---
_id: '2302'
abstract:
- lang: eng
  text: '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.'
article_processing_charge: No
author:
- first_name: Thomas A
  full_name: Henzinger, Thomas A
  id: 40876CD8-F248-11E8-B48F-1D18A9856A87
  last_name: Henzinger
  orcid: 0000−0002−2985−7724
- first_name: Maria
  full_name: Mateescu, Maria
  id: 3B43276C-F248-11E8-B48F-1D18A9856A87
  last_name: Mateescu
citation:
  ama: Henzinger TA, Mateescu M. The propagation approach for computing biochemical
    reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>.
    2012;10(2):310-322. doi:<a href="https://doi.org/10.1109/TCBB.2012.91">10.1109/TCBB.2012.91</a>
  apa: Henzinger, T. A., &#38; Mateescu, M. (2012). The propagation approach for computing
    biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology
    and Bioinformatics</i>. IEEE. <a href="https://doi.org/10.1109/TCBB.2012.91">https://doi.org/10.1109/TCBB.2012.91</a>
  chicago: Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for
    Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational
    Biology and Bioinformatics</i>. IEEE, 2012. <a href="https://doi.org/10.1109/TCBB.2012.91">https://doi.org/10.1109/TCBB.2012.91</a>.
  ieee: T. A. Henzinger and M. Mateescu, “The propagation approach for computing biochemical
    reaction networks,” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>,
    vol. 10, no. 2. IEEE, pp. 310–322, 2012.
  ista: Henzinger TA, Mateescu M. 2012. The propagation approach for computing biochemical
    reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics.
    10(2), 310–322.
  mla: Henzinger, Thomas A., and Maria Mateescu. “The Propagation Approach for Computing
    Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology
    and Bioinformatics</i>, vol. 10, no. 2, IEEE, 2012, pp. 310–22, doi:<a href="https://doi.org/10.1109/TCBB.2012.91">10.1109/TCBB.2012.91</a>.
  short: T.A. Henzinger, M. Mateescu, IEEE ACM Transactions on Computational Biology
    and Bioinformatics 10 (2012) 310–322.
corr_author: '1'
date_created: 2018-12-11T11:56:52Z
date_published: 2012-07-03T00:00:00Z
date_updated: 2025-09-29T14:17:43Z
day: '03'
department:
- _id: ToHe
- _id: CaGu
doi: 10.1109/TCBB.2012.91
ec_funded: 1
external_id:
  isi:
  - '000323504100006'
  pmid:
  - '22778152'
intvolume: '        10'
isi: 1
issue: '2'
language:
- iso: eng
month: '07'
oa_version: None
page: 310 - 322
pmid: 1
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '267989'
  name: Quantitative Reactive Modeling
publication: IEEE ACM Transactions on Computational Biology and Bioinformatics
publication_status: published
publisher: IEEE
publist_id: '4625'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The propagation approach for computing biochemical reaction networks
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 10
year: '2012'
...