M L Neal1, M Galdzicki, J T Gallimore, H M Sauro. 1. Department of Bioengineering, University of Washington, Seattle, WA 98195, USA and Department of Computer Science, Wofford College, Spartanburg, SC 29303, USA.
Abstract
SUMMARY: We describe libSBMLReactionFinder, a C library for retrieving specific biochemical reactions from the curated systems biology markup language models contained in the BioModels database. The library leverages semantic annotations in the database to associate reactions with human-readable descriptions, making the reactions retrievable through simple string searches. Our goal is to provide a useful tool for quantitative modelers who seek to accelerate modeling efforts through the reuse of previously published representations of specific chemical reactions. AVAILABILITY AND IMPLEMENTATION: The library is open-source and dual licensed under the Mozilla Public License Version 2.0 and GNU General Public License Version 2.0. Project source code, downloads and documentation are available at http://code.google.com/p/lib-sbml-reaction-finder.
SUMMARY: We describe libSBMLReactionFinder, a C library for retrieving specific biochemical reactions from the curated systems biology markup language models contained in the BioModels database. The library leverages semantic annotations in the database to associate reactions with human-readable descriptions, making the reactions retrievable through simple string searches. Our goal is to provide a useful tool for quantitative modelers who seek to accelerate modeling efforts through the reuse of previously published representations of specific chemical reactions. AVAILABILITY AND IMPLEMENTATION: The library is open-source and dual licensed under the Mozilla Public License Version 2.0 and GNU General Public License Version 2.0. Project source code, downloads and documentation are available at http://code.google.com/p/lib-sbml-reaction-finder.
Authors: M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang Journal: Bioinformatics Date: 2003-03-01 Impact factor: 6.937
Authors: Chen Li; Marco Donizelli; Nicolas Rodriguez; Harish Dharuri; Lukas Endler; Vijayalakshmi Chelliah; Lu Li; Enuo He; Arnaud Henry; Melanie I Stefan; Jacky L Snoep; Michael Hucka; Nicolas Le Novère; Camille Laibe Journal: BMC Syst Biol Date: 2010-06-29
Authors: Maxwell L Neal; Michael T Cooling; Lucian P Smith; Christopher T Thompson; Herbert M Sauro; Brian E Carlson; Daniel L Cook; John H Gennari Journal: PLoS Comput Biol Date: 2014-10-02 Impact factor: 4.475
Authors: Laurence Loewe; Katherine S Scheuer; Seth A Keel; Vaibhav Vyas; Ben Liblit; Bret Hanlon; Michael C Ferris; John Yin; Inês Dutra; Anthony Pietsch; Christine G Javid; Cecilia L Moog; Jocelyn Meyer; Jerdon Dresel; Brian McLoone; Sonya Loberger; Arezoo Movaghar; Morgaine Gilchrist-Scott; Yazeed Sabri; Dave Sescleifer; Ivan Pereda-Zorrilla; Andrew Zietlow; Rodrigo Smith; Samantha Pietenpol; Jacob Goldfinger; Sarah L Atzen; Erika Freiberg; Noah P Waters; Claire Nusbaum; Erik Nolan; Alyssa Hotz; Richard M Kliman; Ayalew Mentewab; Nathan Fregien; Martha Loewe Journal: Ann N Y Acad Sci Date: 2016-12-05 Impact factor: 5.691
Authors: N Juty; R Ali; M Glont; S Keating; N Rodriguez; M J Swat; S M Wimalaratne; H Hermjakob; N Le Novère; C Laibe; V Chelliah Journal: CPT Pharmacometrics Syst Pharmacol Date: 2015-02-26