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Literature DB >> 35352101

Hybrid modelling of biological systems: current progress and future prospects.

Fei Liu¹, Monika Heiner², David Gilbert³.

Abstract

Integrated modelling of biological systems is becoming a necessity for constructing models containing the major biochemical processes of such systems in order to obtain a holistic understanding of their dynamics and to elucidate emergent behaviours. Hybrid modelling methods are crucial to achieve integrated modelling of biological systems. This paper reviews currently popular hybrid modelling methods, developed for systems biology, mainly revealing why they are proposed, how they are formed from single modelling formalisms and how to simulate them. By doing this, we identify future research requirements regarding hybrid approaches for further promoting integrated modelling of biological systems.

Entities: Chemical

Keywords: biological modelling; hybrid modelling; modelling formalisms

Mesh：

Year: 2022 PMID： 35352101 PMCID： PMC9116374 DOI： 10.1093/bib/bbac081

Source DB: PubMed Journal: Brief Bioinform ISSN： 1467-5463 Impact factor: 13.994

Keyword Cloud
References

63 in total

1. A fuzzy logic approach to analyzing gene expression data.

Authors: P J Woolf; Y Wang
Journal: Physiol Genomics Date: 2000-06-29 Impact factor: 3.107

2. Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle.

Authors: Zhen Liu; Yang Pu; Fei Li; Clifford A Shaffer; Stefan Hoops; John J Tyson; Yang Cao
Journal: J Chem Phys Date: 2012-01-21 Impact factor: 3.488

3. SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks.

Authors: Albert Gevorgyan; Michael E Bushell; Claudio Avignone-Rossa; Andrzej M Kierzek
Journal: Bioinformatics Date: 2010-12-09 Impact factor: 6.937

4. SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.

Authors: M Ander; P Beltrao; B Di Ventura; J Ferkinghoff-Borg; M Foglierini; A Kaplan; C Lemerle; I Tomás-Oliveira; L Serrano
Journal: Syst Biol (Stevenage) Date: 2004-06

Hybrid modelling of biological systems: current progress and future prospects.

1. A fuzzy logic approach to analyzing gene expression data.

2. Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle.

3. SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks.

4. SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.

5. Gene Expression Integration into Pathway Modules Reveals a Pan-Cancer Metabolic Landscape.

6. Modeling formalisms in Systems Biology.

7. Rule-based multi-level modeling of cell biological systems.

Review 8. A Review of Cell-Based Computational Modeling in Cancer Biology.

9. Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking.

10. Coloured Petri nets for multilevel, multiscale and multidimensional modelling of biological systems.