Comparison of approaches for parameter identifiability analysis of biological systems

被引:128
作者
Raue, Andreas [1 ,2 ]
Karlsson, Johan [3 ]
Saccomani, Maria Pia [4 ]
Jirstrand, Mats [3 ]
Timmer, Jens [1 ,5 ,6 ]
机构
[1] Univ Freiburg, Inst Phys, D-79104 Freiburg, Germany
[2] Merrimack Pharmaceut Inc, Cambridge, MA 02139 USA
[3] Fraunhofer Chalmers Res Ctr Ind Math, SE-41288 Gothenburg, Sweden
[4] Univ Padua, Dept Informat Engn, I-35131 Padua, Italy
[5] Univ Freiburg, BIOSS Ctr Biol Signalling Studies, D-79104 Freiburg, Germany
[6] Univ Freiburg, Zentrum Biosyst Anal ZBSA, D-79104 Freiburg, Germany
基金
欧盟第七框架计划;
关键词
OBSERVABILITY; LIKELIHOOD; MODELS; RANGE;
D O I
10.1093/bioinformatics/btu006
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Modeling of dynamical systems using ordinary differential equations is a popular approach in the field of Systems Biology. The amount of experimental data that are used to build and calibrate these models is often limited. In this setting, the model parameters may not be uniquely determinable. Structural or a priori identifiability is a property of the system equations that indicates whether, in principle, the unknown model parameters can be determined from the available data. Results: We performed a case study using three current approaches for structural identifiability analysis for an application from cell biology. The approaches are conceptually different and are developed independently. The results of the three approaches are in agreement. We discuss strength and weaknesses of each of them and illustrate how they can be applied to real world problems.
引用
收藏
页码:1440 / 1448
页数:9
相关论文
共 17 条
[1]   Minimal output sets for identifiability [J].
Anguelova, Milena ;
Karlsson, Johan ;
Jirstrand, Mats .
MATHEMATICAL BIOSCIENCES, 2012, 239 (01) :139-153
[2]   Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range [J].
Bachmann, Julie ;
Raue, Andreas ;
Schilling, Marcel ;
Boehm, Martin E. ;
Kreutz, Clemens ;
Kaschek, Daniel ;
Busch, Hauke ;
Gretz, Norbert ;
Lehmann, Wolf D. ;
Timmer, Jens ;
Klingmueller, Ursula .
MOLECULAR SYSTEMS BIOLOGY, 2011, 7
[3]   Covering a Broad Dynamic Range: Information Processing at the Erythropoietin Receptor [J].
Becker, Verena ;
Schilling, Marcel ;
Bachmann, Julie ;
Baumann, Ute ;
Raue, Andreas ;
Maiwald, Thomas ;
Timmer, Jens ;
Klingmueller, Ursula .
SCIENCE, 2010, 328 (5984) :1404-1408
[4]  
BELLMAN R, 1970, Mathematical Biosciences, V7, P329, DOI 10.1016/0025-5564(70)90132-X
[5]   DAISY:: A new software tool to test global identifiability of biological and physiological systems [J].
Bellu, Giuseppina ;
Saccomani, Maria Pia ;
Audoly, Stefania ;
D'Angio, Leontina .
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, 2007, 88 (01) :52-61
[6]  
Karlsson J, 2012, P 16 IFAC S SYST ID
[7]   Likelihood based observability analysis and confidence intervals for predictions of dynamic models [J].
Kreutz, Clemens ;
Raue, Andreas ;
Timmer, Jens .
BMC SYSTEMS BIOLOGY, 2012, 6
[8]  
Lindskog P., 1996, THESIS LINKOPING U S
[9]   Dynamical modeling and multi-experiment fitting with PottersWheel [J].
Maiwald, Thomas ;
Timmer, Jens .
BIOINFORMATICS, 2008, 24 (18) :2037-2043
[10]   SYSTEM IDENTIFIABILITY BASED ON POWER-SERIES EXPANSION OF SOLUTION [J].
POHJANPALO, H .
MATHEMATICAL BIOSCIENCES, 1978, 41 (1-2) :21-33