Abstract

Short Communication

Computational Models in Systems and Synthetic Biology: Short Overview

Marian Gheorghe*

Published: 18 January, 2024 | Volume 8 - Issue 1 | Pages: 001-002

Computational models used in specifying biological systems represent a complement and become an alternative to more widely used mathematical models. Amongst some of the advantages brought by these computational models, one can mention their executable semantics and mechanistic way of describing biological system phenomena. This short overview report enumerated some of the computational models utilised so far in systems and synthetic biology, the associated analysis and formal verification methods and tools, and a way of facilitating a broader use of this alternative approach.

Read Full Article HTML DOI: 10.29328/journal.abb.1001037 Cite this Article Read Full Article PDF

Keywords:

System and synthetic biology; Executable biology; Computational models; Formal methods; Model checking; User-friendly modelling; Healthcare; Cyber-physical systems

References

  1. Garavel H, Beek MHT, Van de Pol J. The 2020 Expert Survey on Formal Methods, Formal Methods for Industrial Critical Systems (FMICS 2020). LNCS 12327, Springer 2020. 
  2. Bartocci E, Lió P. Computational Modeling, Formal Analysis, and Tools for Systems Biology. PLoS Comput Biol. 2016 Jan 21;12(1):e1004591. doi: 10.1371/journal.pcbi.1004591. PMID: 26795950; PMCID: PMC4721667.
  3. Konur S, Gheorghe M, Krasnogor N. Verifiable biology. J R Soc Interface. 2023 May;20(202):20230019. doi: 10.1098/rsif.2023.0019. Epub 2023 May 10. PMID: 37160165; PMCID: PMC10169095.
  4. Mitra ED, Suderman R, Colvin J, Ionkov A, Hu A, Sauro HM, Posner RG, Hlavacek WS. PyBioNetFit and the Biological Property Specification Language. iScience. 2019 Sep 27; 19:1012-1036. doi: 10.1016/j.isci.2019.08.045. Epub 2019 Aug 28. PMID: 31522114; PMCID: PMC6744527.
  5. Hall BA, Fisher J. Constructing and Analyzing Computational Models of Cell Signaling with BioModelAnalyzer. Curr Protoc Bioinformatics. 2020 Mar; 69(1):e95. doi: 10.1002/cpbi.95. PMID: 32078258.
  6. Konur S, Gheorghe M, Dragomir C, Mierla L, Ipate F, Krasnogor N. Qualitative and quantitative analysis of systems and synthetic biology constructs using P systems. ACS Synth Biol. 2015 Jan 16;4(1):83-92. doi: 10.1021/sb500134w. Epub 2014 Aug 14. PMID: 25090609.

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