---
res:
bibo_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.@eng'
bibo_authorlist:
- foaf_Person:
foaf_givenName: Thomas A
foaf_name: Henzinger, Thomas A
foaf_surname: Henzinger
foaf_workInfoHomepage: http://www.librecat.org/personId=40876CD8-F248-11E8-B48F-1D18A9856A87
orcid: 0000−0002−2985−7724
- foaf_Person:
foaf_givenName: Maria
foaf_name: Mateescu, Maria
foaf_surname: Mateescu
foaf_workInfoHomepage: http://www.librecat.org/personId=3B43276C-F248-11E8-B48F-1D18A9856A87
bibo_doi: 10.1109/TCBB.2012.91
bibo_issue: '2'
bibo_volume: 10
dct_date: 2012^xs_gYear
dct_language: eng
dct_publisher: IEEE@
dct_title: The propagation approach for computing biochemical reaction networks@
fabio_hasPubmedId: '22778152'
...