The following languages have to our knowledge so far
been used with SED-ML. To specify the language of a model
in the Model class, please use the according URN given.
The general scheme for a language URN in SED-ML is urn:sedml:language:{ language
name and version }.
| Language | URN | Specification |
|---|---|---|
| Abstract Petri net notation (APNN) (generic) | urn:sedml:language:apnn |
https://ls4-www.cs.tu-dortmund.de/APNN-TOOLBOX/ |
| Berkeley Logic Interchange Format (BLIF) (generic) | urn:sedml:language:bngl |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.115.9222 |
| BioNetGen Language (BNGL) (generic) | urn:sedml:language:bngl |
https://bionetgen.org |
| BoolNet (generic) | urn:sedml:language:boolnet |
https://cran.r-project.org/web/packages/BoolNet/index.html |
| BooleanNet (generic) | urn:sedml:language:booleannet |
https://github.com/ialbert/booleannet |
| CNET (generic) | urn:sedml:language:cnet |
https://people.kth.se/~dubrova/bns.html |
| CellML (generic) | urn:sedml:language:cellml |
http://www.cellml.org/specifications/ |
| CellML 1.0 | urn:sedml:language:cellml.1_0 |
http://www.cellml.org/specifications/cellml_1.0 |
| CellML 1.1 | urn:sedml:language:cellml.1_1 |
https://www.cellml.org/specifications/cellml_1.1 |
| CellML 2.0 | urn:sedml:language:cellml.2_0 |
https://www.cellml.org/specifications/cellml_2.0 |
| GENESIS (generic) | urn:sedml:language:genesis |
http://genesis-sim.org/ |
| GINsim Markup Language (GINML) (generic) | urn:sedml:language:ginml |
https//ginsim.org |
| Genetic Network Analyzer (GNA) (generic) | urn:sedml:language:gna |
http://ibis.inrialpes.fr/people/dejong/GNA/user/ch03.html |
| High Order Calculator (HOC) (generic) | urn:sedml:language:hoc |
https://www.neuron.yale.edu/neuron/static/new_doc/programming/hoc.html |
| Integrated Net Analyzer (INA) (generic) | urn:sedml:language:ina |
https://www2.informatik.hu-berlin.de/~starke/ina.html |
| Kappa (generic) | urn:sedml:language:kappa |
https://kappalanguage.org/ |
| Low Entropy Model Specification (LEMS) (generic) | urn:sedml:language:lems |
https://github.com/LEMS/LEMS |
| MaBoSS (generic) | urn:sedml:language:maboss |
https://maboss.curie.fr/ |
| Mass Action Stoichiometric Simulation (MASS) (generic) | urn:sedml:language:mass |
https://masspy.readthedocs.io/en/stable/tutorials/reading_writing_models.html |
| Morpheus Markup Language (MorpheusML) (generic) | urn:sedml:language:morpheusml |
https://morpheus.gitlab.io/ |
| NEURON MODeling Language (generic) | urn:sedml:language:nmodl |
https://bluebrain.github.io/nmodl/ |
| Neocortical Simulator (NCS) (generic) | urn:sedml:language:ncs |
https://github.com/BrainComputationLab/ncs |
| NeuroML (generic) | urn:sedml:language:neuroml |
https://docs.neuroml.org/Userdocs/Specification.html |
| NeuroML Version 1.8.1 Level 1 | urn:sedml:language:neuroml.version-1_8_1.level-1 |
https://docs.neuroml.org/Userdocs/NeuroMLv1.html |
| NeuroML Version 1.8.1 Level 2 | urn:sedml:language:neuroml.version-1_8_1.level-2 |
https://docs.neuroml.org/Userdocs/NeuroMLv1.html |
| NeuroML Version 1.8.1 Level 3 | urn:sedml:language:neuroml.version-1_8_1.level-3 |
https://docs.neuroml.org/Userdocs/NeuroMLv1.html |
| NeuroML Version 2.1 | urn:sedml:language:neuroml.version-2_1 |
https://docs.neuroml.org/Userdocs/NeuroMLv2.html |
| NuSMV (generic) | urn:sedml:language:nusmv |
https://nusmv.fbk.eu/NuSMV/userman/index-v2.html |
| Petri Net Markup Language (PNML) (generic) | urn:sedml:language:pnml |
https://www.pnml.org/ |
| Pharmacometrics Markup Language (pharmML) (generic) | urn:sedml:language:pharmml |
http://www.pharmml.org/ |
| Pint (generic) | urn:sedml:language:pint |
https://loicpauleve.name/pint/ |
| Resource Balance Analysis (RBA) (generic) | urn:sedml:language:rba |
https://rba.inrae.fr/ |
| SBML Level 1 Version 1 | urn:sedml:language:sbml.level-1.version-1 |
http://sbml.org/Special/specifications/sbml-level-1/version-1/html/ |
| SBML Level 1 Version 2 | urn:sedml:language:sbml.level-1.version-2 |
http://sbml.org/Special/specifications/sbml-level-1/version-2/html/ |
| SBML Level 2 Version 1 | urn:sedml:language:sbml.level-2.version-1 |
http://www.sbml.org/specifications/sbml-level-2/version-1/html/ |
| SBML Level 2 Version 2 | urn:sedml:language:sbml.level-2.version-2 |
http://www.sbml.org/specifications/sbml-level-2/version-2/revision-1/sbml-level-2-version-2-rev1.pdf |
| SBML Level 2 Version 3 | urn:sedml:language:sbml.level-2.version-3 |
http://www.sbml.org/specifications/sbml-level-2/version-3/release-1/sbml-level-2-version-3-rel-1.pdf |
| SBML Level 2 Version 4 | urn:sedml:language:sbml.level-2.version-4 |
http://precedings.nature.com/documents/2715/version/1 |
| SBML Level 2 Version 5 | urn:sedml:language:sbml.level-2.version-5 |
http://co.mbine.org/specifications/sbml.level-2.version-5.release-1 |
| SBML Level 3 Version 1 | urn:sedml:language:sbml.level-3.version-1 |
http://precedings.nature.com/documents/4123/version/1 |
| SBML Level 3 Version 2 | urn:sedml:language:sbml.level-3.version-2 |
http://sbml.org/Special/specifications/sbml-level-3/version-2/core/release-1-rc2/sbml-level-3-version-2-core.pdf |
| SLI (generic) | urn:sedml:language:sli |
https://nest-simulator.readthedocs.io/en/stable/sli_docs/programming-in-sli.html |
| Smoldyn (generic) | urn:sedml:language:smoldyn |
http://www.smoldyn.org/ |
| Systems Biology Markup Language (SBML) (generic) | urn:sedml:language:sbml |
http://sbml.org/Special/specifications/ |
| TruthTable (generic) | urn:sedml:language:truthtable |
http://colomoto.org/formats/truthtable.html |
| Virtual Cell Markup Language (VCML) (generic) | urn:sedml:language:vcml |
https://vcell.org |
| XPP ODE (generic) | urn:sedml:language:xpp |
http://www.math.pitt.edu/~bard/xpp/xpp.html |
| Zipped GINsim Markup Language (ZGINML) (generic) | urn:sedml:language:zginml |
https//ginsim.org |
| boolSim (generic) | urn:sedml:language:boolsim |
https://www.vital-it.ch/research/software/boolSim |
To specify the format of a resource please use the according URN given.
The general scheme for a format URN in SED-ML is urn:sedml:format:{ format name }.
| Data Format | URN | More information |
|---|---|---|
| CSV | urn:sedml:format:csv |
|
| HDF (generic) | urn:sedml:format:hdf |
https://portal.hdfgroup.org/display/support/Documentation |
| HDF5 | urn:sedml:format:hdf.version-5 |
https://portal.hdfgroup.org/display/HDF5/HDF5 |
| JSON (generic) | urn:sedml:format:json |
https://www.json.org/ |
| NuML (generic) | urn:sedml:format:numl |
https://github.com/NuML/NuML |
| NuML Level 1 Version 1 | urn:sedml:format:numl.level-1.version-1 |
https://github.com/NuML/NuML/raw/master/numl-spec-l1v1.pdf |
| TSV | urn:sedml:format:tsv |
|
| XLSX (Generic) | urn:sedml:format:xlsx |
https://www.ecma-international.org/publications-and-standards/standards/ecma-376/ |
| XML (Generic) | urn:sedml:format:xml |
https://www.w3.org/XML/ |
| YAML (Generic) | urn:sedml:format:yaml |
https://yaml.org/ |
As described in the SED-ML specification some modeling
languages use predefined symbols or implicit variables. In order to
handle such variables the SED-ML introduced symbol URNs. The general scheme for a symbol
URN in SED-ML is urn:sedml:symbol:{ symbolName }.
| Language | URN | Definition |
|---|---|---|
| SBML | urn:sedml:symbol:time |
Time in SBML is an intrinsic model variable that is addressable in model equations via a csymbol 'time'. |
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