October 5-9, 2014

Abstract

P8.5 Organizing community-based data standards: lessons from developing a successful open standard in systems biology

Michael Hucka (California Institute of Technology)

In computational systems biology, researchers develop simulations of biological phenomena to help understand biological function and help guide future experiments. A vast number of computational modeling and simulation software tools are available today for research in computational systems biology. This wealth of resources is a boon to researchers, but it also presents interoperability problems. Different software tools are implemented in different programming languages, run on different operating systems, express models using different mathematical frameworks, provide different analysis methods, present different user interfaces, and support different data formats. Despite working with different tools, researchers want to disseminate their work widely, as well as reuse and extend the models of other researchers. This situation led in the year 2000 to an effort to create a tool-independent, machine-readable format for representing models in systems biology: SBML, the Systems Biology Markup Language (http://sbml.org). Since that time, SBML has become the de facto standard for its purpose, a lingua franca supported by over 260 software tools worldwide. Its success and general approach has inspired and influenced other community-based standardization efforts.

Open standards are essential for the progress of science in all fields, but it is often difficult for academic researchers to organize and develop successful community-oriented standards. In this poster, I draw on personal experiences with the development of SBML, and discuss some of the lessons learned that may benefit other groups who seek to develop open standards in a community-oriented fashion. Topics include approaches for initiating standardization efforts, strategies for gaining acceptance, warnings about hurdles to expect, and more. The lessons come from both successes (based on what seems to have worked) and failures (based on hindsight).

Mode of presentation: poster

Applicable ADASS XXIV theme category: Other