BioPARKIN - Biology-related Parameter Identification in Large Kinetic Networks

Please always quote using this URN: urn:nbn:de:0297-zib-12706
  • Modelling, parameter identification, and simulation play an important rôle in Systems Biology. In recent years, various software packages have been established for scientific use in both licencing types, open source as well as commercial. Many of these codes are based on inefficient and mathematically outdated algorithms. By introducing the package BioPARKIN recently developed at ZIB, we want to improve this situation significantly. The development of the software BioPARKIN involves long standing mathematical ideas that, however, have not yet entered the field of Systems Biology, as well as new ideas and tools that are particularly important for the analysis of the dynamics of biological networks. BioPARKIN originates from the package PARKIN, written by P.Deuflhard and U.Nowak, that has been applied successfully for parameter identification in physical chemistry for many years.

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Author:Thomas Dierkes, Moritz Wade, Ulrich Nowak, Susanna Röblitz
Document Type:ZIB-Report
Tag:affine invariant Gauss-Newton algorithm; graphical user interface; numerical library; ordinary differential equations; parameter identification; sensitivity analysis; systems biology
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 area) / 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 area) / 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]
Year of first publication:2011
Series (Serial Number):ZIB-Report (11-15)

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