ASSA-PBN 3.0: Analysing Context-Sensitive Probabilistic Boolean Networks

Andrzej Mizera; Jun Pang; Hongyang Qu; Qixia Yuan

doi:10.1007/978-3-319-99429-1_16

ASSA-PBN 3.0: Analysing Context-Sensitive Probabilistic Boolean Networks

Andrzej Mizera, Jun Pang, Hongyang Qu, Qixia Yuan

Nutrition, Microbiome and Immunity

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

1 Citation (Scopus)

Abstract

We present a major new release of ASSA-PBN, a software tool for modelling, simulation, and analysis of probabilistic Boolean networks (PBNs). The new version enables the support for context-sensitive PBNs (CPBNs), which can well balance the uncertainty and stability of the modelled biological systems. It contributes mainly in three aspects. Firstly, it designs a high-level language for specifying CPBNs. Secondly, it implements various simulation-based methods for simulating CPBNs and analysing their long-run dynamics. Last but not least, it provides an efficient method to identify all the attractors of a CPBN. Thanks to its divide and conquer strategy, the implemented detection algorithm can deal with large and realistic biological networks under both synchronous and asynchronous updating schemes.

Original language	English
Title of host publication	Computational Methods in Systems Biology (CMSB 2018). 16th international conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings
Publisher	Springer
Pages	277-284
Number of pages	8
Volume	11095
ISBN (Electronic)	978-3-319-99429-1
ISBN (Print)	978-3-319-99428-4
DOIs	https://doi.org/10.1007/978-3-319-99429-1_16
Publication status	Published - 24 Aug 2018

Publication series

Name	Lecture Notes in Bioinformatics

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10.1007/978-3-319-99429-1_16

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Mizera, A., Pang, J., Qu, H., & Yuan, Q. (2018). ASSA-PBN 3.0: Analysing Context-Sensitive Probabilistic Boolean Networks. In Computational Methods in Systems Biology (CMSB 2018). 16th international conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings (Vol. 11095, pp. 277-284). (Lecture Notes in Bioinformatics). Springer. https://doi.org/10.1007/978-3-319-99429-1_16

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title = "ASSA-PBN 3.0: Analysing Context-Sensitive Probabilistic Boolean Networks",

abstract = "We present a major new release of ASSA-PBN, a software tool for modelling, simulation, and analysis of probabilistic Boolean networks (PBNs). The new version enables the support for context-sensitive PBNs (CPBNs), which can well balance the uncertainty and stability of the modelled biological systems. It contributes mainly in three aspects. Firstly, it designs a high-level language for specifying CPBNs. Secondly, it implements various simulation-based methods for simulating CPBNs and analysing their long-run dynamics. Last but not least, it provides an efficient method to identify all the attractors of a CPBN. Thanks to its divide and conquer strategy, the implemented detection algorithm can deal with large and realistic biological networks under both synchronous and asynchronous updating schemes.",

author = "Andrzej Mizera and Jun Pang and Hongyang Qu and Qixia Yuan",

year = "2018",

month = aug,

day = "24",

doi = "10.1007/978-3-319-99429-1_16",

language = "English",

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volume = "11095",

series = "Lecture Notes in Bioinformatics",

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pages = "277--284",

booktitle = "Computational Methods in Systems Biology (CMSB 2018). 16th international conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings",

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Mizera, A, Pang, J, Qu, H & Yuan, Q 2018, ASSA-PBN 3.0: Analysing Context-Sensitive Probabilistic Boolean Networks. in Computational Methods in Systems Biology (CMSB 2018). 16th international conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings. vol. 11095, Lecture Notes in Bioinformatics, Springer, pp. 277-284. https://doi.org/10.1007/978-3-319-99429-1_16

ASSA-PBN 3.0: Analysing Context-Sensitive Probabilistic Boolean Networks. / Mizera, Andrzej; Pang, Jun; Qu, Hongyang et al.
Computational Methods in Systems Biology (CMSB 2018). 16th international conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings. Vol. 11095 Springer, 2018. p. 277-284 (Lecture Notes in Bioinformatics).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

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AB - We present a major new release of ASSA-PBN, a software tool for modelling, simulation, and analysis of probabilistic Boolean networks (PBNs). The new version enables the support for context-sensitive PBNs (CPBNs), which can well balance the uncertainty and stability of the modelled biological systems. It contributes mainly in three aspects. Firstly, it designs a high-level language for specifying CPBNs. Secondly, it implements various simulation-based methods for simulating CPBNs and analysing their long-run dynamics. Last but not least, it provides an efficient method to identify all the attractors of a CPBN. Thanks to its divide and conquer strategy, the implemented detection algorithm can deal with large and realistic biological networks under both synchronous and asynchronous updating schemes.

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Mizera A, Pang J, Qu H, Yuan Q. ASSA-PBN 3.0: Analysing Context-Sensitive Probabilistic Boolean Networks. In Computational Methods in Systems Biology (CMSB 2018). 16th international conference, CMSB 2018, Brno, Czech Republic, September 12-14, 2018, Proceedings. Vol. 11095. Springer. 2018. p. 277-284. (Lecture Notes in Bioinformatics). doi: 10.1007/978-3-319-99429-1_16

ASSA-PBN 3.0: Analysing Context-Sensitive Probabilistic Boolean Networks

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