Nick Juty

TL;DR: This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.

TL;DR: Recon 2, a community-driven, consensus 'metabolic reconstruction', is described, which is the most comprehensive representation of human metabolism that is applicable to computational modeling and has improved topological and functional features.

TL;DR: Three ontologies created specifically to address the needs of the systems biology community are described, including the Systems Biology Ontology, which provides semantic information about the model components, and the Kinetic Simulation Algorithm Ontology and the Terminology for the Description of Dynamics, which categorizes dynamical features of the simulation results and general systems behavior.

TL;DR: BioModels as discussed by the authors is a repository of mathematical models of biological processes, which is used to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding peer-reviewed publication.

TL;DR: This work describes here the new parallel identification scheme and the updated supporting software infrastructure, and introduces the new Identifiers.org service, which provides directly resolvable identifiers, in the form of Uniform Resource Locators (URLs).