N
Nick Juty
Researcher at European Bioinformatics Institute
Publications - 55
Citations - 6223
Nick Juty is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Interoperability & Computer science. The author has an hindex of 19, co-authored 48 publications receiving 5531 citations. Previous affiliations of Nick Juty include Swiss Institute of Bioinformatics & GlaxoSmithKline.
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Journal ArticleDOI
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.
Journal ArticleDOI
A community-driven global reconstruction of human metabolism
Ines Thiele,Neil Swainston,Ronan M. T. Fleming,Andreas Hoppe,Swagatika Sahoo,Maike K. Aurich,Hulda S. Haraldsdóttir,Monica L. Mo,Ottar Rolfsson,Miranda D. Stobbe,Miranda D. Stobbe,Stefan Gretar Thorleifsson,Rasmus Agren,Christian Bölling,Sergio Bordel,Arvind K. Chavali,Paul D. Dobson,Warwick B. Dunn,Warwick B. Dunn,Lukas Endler,David Hala,Michael Hucka,Duncan Hull,Daniel Jameson,Neema Jamshidi,Jon J. Jonsson,Nick Juty,Sarah M. Keating,Intawat Nookaew,Nicolas Le Novère,Nicolas Le Novère,Naglis Malys,Naglis Malys,Alexander Mazein,Jason A. Papin,Nathan D. Price,Evgeni Selkov,Martin I. Sigurdsson,Evangelos Simeonidis,Evangelos Simeonidis,Nikolaus Sonnenschein,Kieran Smallbone,Anatoly Sorokin,Anatoly Sorokin,Johannes H. G. M. van Beek,Dieter Weichart,Igor Goryanin,Jens Nielsen,Hans V. Westerhoff,Douglas B. Kell,Pedro Mendes,Pedro Mendes,Bernhard O. Palsson,Bernhard O. Palsson +53 more
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.
Journal ArticleDOI
Controlled vocabularies and semantics in systems biology
Mélanie Courtot,Nick Juty,Christian Knüpfer,Dagmar Waltemath,Anna Zhukova,Andreas Dräger,Michel Dumontier,Andrew Finney,Martin Golebiewski,Janna Hastings,Stefan Hoops,Sarah M. Keating,Douglas B. Kell,Samuel Kerrien,James R. Lawson,Allyson L. Lister,James Lu,Rainer Machné,Pedro Mendes,Matthew Pocock,Nicolas Rodriguez,Alice Villéger,Darren J. Wilkinson,Sarala M. Wimalaratne,Camille Laibe,Michael Hucka,Nicolas Le Novère +26 more
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.
Journal ArticleDOI
BioModels: ten-year anniversary
Vijayalakshmi Chelliah,Nick Juty,Ishan Ajmera,Raza Ali,Marine Dumousseau,Mihai Glont,Michael Hucka,Gaël Jalowicki,Sarah M. Keating,Vincent Knight-Schrijver,Audald Lloret-Villas,Kedar Nath Natarajan,Jean-Baptiste Pettit,Nicolas Rodriguez,Michael Schubert,Sarala M. Wimalaratne,Yangyang Zhao,Henning Hermjakob,Nicolas Le Novère,Camille Laibe +19 more
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.
Journal ArticleDOI
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
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).