The propagation approach for computing biochemical reaction networks Journal Article


Author(s): Henzinger, Thomas A; Mateescu, Maria
Article Title: The propagation approach for computing biochemical reaction networks
Affiliation IST Austria
Abstract: We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only "significant" mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables.
Keywords: Formal methods; chemical master equation; mathematical model; Vectors; abstract data type; Abstracts; biochemical reaction networks; Biological system modeling; Computational modeling; Equations; Numerical models; propagation models
Journal Title: IEEE ACM Transactions on Computational Biology and Bioinformatics
Volume: 10
Issue 2
ISSN: 1557-9964
Publisher: IEEE  
Date Published: 2013-08-08
Start Page: 310
End Page: 322
DOI: 10.1109/TCBB.2012.91
Open access: no
IST Austria Authors
  1. Thomas A. Henzinger
    415 Henzinger