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

2020 ◽  
Vol 17 (2-3) ◽  
Author(s):  
Lucian P. Smith ◽  
Stuart L. Moodie ◽  
Frank T. Bergmann ◽  
Colin Gillespie ◽  
Sarah M. Keating ◽  
...  
Keyword(s):  
Systems Biology ◽  
Markup Language ◽  
Biological Models ◽  
The Core ◽  
Systems Biology Markup Language ◽  
Level 3

AbstractBiological models often contain elements that have inexact numerical values, since they are based on values that are stochastic in nature or data that contains uncertainty. 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 packages to extend the Core specification and add additional syntactic constructs. 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.

Systems biology markup language: Level 2 and beyond

2003 ◽  
Vol 31 (6) ◽  
pp. 1472-1473 ◽  
Author(s):  
A. Finney ◽  
M. Hucka
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Chemical Species ◽  
Biochemical Networks ◽  
Markup Language ◽  
Exchange Format ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
Level 1 ◽  
Level 2

The SBML (systems biology markup language) is a standard exchange format for computational models of biochemical networks. We continue developing SBML collaboratively with the modelling community to meet their evolving needs. The recently introduced SBML Level 2 includes several enhancements to the original Level 1, and features under development for SBML Level 3 include model composition, multistate chemical species and diagrams.

scholarly journals Integration of constraints documented in SBML, SBO, and the SBML Manual facilitates validation of biological models

2007 ◽  
Vol 4 (3) ◽  
pp. 252-263 ◽  
Author(s):  
Allyson L. Lister ◽  
Matthew Pocock ◽  
Anil Wipat
Keyword(s):  
Systems Biology ◽  
Representative Sample ◽  
Model Development ◽  
Structural Knowledge ◽  
Markup Language ◽  
Web Ontology Language ◽  
Biological Models ◽  
Computational Approaches ◽  
Ontology Language ◽  
Systems Biology Markup Language

Abstract The creation of quantitative, simulatable, Systems Biology Markup Language (SBML) models that accurately simulate the system under study is a time-intensive manual process that requires careful checking. Currently, the rules and constraints of model creation, curation, and annotation are distributed over at least three separate documents: the SBML schema document (XSD), the Systems Biology Ontology (SBO), and the “Structures and Facilities for Model Definition” document. The latter document contains the richest set of constraints on models, and yet it is not amenable to computational processing. We have developed a Web Ontology Language (OWL) knowledge base that integrates these three structure documents, and that contains a representative sample of the information contained within them. This Model Format OWL (MFO) performs both structural and constraint integration and can be reasoned over and validated. SBML Models are represented as individuals of OWL classes, resulting in a single computationally amenable resource for model checking. Knowledge that was only accessible to humans is now explicitly and directly available for computational approaches. The integration of all structural knowledge for SBML models into a single resource creates a new style of model development and checking.

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

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Michael Hucka ◽  
Frank T. Bergmann ◽  
Andreas Dräger ◽  
Stefan Hoops ◽  
Sarah M. Keating ◽  
...  
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Software Systems ◽  
Markup Language ◽  
Starting Point ◽  
Extensible Markup ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
Translation Errors ◽  
Language Specification

AbstractComputational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

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

2010 ◽  
Author(s):  
Lucian Smith ◽  
Darren Wilkinson ◽  
Michael Hucka ◽  
Frank Bergmann ◽  
Stefan Hoops ◽  
...  
Keyword(s):  
Systems Biology ◽  
Markup Language ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
Language Specification

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

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Michael Hucka ◽  
Frank T. Bergmann ◽  
Andreas Dräger ◽  
Stefan Hoops ◽  
Sarah M. Keating ◽  
...  
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Software Systems ◽  
Markup Language ◽  
Design Changes ◽  
Starting Point ◽  
Extensible Markup ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
Translation Errors

AbstractComputational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the format of annotations, the correction of errata and the addition of clarifications. Other materials and software are available from the SBML project website at http://sbml.org/.

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

2015 ◽  
Vol 12 (2) ◽  
pp. 382-549 ◽  
Author(s):  
Michael Hucka ◽  
Frank T. Bergmann ◽  
Stefan Hoops ◽  
Sarah M. Keating ◽  
Sven Sahle ◽  
...  
Keyword(s):  
Systems Biology ◽  
Computational Models ◽  
Software Systems ◽  
Markup Language ◽  
Starting Point ◽  
Extensible Markup ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
Translation Errors ◽  
Language Specification

Summary Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. 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. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

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

2020 ◽  
Vol 17 (2-3) ◽  
Author(s):  
Fengkai Zhang ◽  
Lucian P. Smith ◽  
Michael L. Blinov ◽  
James Faeder ◽  
William S. Hlavacek ◽  
...  
Keyword(s):  
Systems Biology ◽  
Spatial Information ◽  
Markup Language ◽  
Rule Based ◽  
Fine Grained ◽  
Multiple Components ◽  
Design Changes ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
Definition Of

AbstractRule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains and the states and binding status of the involved components. Conceptually, fine-grained spatial information such as locations can also be provided. Through “wildcards” representing component states, entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states, and multiple compartments. The systems biology markup language (SBML) Level 3 Multi Package Version 1 extends the SBML Level 3 Version 1 core with the “type” concept in the Species and Compartment classes. Therefore, reaction rules may contain species that can be patterns and exist in multiple locations. Multiple software tools such as Simmune and BioNetGen support this standard that thus also becomes a medium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level 3 Multi package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications.

scholarly journals The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core

2015 ◽  
Vol 12 (2) ◽  
pp. 550-602 ◽  
Author(s):  
Ralph Gauges ◽  
Ursula Rost ◽  
Sven Sahle ◽  
Katja Wengler ◽  
Frank T. Bergmann
Keyword(s):  
Systems Biology ◽  
Reaction Network ◽  
Software Tools ◽  
Graphical Form ◽  
Markup Language ◽  
As Species ◽  
Systems Biology Markup Language ◽  
Level 3 ◽  
General Graphs ◽  
Network Diagrams

SummaryMany software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded.The SBML Layout package is based on the principle that reaction network diagrams should be described as representations of entities such as species and reactions (with direct links to the underlying SBML elements), and not as arbitrary drawings or graphs; for this reason, existing languages for the description of vector drawings (such as SVG) or general graphs (such as GraphML) cannot be used.

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