This article is part of the supplement: Symposium of Computations in Bioinformatics and Bioscience (SCBB07)
Quantitative analysis of numerical solvers for oscillatory biomolecular system models
1 Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
2 School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
3 Hematology and Oncology, Winship Cancer Institute, Emory University, Altanta, GA 30322, USA
4 The Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
BMC Bioinformatics 2008, 9(Suppl 6):S17 doi:10.1186/1471-2105-9-S6-S17Published: 28 May 2008
This article provides guidelines for selecting optimal numerical solvers for biomolecular system models. Because various parameters of the same system could have drastically different ranges from 10-15 to 1010, the ODEs can be stiff and ill-conditioned, resulting in non-unique, non-existing, or non-reproducible modeling solutions. Previous studies have not examined in depth how to best select numerical solvers for biomolecular system models, which makes it difficult to experimentally validate the modeling results. To address this problem, we have chosen one of the well-known stiff initial value problems with limit cycle behavior as a test-bed system model. Solving this model, we have illustrated that different answers may result from different numerical solvers. We use MATLAB numerical solvers because they are optimized and widely used by the modeling community. We have also conducted a systematic study of numerical solver performances by using qualitative and quantitative measures such as convergence, accuracy, and computational cost (i.e. in terms of function evaluation, partial derivative, LU decomposition, and "take-off" points). The results show that the modeling solutions can be drastically different using different numerical solvers. Thus, it is important to intelligently select numerical solvers when solving biomolecular system models.
The classic Belousov-Zhabotinskii (BZ) reaction is described by the Oregonator model and is used as a case study. We report two guidelines in selecting optimal numerical solver(s) for stiff, complex oscillatory systems: (i) for problems with unknown parameters, ode45 is the optimal choice regardless of the relative error tolerance; (ii) for known stiff problems, both ode113 and ode15s are good choices under strict relative tolerance conditions.
For any given biomolecular model, by building a library of numerical solvers with quantitative performance assessment metric, we show that it is possible to improve reliability of the analytical modeling, which in turn can improve the efficiency and effectiveness of experimental validations of these models. Also, our study can be extended to study a variety of molecular-level system models for human disease diagnosis and therapeutic treatment.