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The Propagation Approach for Computing Biochemical Reaction Networks
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Thomas A. Henzinger,Maria Mateescu
Issue Date:March 2013
pp. 310-322
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 regardi...
 
SABRE: A Tool for Stochastic Analysis of Biochemical Reaction Networks
Found in: Quantitative Evaluation of Systems, International Conference on
By Frederic Didier, Thomas A. Henzinger, Maria Mateescu, Verena Wolf
Issue Date:September 2010
pp. 193-194
The importance of stochasticity within biological systems has been shown repeatedly during the last years and has raised the need for efficient stochastic tools. We present SABRE, a tool for stochastic analysis of biochemical reaction networks. SABRE imple...
 
Fast Adaptive Uniformization of the Chemical Master Equation
Found in: High Performance Computational Systems Biology, International Workshop on
By Frederic Didier, Thomas A. Henzinger, Maria Mateescu, Verena Wolf
Issue Date:October 2009
pp. 118-127
Within systems biology there is an increasing interest in the stochastic behavior of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous-time Markov chain (CTMC). S...
 
The Propagation Approach for Computing Biochemical Reaction Networks
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Maria Mateescu, Thomas A. Henzinger
Issue Date:March 2013
pp. 310-322
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 regardi...
     
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