The third 'Sydney Computational Biologists' meetup will present a talk from Mike Hucka, who is visiting from Caltech, USA. The talk will take place in the John Shine room, level 6 of the Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst - next to the Garvan Institute for Medical Research. Afterwards, drinks at the nearby Darlo Bar.
SBML and other COMBINE efforts: Standardizing exchange formats for computational models in systems biology
Mike Hucka (Caltech, USA)
A vast number of 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 for systems biology 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. They do not want to hardcode their models as software programs, nor assume everyone uses the same computing environment; they need common exchange formats for representing their models in such a way that a variety of software systems can read and write them.
There exist a number of standardization efforts today with the goal of developing and evolving exchange formats for computational systems biology; they differ along dimensions such as domain of specialization and medium of communication. Many of these efforts are engaged in COMBINE (the COmputational Modeling in BIology NEtwork;http://co.mbine.org), an organization whose main goal is to help coordinate community standardization activities. In this presentation, I will summarize the goals of the core standards represented in COMBINE, provide details about recent developments in SBML (Systems Biology Markup Language; http://sbml.org), and discuss other related efforts in COMBINE. Collectively, these various activities support greater integration and easier interchange in computational systems biology, thereby improving reproducibility of scientific results and scientific progress in general.
Dr. Michael Hucka is a Member of the Professional Staff in Computing and Mathematical Sciences at the California Institute of Technology, in Pasadena, California, USA. His work focuses on developing software standards and infrastructure for scientific domains such as systems biology.
Dr. Hucka is one of the principal developers of the Systems Biology Markup Language (SBML), the most widely-used exchange format for computational models in systems biology. By supporting SBML as input and output formats, different software tools can operate on an identical representation of a model, removing chances for errors in translation and assuring a common starting point for analyses and simulations. SBML thus enables researchers in systems biology to share and build on each other's work more effectively and directly. SBML has become the de facto international standard for this purpose and is widely supported today by software tools, databases, consortia, commercial enterprises, and journal publishers. Dr. Hucka continues to lead and participate in development of SBML and core resources such as software libraries (libSBML), test suites, and other systems.
In addition to his work on SBML, Dr. Hucka has been involved in organizing and cofounding multiple other standardization efforts for systems biology, notably the Systems Biology Graphical Notation (SBGN), the Systems Biology Ontology (SBO), the Minimum Information Requested in the Annotation of biochemical Models (MIRIAM) guidelines, theBioModels.net consortium, and, in its early days, BioModels Database. Dr. Hucka has also been involved in a number of community efforts. Most recently, these have been COMBINE (the Computational Modeling in Biology Network, http://co.mbine.org) and HARMONY (the Hackathon on Resources for Modeling in Biology). Dr. Hucka was also twice a primary organizer of the International Conference on Systems Biology, in 2001 (Pasadena, CA, USA) and 2007 (Long Beach, CA, USA).