Abstract
The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report summarizes the topics and activities of the fourth edition of the annual COMBINE meeting, held in Paris during September 16-20 2013, and attended by a total of 96 people. This edition pioneered a first day devoted to modeling approaches in biology, which attracted a broad audience of scientists thanks to a panel of renowned speakers. During subsequent days, discussions were held on many subjects including the introduction of new features in the various COMBINE standards, new software tools that use the standards, and outreach efforts. Significant emphasis went into work on extensions of the SBML format, and also into community-building. This year’s edition once again demonstrated that the COMBINE community is thriving, and still manages to help coordinate activities between different standards in computational systems biology.
Highlights
The Computational Modeling in Biology Network (COMBINE) [1] coordinates the development of open standards and file formats in computational systems biology and related fields
Systems Biology Markup Language (SBML), CellML, NeuroML and PharmML David Nickerson (Auckland Bioengineering Institute, New Zealand) started day two of the meeting with an introduction to the current state of the CellML project. He gave some recent examples of how CellML is being used in large-scale physiological models
One session dealt with the use of distributions of numerical values in models, with Maciej Swat and Pedro Mendes (University of Manchester, United Kingdom) presenting information about how their software tools used such distributions
Summary
The Computational Modeling in Biology Network (COMBINE) [1] coordinates the development of open standards and file formats in computational systems biology and related fields. The COMBINE standards incorporate a number of related resources, including ontologies such as the Systems Biology Ontology (SBO) [15], and Minimum Information Guidelines such as MIRIAM [16], which are again actively being evolved by the community Many of these standards were originally developed independently, with poor coordination and little or no integration between the different efforts. The COMBINE Forum was launched three years ago and has since has been accepted as the crossstandard community meeting It first took place in 2010, organized by the center for integrative systems biology at the University of Edinburgh, United Kingdom, as a joint event with the 10th SBML Anniversary and a satellite of the 11th ICSB [19]. The last part of his presentation was show cased how logical modeling can be applied to study the differentiation of T-helper cells [27]
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