TY - JOUR
T1 - Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)
AU - le Novère, Nicolas
AU - Hucka, Michael
AU - Anwar, Nadia
AU - Bader, Gary D.
AU - Demir, Emek
AU - Moodie, Stuart
AU - Sorokin, Anatoly
N1 - Funding Information:
The authors acknowledge the contributions of all of the workshop participants. COMBINE 2010 was supported by the British Biotechnology and Biological Sciences Research Council, the NIH National Institute of General Medical Sciences (NIGMS) and the EU ENFIN project.
Funding Information:
The symposium was opened by Hiroaki Kitano, from the Systems Biology Institute of Tokyo (Japan), who, a decade earlier and with funding from the Japan Science and Technology Corporation (JST), initiated the project from which SBML eventually emerged. At this anniversary event, Kitano presented his thoughts on the conditions that made possible the emergence of SBML as a successful worldwide standard. He then described his Garuda project to expand the community software development approach to the entire spectrum of computational modeling activities. After Kitano’s presentation, Pedro Mendes, from the University of Manchester, gave an overview of the earliest attempts to develop quantitative models in biochemistry, encode them, and simulate them using computers. Mendes was one of the earliest contributors to SBML. and Prior to SBML, he contributed to the design of a portable file format for metabolic network models (known as PMB). Hamid Bolouri, from the Fred Hutchinson Cancer Research Center (USA), was the head of the initial SBML Team at the California Institute of Technology beginning in 1999. His presentation focused on CRdata, a software platform for computational systems biology using R and the Amazon cloud [88]. Herbert Sauro, from the University of Washington, was one of the first members of the SBML team along with Michael
PY - 2011
Y1 - 2011
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=83255181846&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=83255181846&partnerID=8YFLogxK
U2 - 10.4056/sigs.2034671
DO - 10.4056/sigs.2034671
M3 - Article
C2 - 22180826
AN - SCOPUS:83255181846
VL - 5
SP - 230
EP - 242
JO - Environmental Microbiomes
JF - Environmental Microbiomes
SN - 1944-3277
IS - 2
ER -