Standard Formats
Displaying: 3 Found: 18 Total: 18
SBML L2V5
Systems Biology Markup Language Level 2 Version 5
Synopsis
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
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 |
Modularity: no
Components Relation
Flat Network:
no
Supported Math
MathML Support: yes
Full MathML Support: no
Description
subset MathML 2.0 standard
Unit Support
Unit Required: no
Support: intrinsic
Description
Annotation Support
Miriram Support: yes
identifiers.org Support: yes
|
Biological
Application
Format
|
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SBML L2V5 |
Webpage
Model 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
Publication date
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.
SBML L3V1 Core
Systems Biology Markup Language Level 3 Version 1 Core
Synopsis
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
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
Annotation Support
Miriram Support: yes
identifiers.org Support: yes
|
Biological
Application
Format
|
|||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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
Publication date
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.
SBML Level 3 Packages
Systems Biology Markup Language Level 3 Packages
Synopsis
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
Authors
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 |
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
Annotation Support
Miriram Support: no
identifiers.org Support: no
Description
Annotation Support is part of the SBML core.
|
Biological
Application
Format
|
||
|---|---|---|
| SBML Level 3 Packages |
Webpage
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
Publication date
Organizations
Links
Webpage
All formats for this class
not defined
Description
The licence agreement is not defined or could not be obtained.
