SED-ML examples

L1V3 examples (in COMBINE archives)

Features:
  • Time course simulation
Model language(s):
  • SBML
Source: Hoffmann A, Levchenko A, Scott ML, Baltimore D (2002). The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. Science 11, 298: 1241-1245.
BioModels: BIOMD0000000140
Features:
  • Time course simulation
  • Model resolution by URI fragments
Model language(s):
  • SBML
Source: Leloup JC, Goldbeter A (1999). Chaos and birhythmicity in a model for circadian oscillations of the PER and TIM proteins in drosophila. Journal of Theoretical Biology 6, 198: 445-459.
BioModels: BIOMD0000000021
Features:
  • Aggregate functions
Model language(s):
  • CellML
Features:
  • Algorithm parameters
  • Aggregate functions
Model language(s):
  • SBML
Features:
  • One step simulation
Model language(s):
  • SBML
Features:
  • Steady-state simulation
  • Repeated task
Model language(s):
  • SBML
Features:
  • Data descriptions
  • Plotting
Model language(s):
  • SBML
Features:
  • Data descriptions
  • Plotting
Model language(s):
  • SBML
Features:
  • Repeated task
Experimental features:
  • Plots of results of repeated tasks
Model language(s):
  • SBML
Features:
  • Model resolution by URI fragments
  • Time course simulation
Model language(s):
  • SBML
Source: Elowitz MB, Leibler S (2000). A synthetic oscillatory network of transcriptional regulators. Nature 403, 6767: 335-338.
BioModels: BIOMD0000000012
Features:
  • Steady-state simulation
  • Repeated task
Experimental features:
  • Plots of results of repeated tasks
Model language(s):
  • SBML
Features:
  • Repeated task
Model language(s):
  • SBML
Experimental features:
  • Plots of results of repeated tasks
Model language(s):
  • CellML
Experimental features:
  • Plots of results of repeated tasks
Model language(s):
  • SBML
Download all of the examples as a .zip file.

Additional examples

BioModels database
Database of models which includes SED-ML files for many entries. Entries with SED-ML files can also be obtained as COMBINE archives.

BioSimulators test suite
Test suite for checking that simulation tools execute SED-ML files and COMBINE archives consistently with the specifications of these formats. The test suite uses a collection of curated COMBINE archives, each of which includes SED-ML files. These examples involve multiple model languages, including BNGL, SBML, SBML-fbc, and SBML-qual. To test simulation tools that involve a broad range of model languages, modeling frameworks, and simulation algorithms, the test suite can generate synthetic COMBINE archives and SED-ML files that are appropriate for testing a particular simulation tool (i.e., SED-ML files that involve model formats and simulation algorithms that the simulator can execute). The test suite can also save these synthetic archives to files for further inspection.

JWS Online simulation database
Database of simulation experiments which can be exported to SED-ML files and COMBINE archives.


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