Fully Automated Attractor Analysis of Cyanobacteria Models

Beneš, Nikola; Brim, Luboš; Pastva, Samuel; Šafránek, David; Troják, Matej; Červený, Jan; Šalagovič, Jakub

doi:10.1109/icstcc.2018.8540762

Cited by 3 publications

(2 citation statements)

References 18 publications

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“…Both tools were successfully used on various biological case studies but so far they have been employed only separately (Pithya [34,37,38,56,57,58,59,60] and Parasim [46,48]). In this paper, we combine their application on a single model for the first time.…”

Section: Methodsmentioning

confidence: 99%

Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway

et al. 2019

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In our previous work, we designed and implemented a synthetic metabolic pathway for 1,2,3-trichloropropane (TCP) biodegradation in Escherichia coli. Significant effects of metabolic burden and toxicity exacerbation were observed on single cell and population levels. Deeper understanding of mechanisms underlying these effects is extremely important for metabolic engineering of efficient microbial cell factories for biotechnological processes. In this paper, we present a novel mathematical model of the pathway. The model addresses for the first time the combined effects of toxicity exacerbation and metabolic burden in the context of bacterial population growth. The model is calibrated with respect to the real data obtained with our original synthetically modified E. coli strain. Using the model, we explore the dynamics of the population growth along with the outcome of the TCP biodegradation pathway considering the toxicity exacerbation and metabolic burden. On the methodological side, we introduce a unique computational workflow utilising algorithmic methods of computer science for the particular modelling problem.

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Section: Methodsmentioning

confidence: 99%

Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway

et al. 2019

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“…We have developed an efficient parallel algorithm for detecting tSCCs in parametrised graphs in [1], and we use this algorithm in our two case studies. We have already successfully applied the digital bifurcation analysis to several models from systems biology [4,5].…”

Section: Introductionmentioning

confidence: 99%

Digital Bifurcation Analysis of TCP Dynamics

Beneš

Brim

Pastva

et al. 2019

Tools and Algorithms for the Construction and Analysis of Systems

Self Cite

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Digital bifurcation analysis is a new algorithmic method for exploring how the behaviour of a parameter-dependent computer system varies with a change in its parameters and, in particular, for identification of bifurcation points where such variation becomes dramatic. We have developed the method in an analogy with the traditional bifurcation theory and have it successfully applied to models taken from systems biology. In this case study paper, we demonstrate the appropriateness and usefulness of the digital bifurcation analysis as a push-button alternative to the classical approaches as traditionally used for analysing the stability of TCP/IP protocols. We consider two typical examples (congestion control and buffer sizes throughput influence) and show that the method provides the same results as obtained with classical non-automatic analytical and numerical methods.

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Study of Piecewise Multi-affine models for Genetic Regulatory Networks via a Lyapunov approach: an LMI framework

Pasquini

Angeli

2020

IFAC-PapersOnLine

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Fully Automated Attractor Analysis of Cyanobacteria Models

Cited by 3 publications

References 18 publications

Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway

Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway

Digital Bifurcation Analysis of TCP Dynamics

Study of Piecewise Multi-affine models for Genetic Regulatory Networks via a Lyapunov approach: an LMI framework

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