Standard Formats
Displaying: 3 Found: 18 Total: 18
NeuroML 2 beta 3
NeuroML 2 beta 3
Synopsis
Description
We have developed a compact, hierarchical, XML-based language called LEMS (Low Entropy Model Specification), that can define the structure and dynamics of a wide range of biological models in a fully machine readable format. We describe how LEMS underpins the latest version of NeuroML and show that this framework can define models of ion channels, synapses, neurons and networks. Unit handling, often a source of error when reusing models, is built into the core of the language by specifying physical quantities in models in terms of the base dimensions. We show how LEMS, together with the open source Java and Python based libraries we have developed, facilitates the generation of scripts for multiple neuronal simulators and provides a route for simulator free code generation. We establish that LEMS can be used to define models from systems biology and map them to neuroscience-domain specific simulators, enabling models to be shared between these traditionally separate disciplines. LEMS and NeuroML 2 provide a new, comprehensive framework for defining computational models of neuronal and other biological systems in a machine readable format, making them more reproducible and increasing the transparency and accessibility of their underlying structure and properties.*
*(Cannon RC et al. Frontiers in Neuroinformatics. 2014;8:79. )
Publication Date
Authors
Organizations
Biological Scales
Scale | molecular | cellular | tissue | organ | organism | ecosystem |
---|---|---|---|---|---|---|
Support | intrinsic | intrinsic | intrinsic | intrinsic | unknown | unknown |
Spatial Representation
Spatial Representation Level | Compartment | Dimensions | Gradients | Spatial Structures |
---|---|---|---|---|
Support | intrinsic | intrinsic | potential | intrinsic |
Advantage
- Automated consistency checking
- Multiscale Models
- Translation from Blender
Modularity: yes
Components Relation
Flat Network:
no
Supported Math
MathML Support: no
Full MathML Support: no
Description
Uses own mathematical grammar.
Unit Support
Unit Required: yes
Support: intrinsic
Description
Annotation Support
Biological
Application
Format
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NeuroML 2 beta 3 |
NeuroML
Description
Model Description Language for Computational Neuroscience
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.
PharmML v0.6
Pharmacometrics Markup Language Version 0.6
Synopsis
Description
The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps.*
*(Swat M et al.. CPT: Pharmacometrics & Systems Pharmacology. 2015;4(6):316-319.)
Publication Date
Authors
Organizations
Biological Scales
Scale | molecular | cellular | tissue | organ | organism | ecosystem |
---|---|---|---|---|---|---|
Support | unknown | intrinsic | intrinsic | intrinsic | intrinsic | unknown |
Spatial Representation
Spatial Representation Level | Compartment | Dimensions | Gradients | Spatial Structures |
---|---|---|---|---|
Support | intrinsic | unknown | unknown | unknown |
Advantage
- Extensible XML scheme
- Interfacing NONMEM/Monolix datasets
- Interfacing UncertML
- Intrinsic Simulation Experiment Description
- Vector/Matrices Support
Modularity: yes
Components Relation
Flat Network:
no
Supported Math
MathML Support: no
Full MathML Support: no
Description
Own mathematical definitions. Support of expression validation.
Unit Support
Unit Required: no
Support: intrinsic
Description
Annotation Support
Miriram Support: no
identifiers.org Support: yes
Description
Any annotations is supposed to be stored in an external RDF file.
Webpage
Publication
Model repository
Specification
Pharmacometrics Markup Language (pharmML)
Description
Format for exchange of pharmacometric models.
Derived from
Publication date
Organizations
Links
Webpage
All formats for this class
Apache License , Version 2.0
Description
For exact licence information see webpage.
Links
License
SBGN AF L1 V1.0
SBGN Activity Flow language Level 1 Version 1.0
Synopsis
Description
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Descriptions, the Entity Relationships and the Activity Flows. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage ranging from textbooks and teaching in high schools to peer reviewed articles in scientific journals. The first level of the SBGN Activity Flow language has been publicly released. Shared by the communities of biochemists, genomic scientists, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signaling pathways, metabolic networks and gene regulatory maps.*
*(Mi, Huaiyu et al.. Available from Nature Precedings (2009))
Publication Date
Authors
Organizations
Biological Scales
Scale | molecular | cellular | tissue | organ | organism | ecosystem |
---|---|---|---|---|---|---|
Support | unknown | unknown | unknown | unknown | unknown | unknown |
Spatial Representation
Spatial Representation Level | Compartment | Dimensions | Gradients | Spatial Structures |
---|---|---|---|---|
Support | intrinsic | unknown | unknown | unknown |
Advantage
- Standardized graphical layout of a model
Modularity: no
Components Relation
Flat Network:
no
Supported Math
Unit Support
Unit Required: no
Support: no support
Annotation Support
Miriram Support: no
identifiers.org Support: no
Description
Additional information on glyphs uses controlled vocabulary from SBO.
Webpage
Specification
Publication
Systems Biology Graphical Notation (SBGN)
Description
Systems Biology Graphical Notation aims at representing networks of biochemical interactions in a standard and unambigious way.
Publication date
Organizations
Links
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.