SBML Test Suite
Stable version: 3.2.0, released 29 June 2016 (see box at right →)
Latest stable version of test cases archive released 29 June 2016.
Development version: 3.3.0 alpha, released 17 Oct. 2016 from GitHub.
The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package. The tests are syntactic and semantic in nature.
Components and facilities
The current SBML Test Suite consists of the following components:
- A collection of SBML models, together with expected results, that can be used to test interpretation of SBML files. There are 3 sets of tests: semantic (for deterministic simulation behavior), stochastic (for stochastic simulation behavior), and syntactic (for basic parsing). The sets of test cases can be downloaded separately as complete archives.
- The SBML Test Runner, a standalone application that can be used to run an application against the collection of semantic test cases, and report successes and failures.
- An online database of test results provided by software authors for their SBML-compatible software packages.
You can download the archive of test cases, then arrange to run them in an SBML-compatible program to produce numerical results. The format of the test cases is described on a separate page. For the semantic test cases, we offer a standalone SBML Test Runner; to use it, first download the applicadtion, configure a wrapper program for the SBML-compatible application you want to test, and run the SBML Test Runner to see the results. A description of the wrapper interface is provided in the SBML Test Runner's built-in help system.
If you are a developer of an SBML-compatible simulation system, we encourage you to upload the results of your tests to the SBML Test Suite Database. This system provides a public database of results for various SBML-compatible software systems, and serves to advertise your software's capabilities.
SBML Test Suite release DOIs
We provide Zenodo DOIs for specific releases, so that you can cite the exact version of the software that you use:
- SBML Test Suite 3.2.0 test case archives:
SBML Test Suite contributors
The SBML Test Suite has been developed over many years, with the contributions of many people. The following are the primary authors of the three separate test-case collections:
- Semantic test suite: Sarah M. Keating (a,b), Lucian P. Smith (b,c), Bruce E. Shapiro (b), Michael Hucka (b), Frank T. Bergmann (d), Brett Olivier (g), Andrew Finney (b)
- Stochastic test suite: Thomas W. Evans (e), Colin S. Gillespie (f), Darren J. Wilkinson (f), Lucian P. Smith (b,c)
- Syntactic test suite: Sarah M. Keating (a,b), Lucian P. Smith (b,c)
Additional contributions are gratefully acknowledged from Ralph Gauges (h), Chris Myers (i), Akira Funahashi (j), Andreas Dräger (k), Roland Keller (k), Fedor Kolpakov (l), Stanley Gu (c), and others in the SBML community.
(a) EMBL-EBI, Hinxton, Cambridgeshire, UK
(b) California Institute of Technology, Pasadena, CA, US
(c) University of Washington, Seattle, WA, US
(d) University of Heidelberg, Heidelberg, DE
(e) University of Liverpool, Liverpool, UK
(f) Newcastle University, Newcastle, UK
(g) Vrije Universiteit Amsterdam, NL
(h) Heidelberg Institute for Theoretical Studies, Heidelberg, DE
(i) University of Utah, Salt Lake City, UT, US
(j) Systems Biology Institute, Tokyo, JP
(k) University of Tuebingen, Tübingen, DE
(l) Institute of Systems Biology, Novosibirsk, RU