An algorithm for initial fluxes of metabolic P systems
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Here a heuristic algorithm for estimating the initial fluxes of biological reactions by starting from experimental data is proposed, that is tested in two case studies.Abstract:
A central issue in systems biology is the study of efficient methods inferring fluxes of biological reactions by starting from experimental data. Among the different techniques proposed in the last years, the theory of Metabolic P systems, which is based on the Log-Gain principle, proved to be helpful for deducing biologi- cal fluxes from temporal series of observed dynamics. According to this approach, the algebraic systems provided by the Log-Gain principle determine the reaction fluxes underlying a system dynamics when initial fluxes are known. Here we propose a heuristic algorithm for estimating the initial fluxes, that is tested in two case studies.read more
Citations
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Journal ArticleDOI
Data analysis pipeline from laboratory to MP models
TL;DR: A workflow for data analysis is introduced to synthesize flux regulation maps of a Metabolic P system from time series of data observed in laboratory, and interesting experimental results came out in the context of their residual analysis for model validation.
Book ChapterDOI
From p to MP systems
TL;DR: A synthetic algebraic formulation of MP system is given, and the log-gain theory of MP systems is outlined, by discussing the research perspectives and the methodological aspects of this approach.
Proceedings ArticleDOI
Metabolic Computing
TL;DR: This paper thinks that this metabolic computing model has both high fault tolerance and sustainability, and proposes two new algorithms, namely bubbling and drifting, which are proposed in this paper.
Book ChapterDOI
Regulation and covering problems in MP systems
TL;DR: Some initial results are reported regarding the efficient computation of regulation fluxes in metabolic P systems by means of Log-gain theory, which shows that the system dynamics can be linearized, in such a way to be described by a recurrence equations system.
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