Abstract
The Computational Modeling in Biology Network (COMBINE), is an initiative to coordinate the development of the various community standards and formats in computational systems biology and related fields. This report summarizes the activities pursued at the first annual COMBINE meeting held in Edinburgh on October 6-9 2010 and the first HARMONY hackathon, held in New York on April 18-22 2011. The first of those meetings hosted 81 attendees. Discussions covered both official COMBINE standards-(BioPAX, SBGN and SBML), as well as emerging efforts and interoperability between different formats. The second meeting, oriented towards software developers, welcomed 59 participants and witnessed many technical discussions, development of improved standards support in community software systems and conversion between the standards. Both meetings were resounding successes and showed that the field is now mature enough to develop representation formats and related standards in a coordinated manner.
Highlights
At the beginning of the 21st century, the life sciences have witnessed a tremendous change in the way research is performed, characterized by the acquisition and analysis of large amounts of quantitative data, as well as the integration of these data within computational models used to understand and investigate living systems
The Systems Biology Graphical Notation (SBGN) [3] is a set of visual languages enabling the graphical representation of biological processes
Day 1, tutorials and poster session The meeting opened with an introduction to the day from Michael Hucka, followed by overview presentations about Systems Biology Markup Language (SBML), BioPAX and SBGN given by principal developers involved in the development of each standard
Summary
At the beginning of the 21st century, the life sciences have witnessed a tremendous change in the way research is performed, characterized by the acquisition and analysis of large amounts of quantitative data, as well as the integration of these data within computational models used to understand and investigate living systems. Day 1, tutorials and poster session The meeting opened with an introduction to the day from Michael Hucka, followed by overview presentations about SBML, BioPAX and SBGN given by principal developers involved in the development of each standard. Frank was followed by Richard Adams, who presented several SED-ML developments: JlibSEDML, a Java-based complement to libSEDML; a new SED-ML Editor; and a SED-ML web service which includes a validator These presentations were followed by David Nickerson, who described the work of the CellML group with SED-ML, and the status of CellML software simulators and model repositories. Robin Haw opened the session with a presentation about community outreach activities He was followed by overview presentations by the principal organizers of the SBGN, SBML and BioPAX efforts, covering the current governance structures of those organizations. The rest of the day consisted of various meetings of scientific advisory boards, editorial committees, additional hacking sessions and ad hoc get-togethers organized by HARMONY attendees
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