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Literature DB >> 32598316

Specifications of standards in systems and synthetic biology: status and developments in 2020.

Falk Schreiber^1,2, Björn Sommer³, Tobias Czauderna², Martin Golebiewski⁴, Thomas E Gorochowski⁵, Michael Hucka⁶, Sarah M Keating⁷, Matthias König⁸, Chris Myers⁹, David Nickerson¹⁰, Dagmar Waltemath¹¹.

Abstract

This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology.

Entities: Chemical

Keywords: ontologies; standards; synthetic biology; systems biology

Mesh：

Year: 2020 PMID： 32598316 PMCID： PMC7756620 DOI： 10.1515/jib-2020-0022

Source DB: PubMed Journal: J Integr Bioinform ISSN： 1613-4516

33 in total

1. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

Authors: Anatoly Sorokin; Nicolas Le Novère; Augustin Luna; Tobias Czauderna; Emek Demir; Robin Haw; Huaiyu Mi; Stuart Moodie; Falk Schreiber; Alice Villéger
Journal: J Integr Bioinform Date: 2015-09-04

2. COMBINE Archive Specification Version 1.

Authors: Frank T Bergmann; Nicolas Rodriguez; Nicolas Le Novère
Journal: J Integr Bioinform Date: 2015-09-04

3. NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail.

Authors: Padraig Gleeson; Sharon Crook; Robert C Cannon; Michael L Hines; Guy O Billings; Matteo Farinella; Thomas M Morse; Andrew P Davison; Subhasis Ray; Upinder S Bhalla; Simon R Barnes; Yoana D Dimitrova; R Angus Silver
Journal: PLoS Comput Biol Date: 2010-06-17 Impact factor: 4.475

4. The BioPAX community standard for pathway data sharing.

Authors: Emek Demir; Michael P Cary; Suzanne Paley; Ken Fukuda; Christian Lemer; Imre Vastrik; Guanming Wu; Peter D'Eustachio; Carl Schaefer; Joanne Luciano; Frank Schacherer; Irma Martinez-Flores; Zhenjun Hu; Veronica Jimenez-Jacinto; Geeta Joshi-Tope; Kumaran Kandasamy; Alejandra C Lopez-Fuentes; Huaiyu Mi; Elgar Pichler; Igor Rodchenkov; Andrea Splendiani; Sasha Tkachev; Jeremy Zucker; Gopal Gopinath; Harsha Rajasimha; Ranjani Ramakrishnan; Imran Shah; Mustafa Syed; Nadia Anwar; Ozgün Babur; Michael Blinov; Erik Brauner; Dan Corwin; Sylva Donaldson; Frank Gibbons; Robert Goldberg; Peter Hornbeck; Augustin Luna; Peter Murray-Rust; Eric Neumann; Oliver Ruebenacker; Oliver Reubenacker; Matthias Samwald; Martijn van Iersel; Sarala Wimalaratne; Keith Allen; Burk Braun; Michelle Whirl-Carrillo; Kei-Hoi Cheung; Kam Dahlquist; Andrew Finney; Marc Gillespie; Elizabeth Glass; Li Gong; Robin Haw; Michael Honig; Olivier Hubaut; David Kane; Shiva Krupa; Martina Kutmon; Julie Leonard; Debbie Marks; David Merberg; Victoria Petri; Alex Pico; Dean Ravenscroft; Liya Ren; Nigam Shah; Margot Sunshine; Rebecca Tang; Ryan Whaley; Stan Letovksy; Kenneth H Buetow; Andrey Rzhetsky; Vincent Schachter; Bruno S Sobral; Ugur Dogrusoz; Shannon McWeeney; Mirit Aladjem; Ewan Birney; Julio Collado-Vides; Susumu Goto; Michael Hucka; Nicolas Le Novère; Natalia Maltsev; Akhilesh Pandey; Paul Thomas; Edgar Wingender; Peter D Karp; Chris Sander; Gary D Bader
Journal: Nat Biotechnol Date: 2010-09-09 Impact factor: 54.908

5. Controlled vocabularies and semantics in systems biology.

Authors: Mélanie Courtot; Nick Juty; Christian Knüpfer; Dagmar Waltemath; Anna Zhukova; Andreas Dräger; Michel Dumontier; Andrew Finney; Martin Golebiewski; Janna Hastings; Stefan Hoops; Sarah Keating; Douglas B Kell; Samuel Kerrien; James Lawson; Allyson Lister; James Lu; Rainer Machne; Pedro Mendes; Matthew Pocock; Nicolas Rodriguez; Alice Villeger; Darren J Wilkinson; Sarala Wimalaratne; Camille Laibe; Michael Hucka; Nicolas Le Novère
Journal: Mol Syst Biol Date: 2011-10-25 Impact factor: 11.429

6. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

Authors: Falk Schreiber; Gary D Bader; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Nicolas Le Novère; Chris Myers; David Nickerson; Björn Sommer; Dagmar Walthemath
Journal: J Integr Bioinform Date: 2016-12-18

7. SBML Level 3 package: Groups, Version 1 Release 1.

Authors: Michael Hucka; Lucian P Smith
Journal: J Integr Bioinform Date: 2016-12-18

8. SBML Level 3 package: Render, Version 1, Release 1.

Authors: Frank T Bergmann; Sarah M Keating; Ralph Gauges; Sven Sahle; Katja Wengler
Journal: J Integr Bioinform Date: 2018-04-02

9. Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.

Authors: Fengkai Zhang; Lucian P Smith; Michael L Blinov; James Faeder; William S Hlavacek; Jose Juan Tapia; Sarah M Keating; Nicolas Rodriguez; Andreas Dräger; Leonard A Harris; Andrew Finney; Bin Hu; Michael Hucka; Martin Meier-Schellersheim
Journal: J Integr Bioinform Date: 2020-07-06

Review 3. Validation Through Collaboration: Encouraging Team Efforts to Ensure Internal and External Validity of Computational Models of Biochemical Pathways.

Authors: Richard Fitzpatrick; Melanie I Stefan
Journal: Neuroinformatics Date: 2022-05-11

3 in total