Browsing by Author "Hucka, Michael"
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- Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)Publication . Waltemath, Dagmar; Bergmann, Frank T.; Chaouiya, Claudine; Czauderna, Tobias; Gleeson, Padraig; Goble, Carole; Golebiewski, Martin; Hucka, Michael; Juty, Nick; Krebs, Olga; Le Novère, Nicolas; Mi, Huaiyu; Moraru, Ion I.; Myers, Chris J.; Nickerson, David; Olivier, Brett G.; Rodriguez, Nicolas; Schreiber, Falk; Smith, Lucian; Zhang, Fengkai; Bonnet, EricThe 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.
- Path2Models: large-scale generation of computational models from biochemical pathway mapsPublication . Büchel, Finja; Rodriguez, Nicolas; Swainston, Neil; Wrzodek, Clemens; Czauderna, Tobias; Keller, Roland; Mittag, Florian; Schubert, Michael; Glont, Mihai; Golebiewski, Martin; van Iersel, Martijn; Keating, Sarah; Rall, Matthias; Wybrow, Michael; Hermjakob, Henning; Hucka, Michael; Kell, Douglas B; Müller, Wolfgang; Mendes, Pedro; Zell, Andreas; Chaouiya, Claudine; Saez-Rodriguez, Julio; Schreiber, Falk; Laibe, Camille; Dräger, Andreas; Le Novère, NicolasSystems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data.
- SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and toolsPublication . Chaouiya, Claudine; Bérenguier, Duncan; Keating, Sarah M; Naldi, Aurélien; van Iersel, Martijn P; Rodriguez, Nicolas; Dräger, Andreas; Büchel, Finja; Cokelaer, Thomas; Kowal, Bryan; Wicks, Benjamin; Gonçalves, Emanuel; Dorier, Julien; Page, Michel; Monteiro, Pedro T; von Kamp, Axel; Xenarios, Ioannis; de Jong, Hidde; Hucka, Michael; Klamt, Steffen; Thieffry, Denis; Le Novère, Nicolas; Saez-Rodriguez, Julio; Helikar, TomášQualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing.
- The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2Publication . Hucka, Michael; Bergmann, Frank T.; Chaouiya, Claudine; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M.; König, Matthias; Novère, Nicolas Le; Myers, Chris J.; Olivier, Brett G.; Sahle, Sven; Schaff, James C.; Sheriff, Rahuman; Smith, Lucian P.; Waltemath, Dagmar; Wilkinson, Darren J.; Zhang, FengkaiComputational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. Release 2 corrects some errors and clarifies some ambiguities discovered in Release 1. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project website at http://sbml.org/.