SED-ML | Examples

Below are several examples of SED-ML files. Each example is provided as a COMBINE archive, which contains both the example SED-ML file and all model and data files involved in the SED-ML file.

For each example, the table below also lists simulation tools which have been verified to be able to execute the example.

Note, because SED-ML files typically describe simulations involving specific model formats and simulation algorithms, each SED-ML file can only be executed by a subset of simulation tools. Information about the capabilities of simulation tools to execute SED-ML files involving specific formats and algorithms is available at BioSimulators. In addition, runBioSimulations provides a web application which can recommend specific tools for executing particular SED-ML files in COMBINE archives.

L1V3 examples (in COMBINE archives)

iKappaB model

Features:

Time course simulation

Model language(s):

SBML

Verified simulation tool(s):

tellurium 2.2.10

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.

DOI: 10.1126/science.1071914

BioModels: BIOMD0000000140

Leloup model of circadian oscillations

Features:

Time course simulation
Model resolution by URI fragments

Model language(s):

SBML

Verified simulation tool(s):

PySCeS 1.2.2
tellurium 2.2.10

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.

DOI: 10.1006/jtbi.1999.0924

BioModels: BIOMD0000000021

Lorentz model (CellML)

Features:

Aggregate functions

Model language(s):

CellML

Verified simulation tool(s):

OpenCOR 2021-10-05

Lorentz model (SBML)

Features:

Algorithm parameters
Aggregate functions

Model language(s):

SBML

Verified simulation tool(s):

tellurium 2.2.10

Oscillatory model

Features:

One step simulation

Model language(s):

SBML

Verified simulation tool(s):

tellurium 2.2.10

Parameter scan

Features:

Steady-state simulation
Repeated task

Model language(s):

SBML

Verified simulation tool(s):

tellurium 2.2.10

Plotting (CSV data)

Features:

Data descriptions
Plotting

Model language(s):

SBML

Verified simulation tool(s):

tellurium 2.2.10

Plotting (NuML data)

Features:

Data descriptions
Plotting

Model language(s):

SBML

Verified simulation tool(s):

tellurium 2.2.10

Repeated stochastic runs

Features:

Repeated task

Experimental features:

Plots of results of repeated tasks

Model language(s):

SBML

Verified simulation tool(s):

GillesPy2 1.6.6
tellurium 2.2.10

Represillator

Features:

Model resolution by URI fragments
Time course simulation

Model language(s):

SBML

Verified simulation tool(s):

tellurium 2.2.10

Source: Elowitz MB, Leibler S (2000). A synthetic oscillatory network of transcriptional regulators. Nature 403, 6767: 335-338.

DOI: 10.1038/35002125

BioModels: BIOMD0000000012

Steady-state scan

Features:

Steady-state simulation
Repeated task

Experimental features:

Plots of results of repeated tasks

Model language(s):

SBML

Verified simulation tool(s):

tellurium 2.2.10

Time course scan

Features:

Repeated task

Model language(s):

SBML

Verified simulation tool(s):

PySCeS 1.2.2
tellurium 2.2.10

Van der Pol oscillator (CellML)

Experimental features:

Plots of results of repeated tasks

Model language(s):

CellML

Verified simulation tool(s):

OpenCOR 2021-10-05

Van der Pol oscillator (SBML)

Experimental features:

Plots of results of repeated tasks

Model language(s):

SBML

Verified simulation tool(s):

PySCeS 1.2.2
tellurium 2.2.10

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.

SED-ML examples

L1V3 examples (in COMBINE archives)

Additional examples