Software Engineering Education for Bioinformatics

Engineering bioinformatics: building reliability, performance and productivity into bioinformatics software

“…1 Umarji et al focus exclusively on the gaps in the education of bioinformatic software developers in software engineering principles. 12 It is important to correctly identify all of the significant causes of the problem. If we start with a false or incomplete diagnosis the treatment is unlikely to be effective.…”

“…Umarji et al have surveyed bioinformatics curricula in the United States and found that "out of a total of 79 program offerings, there were only 2 instances where a software engineering related course was a required part of the curriculum" and that "there was no mention of the role and importance of software engineering in the curricula." 12 …”

“…12 We believe that in addition, educators should target software engineering curricula and create specialized Masters and PhD programs in Bioinformatic Engineering, creating specialized software engineers who can dialog with biologists and bioinformaticians as customers based on a shared understanding of the research environment and the biology domain. Early introduction of software engineering graduates into bioinformatic research programmes would have a positive influence on the software developed as part of such research.…”

Bridging the Chasm

“…As already noted, many developers engaged in sci-entific programming are largely self-taught, or taught by a scientific domain expert. Umarji et al [2009], after conducting a survey of bioinformatics researchers, found that the dissemination of software engineering practices was variable. Their review of educational material for bioinformatics courses also found few references to software engineering, or the risks associated with low quality software.…”

“…Despite this progress in other domains, the adoption of available software engineering practices and tools in scientific programming, the practice of developing software to support scientific work, remains patchy [Umarji et al 2009]. Kelly [2007] referred to the disconnection between much of software engineering practice and scientific programming as a 'chasm'.…”