A Metabolic Specialization of a General Purpose Modelica Library for Biological and Biochemical Systems

In the drug industry the later a substance is discharged from the drug development pipeline, the higher the financial cost. In order to reduce the number of lead compounds a number of systems have been suggested, and in most of these systems modeling and simulation of the lead compound’s effects on different metabolic pathways are essential. In these systems, substances that are expected to be harmful or lethal can be removed at an early stage. Consequently, a reduced number of promising lead compounds can be chosen for the concluding tests. Given Modelica’s previous success with huge and complex systems it is likely that it will also be suitable for modeling, simulation, and visualization of metabolic pathway systems, i.e., those systems used in the drug industry. A Modelica library designed to be used for modeling, simulation, and visualization of metabolic pathways is the special-purpose library Metabolic, an extension of the abstract Modelica library BioChem.

[1]  A Finney,et al.  Systems biology markup language: Level 2 and beyond. , 2003, Biochemical Society transactions.

[2]  P N Judson,et al.  Knowledge-based expert systems for toxicity and metabolism prediction: DEREK, StAR and METEOR. , 1999, SAR and QSAR in environmental research.

[3]  Gilles Klopman,et al.  META. 1. A Program for the Evaluation of Metabolic Transformation of Chemicals , 1994, J. Chem. Inf. Comput. Sci..

[4]  Evgeni Selkov,et al.  MPW: the Metabolic Pathways Database , 1998, Nucleic Acids Res..

[5]  Peter Fritzson,et al.  MathModelica - An Extensible Modeling and Simulation Environment with Integrated Graphics and Literate Programming , 2002 .

[6]  J. Lindon,et al.  Metabonomics: a platform for studying drug toxicity and gene function , 2002, Nature Reviews Drug Discovery.

[7]  Stina Edelfeldt,et al.  Evaluation and Comparison of Ecological Models Simulating Nitrogen Processes in Treatment Wetlands,Implemented in Modelica , 2005 .

[8]  Peter Fritzson,et al.  BioChem - A Biological and Chemical Library for Modelica , 2003 .

[9]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[10]  Minoru Kanehisa,et al.  The KEGG database. , 2002, Novartis Foundation symposium.

[11]  Antje Chang,et al.  BRENDA , the enzyme database : updates and major new developments , 2003 .

[12]  Peter A. Fritzson,et al.  Principles of object-oriented modeling and simulation with Modelica 2.1 , 2004 .

[13]  Terry Gaasterland,et al.  The metabolic pathway collection from EMP: the enzymes and metabolic pathways database , 1996, Nucleic Acids Res..

[14]  Gilles Klopman,et al.  META. 2. A Dictionary Model of Mammalian Xenobiotic Metabolism , 1994, J. Chem. Inf. Comput. Sci..

[15]  Stephen Wolfram,et al.  The Mathematica Book , 1996 .

[16]  Peter D. Karp,et al.  The EcoCyc and MetaCyc databases , 2000, Nucleic Acids Res..

[17]  Tatiana Nikolskaya,et al.  Early prediction of drug metabolism and toxicity: systems biology approach and modeling. , 2004, Drug discovery today.

[18]  Peter Fritzson,et al.  Modelica - a general object-oriented language for continuous and discrete-event system modeling and simulation , 2002, Proceedings 35th Annual Simulation Symposium. SS 2002.