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; and the systems biology graphical notation (SBGN) for visual representations. In a separate effort, the synthetic biology community is developing 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 is important to join these efforts, such that, the synthetic biology community can leverage existing standards enabling the sharing of tools and other infrastructure.
This project will help enable these two communities to meet together at COMBINE's HARMONY 2015 meeting to be held in Wittenberg, Germany on April 20th to 24th (http://co.mbine.org/events/HARMONY_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 SBOL are students based in the US who would otherwise find it difficult to find the funds to attend this meeting. Therefore, this project would help support travel expenses for these US-based students working on the SBOL standard to travel to Germany for HARMONY 2015. Not only would this be a valuable experience for these students, 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. The goals of this workshop will be to (1) develop synergistic relationships between systems and synthetic biology researchers; (2) provide a tighter integration of standard development for systems and synthetic biology; (3) perform outreach to modelers and experimentalists; and (4) discuss a coordinated effort to advocate the use of standards in publications and archival databases to enhance reproducibility of scientific results.
