1. Parameter identification in large kinetic networks with BioPARKIN
- Author
-
Dierkes, Thomas, Röblitz, Susanna, Wade, Moritz, and Deuflhard, Peter
- Subjects
Computer Science - Mathematical Software ,Computer Science - Computational Engineering, Finance, and Science ,Quantitative Biology - Quantitative Methods ,65L09 (Primary) 49M15, 65C20, 65L04, 65L80, 92C42 (Secondary) ,G.1.6 ,G.1.7 ,J.3 - Abstract
Modelling, parameter identification, and simulation play an important role in systems biology. Usually, the goal is to determine parameter values that minimise the difference between experimental measurement values and model predictions in a least-squares sense. Large-scale biological networks, however, often suffer from missing data for parameter identification. Thus, the least-squares problems are rank-deficient and solutions are not unique. Many common optimisation methods ignore this detail because they do not take into account the structure of the underlying inverse problem. These algorithms simply return a "solution" without additional information on identifiability or uniqueness. This can yield misleading results, especially if parameters are co-regulated and data are noisy., Comment: 20 pages, 7 figures, 4 tables; added 1 figure, and revised section 4
- Published
- 2013