Elucidating the role and use of bioinformatics software in life science research

Reviewer: Andrew Brooks

Genome-based research involves large teams of specialists and the use of complex software tools to perform analysis. To better understand the problems associated with using bioinformatics software, ten life science researchers were interviewed. Questions were asked about the goals of their research, the workflows they used, and the tools they used. Participants were also asked to walk through specific examples of how they conducted recent research. Interview materials and photographs of work artifacts were analyzed using the affinity diagram approach. The life science researchers were found to treat their tools almost as black boxes. Without adequate knowledge of the underlying algorithms being used, they resorted to a variety of strategies to select the values of input parameters. For example, one strategy was to begin with default settings and then use a trial-and-error approach. Several of them were found to use both digital and physical notes to keep records of the command-line sequences required when working with Linux-based tools. Other researchers chose to purchase commercial genomics workbenches to reduce the need for command-line skills. A priority for any project was access to bioinformatics experts. If this could not be obtained, some of the life science researchers indicated that this restricted their inquiries to those that they themselves were comfortable answering using their existing tools. A major limitation of this study, as recognized by the authors, was the small sample size. Nevertheless, several important issues have been exposed. This paper is recommended to genomics researchers and developers of bioinformatics software. Online Computing Reviews Service