Article | Proceedings of the 9th International MODELICA Conference; September 3-5; 2012; Munich; Germany | ADGenKinetics: An Algorithmically Differentiated Library for Biochemical Networks Modeling via Simplified Kinetics Formats

Title:
ADGenKinetics: An Algorithmically Differentiated Library for Biochemical Networks Modeling via Simplified Kinetics Formats
Author:
Atiyah Elsheikh: Austrian Institute of Technology, Vienna, Austria
DOI:
10.3384/ecp12076915
Download:
Full text (pdf)
Year:
2012
Conference:
Proceedings of the 9th International MODELICA Conference; September 3-5; 2012; Munich; Germany
Issue:
076
Article no.:
095
Pages:
915-926
No. of pages:
12
Publication type:
Abstract and Fulltext
Published:
2012-11-19
ISBN:
978-91-7519-826-2
Series:
Linköping Electronic Conference Proceedings
ISSN (print):
1650-3686
ISSN (online):
1650-3740
Publisher:
Linköping University Electronic Press; Linköpings universitet


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This work demonstrates the compact but powerful freely available Modelica library ADGenKinetics for descriptive modeling of biochemical reaction networks using simplified kinetics formats. While existing powerful works and guidelines for modeling biochemical reaction networks based on classical mechanistic kinetics already exist; in this work a first attempt of utilizing the power of Modelica constructs for providing a compact implementation of simplified kinetic formats with generalized structured formulas is presented. This gives the opportunity of realizing biochemical reaction networks using few number of reaction components; in contrast to libraries based on classical mechanistic kinetics which require hundreds of reaction components. ADGenKinetics is the first algorithmically differentiated Modelica library that is enhanced with differentiated components by which parameter sensitivities are additionally computed with minimal efforts from the user perspective.

Keywords: Enzyme Kinetics; Biochemical Reaction Networks; Systems Biology; Algorithmic Differentiation

Proceedings of the 9th International MODELICA Conference; September 3-5; 2012; Munich; Germany

Author:
Atiyah Elsheikh
Title:
ADGenKinetics: An Algorithmically Differentiated Library for Biochemical Networks Modeling via Simplified Kinetics Formats
DOI:
http://dx.doi.org/10.3384/ecp12076915
References:
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Proceedings of the 9th International MODELICA Conference; September 3-5; 2012; Munich; Germany

Author:
Atiyah Elsheikh
Title:
ADGenKinetics: An Algorithmically Differentiated Library for Biochemical Networks Modeling via Simplified Kinetics Formats
DOI:
http://dx.doi.org/10.3384/ecp12076915
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