SBML Level 3: an extensible format for the exchange and reuse of biological models-Reference-Cited by-同舟云学术

SBML Level 3: an extensible format for the exchange and reuse of biological models

Published:2020-08 Issue:8 Volume:16 Page:
ISSN:1744-4292
Container-title:Molecular Systems Biology
language:en
Short-container-title:Mol Syst Biol

Author:

Keating Sarah M¹²³^ORCID,Waltemath Dagmar⁴^ORCID,König Matthias⁵^ORCID,Zhang Fengkai⁶^ORCID,Dräger Andreas⁷⁸⁹^ORCID,Chaouiya Claudine¹⁰¹¹^ORCID,Bergmann Frank T³^ORCID,Finney Andrew¹²,Gillespie Colin S¹³^ORCID,Helikar Tomáš¹⁴^ORCID,Hoops Stefan¹⁵^ORCID,Malik‐Sheriff Rahuman S²^ORCID,Moodie Stuart L¹⁶^ORCID,Moraru Ion I¹⁷^ORCID,Myers Chris J¹⁸^ORCID,Naldi Aurélien¹⁹^ORCID,Olivier Brett G¹³²⁰^ORCID,Sahle Sven³,Schaff James C²¹^ORCID,Smith Lucian P¹²²^ORCID,Swat Maciej J²³,Thieffry Denis¹⁹^ORCID,Watanabe Leandro¹⁸^ORCID,Wilkinson Darren J¹³²⁴^ORCID,Blinov Michael L¹⁷^ORCID,Begley Kimberly²⁵^ORCID,Faeder James R²⁶^ORCID,Gómez Harold F²⁷,Hamm Thomas M⁷⁸^ORCID,Inagaki Yuichiro²⁸^ORCID,Liebermeister Wolfram²⁹^ORCID,Lister Allyson L³⁰^ORCID,Lucio Daniel³¹^ORCID,Mjolsness Eric³²^ORCID,Proctor Carole J³³^ORCID,Raman Karthik³⁴³⁵³⁶^ORCID,Rodriguez Nicolas³⁷^ORCID,Shaffer Clifford A³⁸^ORCID,Shapiro Bruce E³⁹,Stelling Joerg⁴⁰^ORCID,Swainston Neil⁴¹^ORCID,Tanimura Naoki⁴²,Wagner John⁴³,Meier‐Schellersheim Martin⁶^ORCID,Sauro Herbert M²²^ORCID,Palsson Bernhard⁴⁴^ORCID,Bolouri Hamid⁴⁵,Kitano Hiroaki⁴⁶⁴⁷^ORCID,Funahashi Akira⁴⁸^ORCID,Hermjakob Henning²^ORCID,Doyle John C¹^ORCID,Hucka Michael¹^ORCID,Adams Richard R,Allen Nicholas A,Angermann Bastian R,Antoniotti Marco,Bader Gary D,Červený Jan,Courtot Mélanie,Cox Chris D,Dalle Pezze Piero,Demir Emek,Denney William S,Dharuri Harish,Dorier Julien,Drasdo Dirk,Ebrahim Ali,Eichner Johannes,Elf Johan,Endler Lukas,Evelo Chris T,Flamm Christoph,Fleming Ronan MT,Fröhlich Martina,Glont Mihai,Gonçalves Emanuel,Golebiewski Martin,Grabski Hovakim,Gutteridge Alex,Hachmeister Damon,Harris Leonard A,Heavner Benjamin D,Henkel Ron,Hlavacek William S,Hu Bin,Hyduke Daniel R,Jong Hidde,Juty Nick,Karp Peter D,Karr Jonathan R,Kell Douglas B,Keller Roland,Kiselev Ilya,Klamt Steffen,Klipp Edda,Knüpfer Christian,Kolpakov Fedor,Krause Falko,Kutmon Martina,Laibe Camille,Lawless Conor,Li Lu,Loew Leslie M,Machne Rainer,Matsuoka Yukiko,Mendes Pedro,Mi Huaiyu,Mittag Florian,Monteiro Pedro T,Natarajan Kedar Nath,Nielsen Poul MF,Nguyen Tramy,Palmisano Alida,Pettit Jean‐Baptiste,Pfau Thomas,Phair Robert D,Radivoyevitch Tomas,Rohwer Johann M,Ruebenacker Oliver A,Saez‐Rodriguez Julio,Scharm Martin,Schmidt Henning,Schreiber Falk,Schubert Michael,Schulte Roman,Sealfon Stuart C,Smallbone Kieran,Soliman Sylvain,Stefan Melanie I,Sullivan Devin P,Takahashi Koichi,Teusink Bas,Tolnay David,Vazirabad Ibrahim,Kamp Axel,Wittig Ulrike,Wrzodek Clemens,Wrzodek Finja,Xenarios Ioannis,Zhukova Anna,Zucker Jeremy,

Affiliation:

1. Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA

2. European Bioinformatics Institute European Molecular Biology Laboratory (EMBL‐EBI) Hinxton UK

3. BioQuant/COS Heidelberg University Heidelberg Germany

4. Medical Informatics Institute for Community Health University Medicine Greifswald Greifswald Germany

5. Institute for Theoretical Biology Humboldt‐University Berlin Berlin Germany

6. Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bethesda MDUSA

7. Computational Systems Biology of Infection and Antimicrobial‐Resistant Pathogens Institute for Biomedical Informatics (IBMI) University of Tübingen Tübingen Germany

8. Department of Computer Science University of Tübingen Tübingen Germany

9. German Center for Infection Research (DZIF) Tübingen Germany

10. Aix‐Marseille Université CNRS Centrale Marseille Marseille France

11. Instituto Gulbenkian de Ciência Oeiras Portugal

12. ANSYS UK Ltd Milton Park Oxfordshire UK

13. School of Mathematics, Statistics and Physics Newcastle University Newcastle upon Tyne UK

14. Department of Biochemistry University of Nebraska–LincolnLincoln NE USA

15. Biocomplexity Institute & Initiative University of Virginia Charlottesville VA USA

16. Eight Pillars Ltd Edinburgh UK

17. Center for Cell Analysis and Modeling UConn Health Farmington CTUSA

18. Department of Electrical and Computer Engineering University of Utah Salt Lake CityUT USA

19. Institut de Biologie de l'ENS (IBENS) Département de Biologie École Normale Supérieure CNRS INSERM Université PSL Paris France

20. SysBioLab AIMMS Vrije Universiteit Amsterdam Amsterdam the Netherlands

21. Applied BioMath, LLC Concord MAUSA

22. Department of Bioengineering University of Washington Seattle WAUSA

23. Simcyp (a Certara company) Sheffield South Yorkshire UK

24. The Alan Turing Institute British Library London UK

25. California Institute of Technology Pasadena CAUSA

26. Department of Computational and Systems Biology University of Pittsburgh Pittsburgh PAUSA

27. Department of Biosystems Science and Engineering ETH Zürich Basel Switzerland

28. Management & IT Consulting Division Mizuho Information & Research Institute, Inc.Tokyo Japan

29. Université Paris‐Saclay INRAE MaIAGEJouy‐en-Josas France

30. Oxford e‐Research Centre (OeRC) Department of Engineering Science University of Oxford Oxford UK

31. College of Sciences NC State University RaleighNC USA

32. Department of Computer Science University of California Irvine CAUSA

33. Institute of Cellular Medicine Newcastle University Newcastle upon Tyne UK

34. Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Indian Institute of Technology (IIT) Madras Chennai India

35. Initiative for Biological Systems Engineering (IBSE) IIT Madras Chennai India

36. Robert Bosch Centre for Data Science and Artificial Intelligence (RBC‐DSAI) IIT Madras Chennai India

37. The Babraham Institute Cambridge UK

38. Department of Computer Science Virginia Tech Blacksburg VAUSA

39. Department of Mathematics California State University Northridge CAUSA

40. Department of Biosystems Science and Engineering SIB Swiss Institute of Bioinformatics ETH Zürich Basel Switzerland

41. Institute of Integrative Biology University of Liverpool Liverpool UK

42. Science Solutions Division Mizuho Information & Research Institute, Inc. Tokyo Japan

43. IBM Research Australia Melbourne Vic. Australia

44. Department of Bioengineering University of California San Diego La Jolla CA USA

45. Systems Immunology Benaroya Research Institute at Virginia Mason Seattle WAUSA

46. The Systems Biology Institute Tokyo Japan

47. Okinawa Institute of Science and Technology Okinawa Japan

48. Department of Biosciences and Informatics Keio University Yokohama Kanagawa Japan

Publisher

EMBO

Subject

Applied Mathematics,Computational Theory and Mathematics,General Agricultural and Biological Sciences,General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,Information Systems

Link

https://onlinelibrary.wiley.com/doi/pdf/10.15252/msb.20199110

Reference121 articles.

1. Gene Ontology: tool for the unification of biology

2. Comparing simulation results of SBML capable simulators

3. COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

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

5. A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

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