H
Herbert M. Sauro
Researcher at University of Washington
Publications - 185
Citations - 12018
Herbert M. Sauro is an academic researcher from University of Washington. The author has contributed to research in topics: Synthetic biology & SBML. The author has an hindex of 46, co-authored 172 publications receiving 11280 citations. Previous affiliations of Herbert M. Sauro include Lawrence Berkeley National Laboratory & University of Edinburgh.
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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Michael Hucka,Andrew Finney,Herbert M. Sauro,Hamid Bolouri,Hamid Bolouri,John Doyle,Hiroaki Kitano,Adam P. Arkin,Benjamin Bornstein,Dennis Bray,Athel Cornish-Bowden,Autumn A. Cuellar,S. Dronov,E. D. Gilles,Martin Ginkel,V. Gor,Igor Goryanin,W. J. Hedley,T. C. Hodgman,J.-H.S. Hofmeyr,Peter Hunter,Nick Juty,J. L. Kasberger,Andreas Kremling,Ursula Kummer,N Le Novère,Leslie M. Loew,D. Lucio,Pedro Mendes,E. Minch,Eric Mjolsness,Yoichi Nakayama,Melanie R. Nelson,Poul M. F. Nielsen,T. Sakurada,James C. Schaff,Bruce E. Shapiro,Thomas S. Shimizu,H. D. Spence,Jörg Stelling,Koichi Takahashi,Masaru Tomita,John Wagner,J. Wang +43 more
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.
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The Systems Biology Graphical Notation
Nicolas Le Novère,Michael Hucka,Huaiyu Mi,Stuart L. Moodie,Falk Schreiber,Falk Schreiber,Anatoly Sorokin,Emek Demir,Katja Wegner,Mirit I. Aladjem,Sarala M. Wimalaratne,Frank T Bergman,Ralph Gauges,Peter Ghazal,Hideya Kawaji,Lu Li,Yukiko Matsuoka,Alice Villéger,Sarah Elizabeth Boyd,Laurence Calzone,Mélanie Courtot,Ugur Dogrusoz,Tom C. Freeman,Akira Funahashi,Samik Ghosh,Akiya Jouraku,Sohoung Kim,Fedor A. Kolpakov,Augustin Luna,Sven Sahle,Esther Schmidt,Steven Watterson,Steven Watterson,Guanming Wu,Igor Goryanin,Douglas B. Kell,Chris Sander,Herbert M. Sauro,Jacky L. Snoep,Kurt W. Kohn,Hiroaki Kitano +40 more
TL;DR: The Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists, believes that it will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge.
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BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
Nicolas Le Novère,Benjamin Bornstein,Alexander Broicher,Mélanie Courtot,Marco Donizelli,Harish Dharuri,Lu Li,Herbert M. Sauro,Maria J. Schilstra,Bruce E. Shapiro,Jacky L. Snoep,Michael Hucka +11 more
TL;DR: TheBioModels Database (), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems.
Journal ArticleDOI
Minimum information requested in the annotation of biochemical models (MIRIAM)
Nicolas Le Novère,Andrew Finney,Michael Hucka,Upinder S. Bhalla,Fabien Campagne,Julio Collado-Vides,Edmund J. Crampin,Matt D. B. Halstead,Edda Klipp,Pedro Mendes,Poul M. F. Nielsen,Herbert M. Sauro,Bruce E. Shapiro,Jacky L. Snoep,Hugh D. Spence,Barry L. Wanner +15 more
TL;DR: These rules define procedures for encoding and annotating models represented in machine-readable form to enable users to have confidence that curated models are an accurate reflection of their associated reference descriptions and to facilitate model reuse and composition into large subcellular models.
Journal ArticleDOI
Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration
Herbert M. Sauro,Michael Hucka,Andrew Finney,Cameron Wellock,Hamid Bolouri,John Doyle,Hiroaki Kitano +6 more
TL;DR: The SBW architecture, a selection of current modules, including Jarnac, JDesigner, and SBWMeta-tool, and the close integration of SBW into BioSPICE, which enables both frameworks to share tools and compliment and strengthen each others capabilities are described.