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Parameter identification in large kinetic networks with BioPARKIN

Please always quote using this URN:urn:nbn:de:0296-matheon-12398
  • Motivation. 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. Results. The Gauss-Newton method presented in this paper monitors the numerical rank of the Jacobian and converges locally, for the class of adequate problems, to a solution that is unique within the subspace of identifiable parameters. This method has been implemented in BioPARKIN, a software package that combines state-of-the-art numerical algorithms with compliance to system biology standards, most importantly SBML, and an accessible interface. Availability. The software package BioPARKIN is available for download at http://bioparkin.zib.de .

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Metadaten
Author:Thomas Dierkes, Susanna Röblitz, Moritz Wade, Peter Deuflhard
URN:urn:nbn:de:0296-matheon-12398
Referee:Alexander Bockmayr
Document Type:Preprint, Research Center Matheon
Language:English
Date of first Publication:2013/07/20
Release Date:2013/07/20
Tag:affine invariant Gauss-Newton algorithm; graphical user interface; numerical library; ordinary differential equations; parameter identification; sensitivity analysis; systems biology
Institute:Zuse Institute Berlin (ZIB)
MSC-Classification:65-XX NUMERICAL ANALYSIS / 65Lxx Ordinary differential equations / 65L09 Inverse problems
68-XX COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section {04 in that areag 68-00 General reference works (handbooks, dictionaries, bibliographies, etc.) / 68Nxx Software / 68N19 Other programming techniques (object-oriented, sequential, concurrent, automatic, etc.)
68-XX COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section {04 in that areag 68-00 General reference works (handbooks, dictionaries, bibliographies, etc.) / 68Uxx Computing methodologies and applications / 68U20 Simulation [See also 65Cxx]
92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92Cxx Physiological, cellular and medical topics / 92C42 Systems biology, networks
92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92Cxx Physiological, cellular and medical topics / 92C45 Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) [See also 80A30]
Preprint Number:1024
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