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
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 |
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
Biological
Application
Format
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SBML L3V1 Core |
Webpage
Specification
Model repository
Software Repository
libSBML
Programming language
C++Dependend apis
- libSBML - Java
- libSBML - Python
- libSBML - Matlab
- libSBML - Octave
Links
API
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.