Software engineering education for bioinformatics

Proceedings - 22nd Conference on Software Engineering Education and Training, CSEET 2009

Volumn , Issue , 2009, Pages 216-223

  Umarji, Medha ^a   Seaman, Carolyn ^a   Koru, A Gunes ^a   Liu, Hongfang ^b  

^a GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

^b Baltimore County   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; CURRICULA; ENGINEERING EDUCATION; SURVEYS;

BIOINFORMATICS PROGRAMS; BIOINFORMATICS SOFTWARE; DEPENDABLE SOFTWARES; ENGINEERING EDUCATORS; ENGINEERING STANDPOINT; EXPLORATORY SURVEYS; EXTREME PROGRAMMING; SOFTWARE ENGINEERING PRACTICES;

SOFTWARE ENGINEERING;

EID: 67649996076     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/cseet.2009.44     Document Type: Conference Paper

References (25)

1. D. Counsell, "A review of bioinformatics education in the UK," Briefings in Bioinformatics, vol. 4, pp. 7-21, 2003.
2. J. Segal and C. Morris, "Developing Scientific Software," IEEE Softw., vol. 25, pp. 18-20, 2008.
3. R. Sanders and D. Kelly, "Dealing with Risk in Scientific Software Development," Software, IEEE, vol. 25, pp. 21-28, 2008.
4. C. Letondal and W. Mackay, "Participatory programming and the scope of mutual responsibility: balancing scientific, design and software commitment," in Proceedings of the eighth conference on Participatory design: Artful integration: interweaving media, materials and practices - Volume 1. Toronto, Ontario, Canada: ACM, 2004.
5. International Society for Computational Biology, "ISCB listing of degree/certificate programs worldwide," International Society for Computational Biology, La Jolla (California) October 5, 2005.
6. D. T. Burhans and G. R. Skuse, "The role of computer science in undergraduate bioinformatics education," SIGCSE Bull, vol. 36, pp. 417-421, 2004.
7. T. Doom, M. Raymer, D. Krane, and O. Garcia, "A proposed undergraduate bioinformatics curriculum for computer scientists," in Proceedings of the 2002 ACM Special Interest Group on Computer Science Education (SIGCSE 2002). Covington, Kentucky, 2002.
8. B. Hemminger, T. Losi, and A. Bauers, "Survey of bioinformatics programs in the United States," Journal of the American Society for Information Science and Technology, vol. 30, pp. 12-13, 2005.
9. R. B. Altman, "A curriculum for bioinformatics: The time is ripe.," Bioinformatics, vol. 14 pp. 549-550, 1998.
10. S. Ranganathan and e52., "Bioinformatics education-Perspectives and challenges," PLoS ComputBiol, vol. 1, 2005.
11. K. Beck, Extreme programming explained: embrace change. Boston, MA, USA: Addison-Wesley Longman Publishing Co., Inc, 1999.
12. R. Kendall, J. C. Carver, D. Fisher, D. Henderson, A. Mark, D. Post, C. E. Rhoades, and S. Squires, "Development of a Weather Forecasting Code: A Case Study," Software, IEEE, vol. 25, pp. 59-65, 2008.
13. M. Pocock, "BioJava Toolkit Progress," in Bioinformatics Open Source Conference, 2002.
14. K. S. Ackroyd, S. H. Kinder, G. R. Mant, M. C. Miller, C. A. Ramsdale, and P. C. Stephenson, "Scientific Software Development at a Research Facility," Software, IEEE, vol. 25, pp. 44-51,2008.
15. R. C. Gentleman, V. J. Carey, D. M. Bates, B. Bolstad, M. Dettling, S. Dudoit, B. Ellis, L. Gautier, Y. Ge, J. Gentry, K. Hornik, T. Hothorn, W. Huber, S. Iacus, R. Irizarry, F. Leisch, C. Li, M. Maechler, A. J. Rossini, G. Sawitzki, C. Smith, G. Smyth, L. Tierney, J. Y. H. Yang, and J. Zha, "Bioconductor: open software development for computational biology and bioinformatics," Genome Biology, vol. vol. 5, 2004.
16. S. M. Baxter, S. W. Day, J. S. Fetrow, and S. J. Reisinger, "Scientific Software Development is Not an Oxymoron," PloS Computational Biology, vol. 2, 2006.
17. P. v. Heusden, "Applying software validation techniques to Bioperl," in Bioinformatics Open Source Conference, 2004.
18. A. G. Koru, K. El-Emam, A. Neisa, and M. Umarji, "A survey of quality assurance practices in biomedical open source projects," Journal of Medical Internet Research, vol. 9, pp. e8, May, 2007.
19. S. M. Baxter, S. W. Day, J. S. Fetrow, and S. J. Reisinger, "Scientific Software Development is Not an Oxymoron," PloS Computational Biology, vol. 2, September, 2006.
20. A. G. Koru and J. Tian, "Comparing High-Change Modules and Modules with the Highest Measurement Values in Two Large-Scale Open-Source Products," IEEE Transactions on Software Engineering, vol. 31, pp. 625-642, 2005.
21. J. Segal, "When Software Engineers Met Research Scientists: A Case Study," Empirical Softw. Engg., vol. 10, pp. 517-536, 2005.
22. M. Vigder, N. G. Vinson, J. Singer, D. Stewart, and K. Mews, "Supporting Scientists' Everyday Work: Automating Scientific Workflows," Software, IEEE, vol. 25, pp. 52- 58,2008.
23. J. Barker and J. Thornton, "Software Engineering Challenges in Bioinformatics," in International Conference on Software Engineering (Keynote address). Edinburgh, Scotland, UK, 2004.
24. L. Stein, "Bioinformatics: Gone in 2012.," in O'Reilly Bioinformatics Technology Conference (Keynote Address). San Diego CA, 2003.
25. D. Kane, "Introducing Agile Development into Bioinformatics: An Experience Report," Conference on Agile Development, Washington DC, USA 2003.