Standard Formats

Displaying: 1 Found: 1 Total: 18


SBML L3V1 Core


Systems Biology Markup Language Level 3 Version 1 Core

Synopsis

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

Description

Systems Biology Markup Language (SBML), a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others.*

*(M. Hucka et al. Bioinformatics (2003) 19 (4): 524-531)

Publication Date

10/2010

Authors

Hucka, Michael
T. Bergmann, Frank
Hoops, Stefan
M. Keating, Sarah
Sahle, Sven
C. Schaff, James
P. Smith, Lucian
J. Wilkinson, Darren

Organizations


Biological Scales

Scale molecular cellular tissue organ organism ecosystem
Support intrinsic potential potential unknown unknown potential

Spatial Representation

Spatial Representation Level Compartment Dimensions Gradients Spatial Structures
Support intrinsic intrinsic unknown unknown

Modeling Formalisms for this format

Software support for this format

Examples for this format


Advantage

  • Multiscale Models
  • Extensible XML scheme

Modularity: no


Components Relation
Flat Network: no


Supported Math

MathML Support: yes

Full MathML Support: no


Unit Support

Unit Required: no

Support: intrinsic

Description

units are more like a form of annotation; every transformation of values implied by units must be encoded explicitly

Annotation Support

Miriram Support: yes

identifiers.org Support: yes


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 - Python


Programming language

Python

Depends on api

libSBML

Links

API

libSBML - Matlab


Programming language

Matlab

Depends on api

libSBML

Links

API

libSBML - Octave


Programming language

Octave

Depends on api

libSBML

Links

API

libSBML


SBML


Validation Portal

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

Free and Open


Description

Not closely defiened license allowing for free use and open participation. The product is viewed as community effort.