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Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1

Lucian P Smith, Stuart L Moodie, Frank T Bergmann, Colin Gillespie, Sarah M Keating, Matthias König, Chris J Myers, Maciek J Swat, Darren J Wilkinson, Michael Hucka
2020 Journal of Integrative Bioinformatics  
The Systems Biology Markup Language (SBML) Level 3 Core specification does not include an explicit mechanism to include inexact or stochastic values in a model, but it does provide a mechanism for SBML  ...  The SBML Distributions package for SBML Level 3 adds the necessary features to allow models to encode information about the distribution and uncertainty of values underlying a quantity.  ...  model using SBML Level 3 Version 1 and this 9 version of the Distributions package: 10 11 <?  ... 
doi:10.1515/jib-2020-0018 pmid:32750035 fatcat:b7qouaimvnfctk2tukti76mjry

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core

Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath (+1 others)
2018 Journal of Integrative Bioinformatics  
This document provides the specification for Version 2 of SBML Level 3 Core.  ...  The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange.  ...  Acknowledgments 1 The development of SBML was originally funded by the Japan Science and Technology Agency (JST) under  ... 
doi:10.1515/jib-2017-0081 pmid:29522418 fatcat:qcedcbjwlrhbjllcyz7afacbbq

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Michael Hucka, Michael Hucka, Frank Bergmann, Stefan Hoops, Sarah Keating, Sven Sahle, James Schaff, Lucian Smith, Darren Wilkinson
2010 Nature Precedings  
Notifications of new releases are broadcast on the mailing list sbml-announce@sbml.org The latest release of the SBML Level 3 Version 1 Core specification is available at  ...  Corrections and other changes to this SBML language specification may appear over time.  ...  in the SBML file. 1 . 1 The modular nature of SBML Level 3 Version 1 Core means that data that in SBML Level 2 could only 40 be stored in annotations may now be supported using a full SBML Level 3 package  ... 
doi:10.1038/npre.2010.4959.1 fatcat:rcwt3kprijabhcyjusdehuts3a

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Michael Hucka, Frank T Bergmann, Stefan Hoops, Sarah M Keating, Sven Sahle, James C Schaff, Lucian P Smith, Darren J Wilkinson
2015 Journal of Integrative Bioinformatics  
This document provides the specification for Version 1 of SBML Level 3 Core.  ...  The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems.  ...  (Germany), the University of Heidelberg (Germany), the European Molecular Biology Laboratory's European Bioinformatics Institute (UK), the Molecular  ... 
doi:10.2390/biecoll-jib-2015-266 pmid:26528564 pmcid:PMC5451324 fatcat:5ynhdioiubhhznpnftlv667aom

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Michael Hucka, Lucian Smith, Darren Wilkinson, Michael Hucka, Frank Bergmann, Stefan Hoops, Sarah Keating, Sven Sahle, James Schaff
2010 Nature Precedings  
Notifications of new releases are broadcast on the mailing list sbml-announce@sbml.org The latest release of the SBML Level 3 Version 1 Core specification is available at  ...  Corrections and other changes to this SBML language specification may appear over time.  ...  in the SBML file. 1 . 1 The modular nature of SBML Level 3 Version 1 Core means that data that in SBML Level 2 could only 40 be stored in annotations may now be supported using a full SBML Level 3 package  ... 
doi:10.1038/npre.2010.4959 fatcat:jxmfygtfrnchlhhgokdi2rtns4

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath (+1 others)
2018 Journal of Integrative Bioinformatics  
This document provides the specification for Release 2 of Version 1 of SBML Level 3 Core.  ...  The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange.  ...  Level 3 Version 1 58 Core, but the identifiers are available for possible use by SBML Level 3 packages.  ... 
doi:10.1515/jib-2017-0080 fatcat:xlg2o5uarrhizeili4asdxujae

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Michael Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith, Darren J. Wilkinson
2015 Journal of Integrative Bioinformatics  
This document provides the specification for Version 1 of SBML Level 3 Core.  ...  The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems.  ...  in the SBML file. 1 . 1 The modular nature of SBML Level 3 Version 1 Core means that data that in SBML Level 2 could only 40 be stored in annotations may now be supported using a full SBML Level 3 package  ... 
doi:10.1515/jib-2015-266 fatcat:agyvbsnlwvhkxkk4dtslsmilxq

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff (+5 others)
2019 Journal of Integrative Bioinformatics  
This document provides the specification for Release 2 of Version 2 of SBML Level 3 Core.  ...  The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange.  ...  Acknowledgments 1 The development of SBML was originally funded by the Japan Science and Technology Agency (JST) under  ... 
doi:10.1515/jib-2019-0021 pmid:31219795 pmcid:PMC6798823 fatcat:dvpppkkxdjfndcwf3qxhstc2km

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate)

Michael Hucka, Michael Hucka, Frank Bergmann, Stefan Hoops, Sarah Keating, Sven Sahle, Darren Wilkinson
2010 Nature Precedings  
Notifications of new releases are broadcast on the mailing list sbml-announce@sbml.org The latest release of the SBML Level 3 Version 1 Core specification is available at  ...  Corrections and other changes to this SBML language specification may appear over time.  ...  The modular nature of SBML Level 3 Version 1 Core means that data that in SBML Level 2 could only be stored in annotations may now be supported using a full SBML Level 3 package.  ... 
doi:10.1038/npre.2010.4123 fatcat:vzwadsu2hzayzf7542h7zddsty

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate)

Michael Hucka, Michael Hucka, Frank Bergmann, Stefan Hoops, Sarah Keating, Sven Sahle, Darren Wilkinson
2010 Nature Precedings  
Notifications of new releases are broadcast on the mailing list sbml-announce@sbml.org The latest release of the SBML Level 3 Version 1 Core specification is available at  ...  Corrections and other changes to this SBML language specification may appear over time.  ...  The modular nature of SBML Level 3 Version 1 Core means that data that in SBML Level 2 could only be stored in annotations may now be supported using a full SBML Level 3 package.  ... 
doi:10.1038/npre.2010.4123.1 fatcat:wwzvuqymdjck5chu5u53thzcr4

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

Michael Hucka, Andrew Finney, Stefan Hoops, Sarah Keating, Nicolas Le Novere
2007 Nature Precedings  
-2/version-3/ This release of the specification is available at http://sbml.org/specifications/sbml-level-2/version-3/release-1/ The list of known issues in all releases of SBML Level 2 Version 3 is available  ...  Notifications of new releases are broadcast on the mailing list sbml-announce@sbml.org The latest release of the SBML Level 2 Version 3 specification is available at http://sbml.org/specifications/sbml-level  ...  or attributes in the SBML namespace that are not 21 defined in this SBML Level 2 Version 3 Release 1 specification.  ... 
doi:10.1038/npre.2007.58.1 fatcat:mgdu7fr4wjgprmo4nksfuihiji

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

Nicolas Le Novère, Michael Hucka, Stefan Hoops, Sarah Keating, Sven Sahle, Darren Wilkinson
2008 Nature Precedings  
-2/version-4/ This release of the specification is available at http://sbml.org/specifications/sbml-level-2/version-4/release-1/ The list of known issues in all releases of SBML Level 2 Version 4 is available  ...  Notifications of new releases are broadcast on the mailing list sbml-announce@sbml.org The latest release of the SBML Level 2 Version 4 specification is available at http://sbml.org/specifications/sbml-level  ...  in the instance of the Section 6 now includes these qualifiers. 7 • Since the time that SBML Level 2 Version 3 Release 2 was issued, the Systems Biology Ontology 8 (SBO) underwent reorganization and  ... 
doi:10.1038/npre.2008.2715.1 fatcat:nlbdkuhuu5bozgtpzfofadmequ

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

Michael Hucka, Andrew Finney, Stefan Hoops, Sarah Keating, Nicolas Le Novere
2007 Nature Precedings  
-2/version-3/ This release of the specification is available at http://sbml.org/specifications/sbml-level-2/version-3/release-1/ The list of known issues in all releases of SBML Level 2 Version 3 is available  ...  Notifications of new releases are broadcast on the mailing list sbml-announce@sbml.org The latest release of the SBML Level 2 Version 3 specification is available at http://sbml.org/specifications/sbml-level  ...  or attributes in the SBML namespace that are not 21 defined in this SBML Level 2 Version 3 Release 1 specification.  ... 
doi:10.1038/npre.2007.58.2 fatcat:fpm75djjxjcwlcd3ogkbvbjjpq

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project

M. Hucka, A. Finney, J.C. Doyle, H. Kitano, B.L. Kovitz, B.E. Shapiro, A. Funahashi, J. Matthews, B.J. Bornstein, S.M. Keating, M.J. Schilstra
2004 IEE Proceedings - Systems Biology  
Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers.  ...  The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively.  ...  We developed the Systems Biology Markup Language (SBML) in an effort to address these problems.  ... 
doi:10.1049/sb:20045008 pmid:17052114 fatcat:643mmve5avaoroecfrbx43t2xm

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Michael Hucka, Frank T Bergmann, Andreas Dräger, Stefan Hoops, Sarah M Keating, Nicolas Le Novère, Chris J Myers, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Dagmar Waltemath (+1 others)
2015 Journal of Integrative Bioinformatics  
The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems.  ...  This document provides the specification for Version 5 of SBML Level 2.  ...  Acknowledgments The development of SBML was originally funded entirely by the Japan Science and Technology Agency (JST) under the ERATO Kitano Symbiotic Systems Project during the years .  ... 
doi:10.2390/biecoll-jib-2015-271 pmid:26528569 pmcid:PMC5457286 fatcat:vx6dfed6xnam3plmtngauwd3ei
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