Standard Formats

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SBML Level 3 Packages

Systems Biology Markup Language Level 3 Packages

Synopsis

Extension of the SBML level 3 core functionality through external modules.

Description

SBML level 3 is a modular language with an extensible XML schema. The core functionality may be extended through individual packages. Only packages which are labeled as released are included.

 

List of included packages and their functionality*:

Hierarchical Model Composition: A means for defining how a model is composed from other models. 

Flux Balance Constraints: Support for constraint-based (a.k.a. steady-state) models.

Groups: A means for grouping elements Layout: Support for storing the spatial topology of a network diagram: adjunct to the render package.

Qualitative Models: Support for models wherein species do not represent quantity of matter & processes are not reactions per se

 

For a complete list of available packages visit the SBML webpage.

(*15.02.2016 - http://sbml.org/Documents/Specifications)

Publication Date

10/2010

Authors

Hucka, Michael
T. Bergmann, Frank
Hoops, Stefan
M. Keating, Sarah
Sahle, Sven
P. Smith, Lucian
Myers, Chris
P. van Iersel, Martijn
Finney, Andrew
Ginkel, Martin
Moraru, Ion
Liebermeister, Wolfram
Olivier, Brett G.
Gauges, Ralph
Rost, Ursula
Wengler, Katja
Chaouiya, Claudine
Berenguier, Duncan
Naldi, Aurélien
Thieffry, Denis

Organizations

Biological Scales

Scale molecular cellular tissue organ organism ecosystem
Support undefined undefined undefined undefined undefined undefined

Spatial Representation

Spatial Representation Level Compartment Dimensions Gradients Spatial Structures
Support undefined undefined undefined undefined

Modeling Formalisms for this format

Software support for this format

Examples for this format

Advantage

  • Model components reusability
  • Flexible component grouping
  • Standardized graphical layout of a model

Modularity: yes

Components Relation
Flat Network: no

Supported Math

MathML Support: no

Full MathML Support: no

Description

Math Support is part of the SBML core.

Unit Support

Unit Required: no

Support: undefined

Description

Unit support is part of the SBML core.

Annotation Support

Miriram Support: no

identifiers.org Support: no

Description

Annotation Support is part of the SBML core.

There are no transformations available!

libSBML

Programming language

C++

Dependend apis

  • libSBML - Java
  • libSBML - Python
  • libSBML - Matlab
  • libSBML - Octave

Links

API

libSBML - Java

Programming language

Java

Depends on api

libSBML

Links

API

libSBML

libSBML

Systems Biology Markup Language (SBML)

Description

Representation of biological processes as a set of processes, that are converting pools of entities into other pools entities. 

Derived from

XML

Publication date

03/2001

Organizations

Links

Webpage

All formats for this class

not defined

Description

The licence agreement is not defined or could not be obtained.