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A test suite for SED-ML, modeled after the SBML test suite.

The test suite contains of two main parts:

  • archives: combine archives containing SED-ML bases simulation experiments
  • cases: individual test cases similar to the SBML test suite

Each test is in a numbered directory in the cases/ directory. When possible, both SBML and CellML versions are present; the focus being on the SED-ML itself rather than the modeling language it points to. Each directory may contain the following files, where xxxxx is the number of the directory (i.e. 00001):

file description
xxxxx-info.txt Information about the test itself, including a summary of what is being tested (see below).
xxxxx-sedml-cellml.xml The version of the SED-ML test that points to the CellML model
xxxxx-sedml-sbml.xml The version of the SED-ML test that points to the SBML model
xxxxx-results.csv The output from any <report> element in the SED-ML
xxxxx-cellml[xx].xml Any CellML models
xxxxx-sbml[xx].xml Any SBML models

The format of the info file is as follows:

title description
category: Test Not sure if this is needed--taken from the SBML test suite, and they're all 'test' there
synopsis: A short text description of the test.
sbml: xxxxx-sedml-sbml.xml The version of the test that points to SBML
cellml: xxxxx-sedml-cellml.xml The version of the test that points to CellML
componentTags: A list of the actual SED-ML classes used in the file
testTags: A list of particular SED-ML interactions or uses that cannot be summarized by simply listing the components
testType: TimeCourse Not sure if this is needed either--might be covered by the componentTags?
description: A longer description of the test. May include an Antimony version of the model, and a phraSED-ML version of the SED-ML, if people don't think it's too cheesy to include my own stuff here ;-) This is exactly the sort of context where those languages are particularly useful, though.

The contributions folder is for people to upload SED-ML files or Combine Archives they think might be useful to add to the suite proper.


A test suite for SED-ML




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