Forums

Dear SBML people,

We are pleased to announce an update to the SBML Test Suite, available now. The update features the following changes:

1) Additional test cases, bringing the total to 1123 tests.
2) Corrections to a number of cases (see the notes below).
3) Improvements to the meaning and clarity of several test tags
4) Updated online evaluation system at
http://sbml.org/Facilities/Online_SBML_Test_Suite

Beware that the online system is not terribly fast. We're in the process of upgrading our servers, so that will change, but it will take a while longer to finish the move.

Please report any issues or questions, either to sbml-team@caltech.edu (if it seems to be a specific problem with the system or test cases) or to the sbml-interoperability@caltech.edu mailing list (if it seems to be a philosophical issue or general point).

Here is the change log since the last update.

* Bug fixes:

- Models 00056, 00112, 00288, 00293, and 00294 had reactions with
kinetic laws that went negative, but which were flagged
'reversible=false'. They are now correctly flagged as
'reversible=true'.

- Several L1 versions of tests with algebraic rules were ambiguous
due to L1 not having the 'constant' flag. These models have been
removed.

* Changes since last update:

- Several new models tagged ReversibleReaction where a kinetic law
now goes negative.

- Tests with assigned stoichiometries have been split into two tests:
one for the L2 versions using the StoichiometryMath construct,
and one for the L3 version using rules and events to assign values
to the speciesReference id.

- The definitions of several tags have been tweaked to be clearer
and more useful. See docs\src\tags-documentation\Tags.txt for
the new definitions.

- As part of the above, many test cases have been re-tagged to
reflect the new definitions.

- Tests that assigned stoichiometries to speciesReference elements
have been split into L2 versions (using the StoichiometryMath
construct) and L3 versions (which use the speciesReference id in
rules and events to change or set the stoichiometry).

- A new program, 'generateTestsFrom' was written which takes an SBML
model as input and outputs the different translations of that model,
a generic 'settings' file, and a model description file with what
tags it can deduce from the SBML model. See src\utilities\c++\

- A new program, 'checkTestCases' was written which analyzes the
contents of a test case directory and determines whether the tags
are correct, the models are valid and present, and the settings
file is of the right basic format. See src\utilities\c++\

- We changed some cases' tolerances, because some developers
reported the cases had excessively stringent tolerances.

* New cases:

- New cases with the AssignedVariableStoichiometry tag (both L2
and L3 versions)

- New cases with the FastReaction tag

- New cases with delay equations with variable delays.

- New cases with both the HasOnlySubstanceUnits and
NonUnityCompartment tags.

- New cases with the ReversibleReaction tag where the kinetic law
goes negative during the requested simulation (as per the new
definition of the ReversibleReaction tag).

- One new 'kitchen sink' test (1000) which tests almost all tags
in one complicated model.

Note: the syntax of some gnuplot commands changed from version 4.4
to 4.6, and the script in src/utilities/plotresults/plotresults.sh
will currently not work in gnuplot 4.6. Make sure to use 4.4 if you
attempt to recreate the plots using the scripts provided in the
SBML Test Suite source directory.

-------------

Finally, we thank all the people who tried the test suite and provided feedback and corrections.

Mike and Lucian
____________________________________________________________
To manage your sbml-discuss list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/sbml-discuss

For a web interface to the sbml-discuss mailing list, visit
http://sbml.org/Forums/

For questions or feedback about the sbml-discuss list,
contact sbml-team@caltech.edu