Organizing Community-Based Data Standards: Lessons from Developing a Successful Open Standard in Systems Biology
In common with many fields, including astronomy, a vast number of software tools for computational modeling and simulation are available today in systems biology. This wealth of resources is a boon to researchers, but it also presents interoperability problems. Despite working with different software 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 file format for representing models: SBML, the Systems Biology Markup Language. SBML has since become the de facto standard for its purpose. Its success and general approach has inspired and influenced other community-oriented standardization efforts in systems biology. Open standards are essential for the progress of science in all fields, but it is often difficult for academic researchers to organize successful community-based standards. I draw on personal experiences from the development of SBML and summarize some of the lessons learned, in the hope that this may be useful to other groups seeking to develop open standards in a community-oriented fashion.
Additional Information© 2015 Astronomical Society of the Pacific. The original SBML development team consisted of Hamid Bolouri, Andrew M. Finney, Herbert M. Sauro and the author; John C. Doyle (Caltech) and Hiroaki Kitano (Systems Biology Institute, Japan) were the principal investigators. Development of SBML has been continued by many people over the years, notably the SBML Editors (past and present): Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, James C. Schaff, Sven Sahle, Lucian Smith, Dagmar Waltemath, and Darren J. Wilkinson. Main SBML development is currently funded by NIH grant R01GM070923.
Published - 495-0575.pdf