The parameter estimator takes a biological model, experimental data, and the relationship between the model and data. Using this information the parameter estimator uses numerical tools to vary the parameters to the model looking for the parameters that best fit the experimental data.
The user of the parameter estimator must give the estimator a biological model in the form of ordinary differential equations, experimental data in the form of numbers, and the relationship between the model and data in the form of FORTRAN 90 code. The first two of these is fairly trivial for someone already involved in biological models. The last can be a difficult task for anyone not familiar with both biological modelling and FORTRAN 90. The difficulty of this task may be addressed in a larger project involving the parameter estimator but is beyond the scope of the this research.
The parameter estimator depends on ODRPACK for minimizing the error between the model data and experimental data. The parameter estimator depends on LSODAR to solve the system of ODE's numerically. The solutions are used to generate model data which is fed into ODRPACK as information used to adjust the parameters. There is a system diagram showing how everything fits together inside the parameter estimator.
Papers
Estimating Rate Constants in
Cell Cycle Models describes the first version of the parameter estimator and
the results of using the parameter estimator on a simple 3 parameter model.
Parameter Estimation In Biological Cell Cycle Models Using Deterministic Optimization describes in detail the parameter estimator and 3 models where parameter estimation was done. Source code is included in this thesis (as of 2001-11-05 this is a work in progress).
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