELOPMENT;

SOFTWARE DESIGN;

ALGORITHM; BIOLOGY; COMPUTER ANALYSIS; COMPUTER PROGRAM; INFORMATION PROCESSING; INFORMATION SYSTEM; QUALITY CONTROL; SHORT SURVEY; ARTICLE; RESEARCH;

RESEARCH; SOFTWARE DESIGN;

EID: 33749320683     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0020087     Document Type: Short Survey

References (27)

1. Wilson GV (2006) Software carpentry. Available: http://www.scipy.org. Accessed 10 July 2006.
2. Wilson GV (2005) Where's the real bottleneck in scientific computing? Am Sci 94: 5.
3. Morris RW, Bean CA, Farber GK, Gallahan D, Jakobsson E, et al. (2005) Digital biology: An emerging and promising discipline. Trends Biotechnol 23: 113-117. DOI: 10.1016/j.tibtech.2005.01.005
4. Eddy S (2005) "Antedisciplinary" science. PLoS Comput Biol 1: DOI: 10.1371/journal.pcbi.0010006
5. Huerta MF, Farber GK, Wilder EL, Dushanka V, Kleinman PA, et al. (2005) NIH roadmap interdisciplinary research initiatives. PLoS Comput Biol 1: DOI: 10.1371/journal.pcbi.0010059
6. Cassman M, Arkin A, Katagiri F, Lauffenburger D, Doyle FJ, et al. (2005) Barriers to progress in systems biology. Nature 438: 1079.
7. Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, et al. (2006) Top-down standards will not serve systems biology. Nature 440: 24.
8. Hunt A, Thomas D (2000) The pragmatic programmer: From journeyman to master. Boston: Addison Wesley. 321 p.
9. Berkun S (2005) The art of project management. Sebastopol (California): O'Reilly Media. 488 p.
10. Gamma E, Helm R, Johnson R, Vlissides J (1995) Design patterns: Elements of reusable object-oriented software. Boston: Addison-Wesley.
11. Subversion. Available: http://subversion.tigris.org. Accessed 10 July 2006.
12. Thomas D, Hunt A (2003) Pragmatic version control using CVS. Boston: The Pragmatic Programmers. 176 p.
13. Concurrent Versioning System (CVS). Available: http://www.nongnu.org/cvs. Accessed 10 July 2006.
14. Jira: Bug tracking, issue tracking, and project management. Available: http://www.atlassian.com/software/jira. Accessed 10 July 2006.
15. Bugzilla. Available: http://www.bugzilla.org. Accessed 10 July 2006.
16. Yang C, Benz RD, Cheeseman MA (2006) Landscape of current toxicity databases and database standards. Curr Opin Drug Discov Devel 9: 124-133.
17. Luciano JS (2005) PAX of mind for pathway researchers. Drug Discov Today 10: 937-942.
18. Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, et al. (2006) The MGED ontology: A resource for semantics-based description of microarray experiments. Bioinformatics 22: 866-873.
19. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, et al. (2005) NCBI GEO: Mining millions of expression profiles - Database and tools. Nucleic Acids Res 33: D562-D566.
20. Parkinson P, Sarkans U, Shojatalab M, Abeygunawardena N, Contrino S, et al. (2005) ArrayExpress - A public repository for microarray gene expression data at the EBI. Nucleic Acids Res 33: D553-D555. DOI: 10.1093/nar/gki056.
21. (2002) Microarray standards at last. Nature 419: 323. DOI: 10.1038/419323a.
22. Xplanner. Available: http://www.xplanner.org. Accessed 10 July 2006.
23. BaseCamp. Available: http://www.basecamphq.com. Accessed 10 July 2006.
24. Schwaber K (2004) Agile project management with Scrum. Redmond (Washington): Microsoft Press. 150 p.
25. Phillips J, Chilukuri R, Fragoso G, Warzel D, Covitz PA (2006) The caCORE Software Development Kit: Streamlining construction of interoperable biomedical information services. BMC Med Inform Decis Mak 6: 2.
26. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol 5: R80.
27. Gentleman RC, Lang TD (2004) Statistical analyses and reproducible research. In: Bioconductor project working papers. Working Paper 2. Available: http://www.bepress.com/bioconductor/paper2. Accessed 10 July 2006. Available: http://www.bioconductor.org/docs/vignettes.html. Accessed 10 July 2006.