The Community for Technology Leaders
RSS Icon
Subscribe
Issue No.06 - November/December (2009 vol.11)
pp: 20-29
Sarah Killcoyne , Institute for Systems Biology
John Boyle , Institute for Systems Biology
ABSTRACT
<p>In the life sciences, the need to balance the costs and benefits of introducing software processes into a research environment presents a distinct set of challenges due to the cultural disconnect between life sciences research and software engineering. The Institute for Systems Biology's research informatics team has studied these challenges and developed a software process to address them.</p>
INDEX TERMS
Software development process, software design, life sciences research, agile, rapid application development
CITATION
Sarah Killcoyne, John Boyle, "Managing Chaos: Lessons Learned Developing Software in the Life Sciences", Computing in Science & Engineering, vol.11, no. 6, pp. 20-29, November/December 2009, doi:10.1109/MCSE.2009.198
REFERENCES
1. C.S.M. Scaffidi and B. Myers, "Estimating the Numbers of End Users and End User Programmers," Proc. 2005 IEEE Symp. Visual Languages and Human-Centric Computing, IEEE CS Press, 2005, pp. 207–214.
2. E.J. Hannay et al., "How Do Scientists Develop and Use Scientific Software?" Proc. 2009 ICSE Workshop on Software Eng. Computational Science and Eng., IEEE CS Press, 2009, pp. 1–8.
3. J. Segal, "When Software Engineers Met Research Scientists: A Case Study," Empirical Software Eng., vol. 10, no. 4, 2005, pp. 517–536.
4. G. Wilson, "Where's the Bottleneck in Scientific Computing?" Am. Scientist, vol. 94. no. 1, 2006, p. 5.
5. D. Kelly, "A Software Chasm: Software Engineering and Scientific Computing," IEEE Software, vol. 24, no. 6, 2007, pp. 120–119.
6. J. Segal, "Professional End User Developers and Software Development Knowledge," tech. report no. 2004/25, Computing Dept., Open Univ., UK, 2004.
7. J. Segal, "Workshop on End-User Software Engineering," Proc. 1st Workshop End-User Software Eng., ACM Press, 2005, p. 698.
8. S.L. Star and K. Ruhleder, "Steps Towards and Ecology of Infrastructure," Proc. ACM Conf. Computer-Supported Cooperative Work, ACM Press, 1994, pp. 253–264.
9. J. Boyle et al., "Adaptable Data Management for Systems Biology Investigations," BMC Bioinformatics, vol. 10, 2009; www.biomedcentral.com/1471-2105/1079.
10. J. Boyle, "Gene-Expression Omnibus Integration and Clustering Tools in SeqExpress," Bioinformatics, vol. 21, no. 10, 2005, pp. 2550–2551.
11. G. Pavlopoulos, A. Wegener, and R. Schneider, "A Survey of Visualization Tools for Biological Network Analysis," BioData Mining, vol. 1, no. 12, 2008; www.biodatamining.org/content/1/112.
12. D.S. Johnson et al., "Genome-Wide Mapping of In-Vivo Protein-DNA Interactions," Science, vol. 316, no. 5830, 2007, pp. 1497–1502.
13. B. Schwanhäusser et al., "Global Analysis of Cellular Protein Translation by Pulsed Silac," Proteomics, vol. 9, no. 1, 2009, pp. 205–209.
14. The Encode Project Consortium, "The Encode (ENCyclopedia Of DNA Elements) Project," Science, vol. 306, no. 5696, 2004, pp. 636–640.
15. K. Beck et. al., Manifesto for Agile Software Development, 2001, www.agilemanifesto.org.
16. J. Boyle et al., "Systems Biology Driven Software Design for the Research Enterprise," BMC Bioinformatics vol. 9, 2008; www.biomedcentral.com/1471-2105/9295.
17. S.L. Star and J.R. Griesemser, "Institutional Ecology, 'Translations' and Boundary Objects: Amateurs and Professionals in Berkeley's Museum of Vertebrate Zoology, 1907–39," Social Studies Science, vol. 19, no. 3, 1989, pp. 387–420.
29 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool