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Virtual Cell - Technology

National Resource for Cell Analysis and Modeling

Testing Framework

Dependable performance, in particular validity and reproducibility of results, are critical requirements for a modeling environment. Extensive testing must be carried out to ensure this performance.

Testing needs to be tailored to particular systems. Not all models will utilize all components within the modeling environment therefore test strategies need to be designed to focus on particular areas. The modular design of the Virtual Cell: modeling framework, math framework and user interface, helps to tackle this issue. The program can be readily decomposed into separate independent components which reduces the complexity of the testing scheme.

Numerics Testing Framework
The numerics testing framework consists of the following:

  • Generate "constructed" solutions by adding explicit forcing functions. This exercises the code for arbitrarily complex models and handles arbitrary analytic geometry using analytic normals.
  • Verify accuracy and convergence against exact solutions
  • Math tests are specified in declarative math language. The code generation eliminates test code maintenance and facilitates regression testing, and makes the numerics more nimble.
  • Regression Testing or verification testing. Old test cases are run against the new version to ensure functionality.
  • Finite difference sensitivities are calculated to verify the accuracy of the Sensitivity Analysis option for ODE simulations.
  • Report generation - extensive reports are generated with the results to the testing scheme.

Expression Testing

  • Evaluate, parse, simplify, differentiate, evaluate intervals, narrow intervals.

Math Verifier

  • Regenerates math for every BioModel in database .
  • Equivalence of math systems (canonical reduced form)

SBML Testing

  • Testing framework to import models from Biomodels.net database (www.ebi.ac.uk/biomodels-main) into COPASI, MathSBML and Virtual Cell; create and run simulations in each tool and report the simulation comparison results between the tools.