Quantitative analysis of numerical solvers for oscillatory biomolecular system models

Background: 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...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Chang F. Quo, May D. Wang
• Keywords: BMCBI 2008, MATLAB Numerical Solvers, Numerical Solvers, Optimal Numerical Solver