Support for COMBINE 2015

University Of Utah, Salt Lake City UT

Investigators

Abstract

Standards for data exchange are critical to the development of any field. They enable researchers and practitioners to exchange information reliably, apply a variety of tools to their problems, and reproduce scientific results. The COmputational MOdeling in Biology NEtwork (COMBINE) was created in 2010 to organize standardization efforts for systems biology. This effort includes, among others, the systems biology markup language (SBML) for mathematical modeling, the biological pathways exchange language (BioPaX) for describing pathways, the systems biology graphical notation (SBGN) for visual representations, and the synthetic biology open language (SBOL). While synthetic biology has many unique requirements, there are also a lot of overlapping features such as the need to construct mathematical models, describe pathways, and provide visual representations. It makes a lot of sense for these efforts to collaborate, such that, the synthetic biology community can leverage existing standards enabling the sharing of tools and other infrastructure. The COMBINE organization holds two workshops per year to discuss standards for biology. The purpose of this grant is to support travel expenses for students, postdoctoral scholars, and participants from underrepresented groups to attend COMBINE 2015 to be held at the University of Utah in Salt Lake City, UT from October 12th to 16th, 2015. Workshops like this one are instrumental in making progress in the development of these standards. Currently, most standardization efforts are either unfunded or only have very limited support. Indeed, the success of these standards has been due to the donation of time from many individuals to participate in discussions, write specifications, serve as standard editors, and attend workshops. Many of these individuals working on the development of standards are students based in the US who would otherwise find it difficult to find the funds to attend this meeting. Therefore, this grant would help support travel, lodging, and registration expenses for these US-based students, postdoctoral scholars, and participants from underrepresented groups working on systems and synthetic biology standards. Not only would this be a valuable experience for these participants, but it would also greatly enhance our goal of bringing together researchers in synthetic biology with those working in systems biology leading to integrated standards and shared software and infrastructure. Intellectual Merit: The major goals of this workshop are: (1) Develop synergistic relationships between systems and synthetic biology researchers. (2) A tighter integration of standard development for systems and synthetic biology. (3) Outreach to modelers and experimentalists. (4) A coordinated effort to advocate the use of standards in publications and archival databases. Broader Impacts: The development of standards has the potential for tremendous broader impact. Standards enable researchers to share models and software tools. They improve science in that results encoded in standards are more readily reproducible. Furthermore, both systems and synthetic biology have numerous potential applications in health, such as a better understanding of diseases and the development of new drugs. This workshop will also be a valuable educational experience for the student participants.