Sharing research models: Using software engineering practices for facilitation

Stephanie P. Bryant · Eric Solano · Susanna Cantor · Philip C. Cooley · Diane K. Wagener

feb 2011 · RTI Press

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Increasingly, researchers are turning to computational models to understand the interplay of important variables on systems' behaviors. Although researchers may develop models that meet the needs of their investigation, application limitations—such as nonintuitive user interface features and data input specifications—may limit the sharing of these tools with other research groups. By removing these barriers, other research groups that perform related work can leverage these work products to expedite their own investigations. The use of software engineering practices can enable managed application production and shared research artifacts among multiple research groups by promoting consistent models, reducing redundant effort, encouraging rigorous peer review, and facilitating research collaborations that are supported by a common toolset. This report discusses three established software engineering practices—the iterative software development process, object-oriented methodology, and unified modeling language—and the applicability of these practices to computational model development. Our efforts to modify the MIDAS TranStat application to make it more user-friendly are presented as an example of how computational models that are based on research and developed using software engineering practices can benefit a broader audience of researchers.

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MS, is a member of the Bioinformatics Group at RTI International, specializing in software development, distributed systems, and high-performance computing.

PhD, is a member of RTI’s Bioinformatics Group, specializing in high-performance computing tools (distributed computing, grids) in simulations, modeling, and programming.

BS, a member of RTI’s Research Computing Division, specializes in system, software, and project documentation, and process and configuration management.

MS, is an RTI Fellow in bioinformatics and highperformance computing.

PhD, is a member of the Genomics, Statistical Genetics, and Environmental Research group at RTI International. Her research includes genomics and proteomics of vaccine response and informatics support for modeling the spread of infectious disease.