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用于生成生物网络的简化计算模型。

Simplified computational model for generating biological networks.

作者信息

Bailey Matthew H J, Ormrod Morley David, Wilson Mark

机构信息

Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford South Parks Road Oxford OX1 3QZ UK

出版信息

RSC Adv. 2020 Oct 16;10(63):38275-38280. doi: 10.1039/d0ra06205g. eCollection 2020 Oct 15.

Abstract

A method to generate and simulate biological networks is discussed. An expanded Wooten-Winer-Weaire bond switching methods is proposed which allows for a distribution of node degrees in the network while conserving the mean average node degree. The networks are characterised in terms of their polygon structure and assortativities (a measure of local ordering). A wide range of experimental images are analysed and the underlying networks quantified in an analogous manner. Limitations in obtaining the network structure are discussed. A "network landscape" of the experimentally observed and simulated networks is constructed from the underlying metrics. The enhanced bond switching algorithm is able to generate networks spanning the full range of experimental observations.

摘要

讨论了一种生成和模拟生物网络的方法。提出了一种扩展的伍滕 - 维纳 - 韦尔键切换方法,该方法允许网络中节点度的分布,同时保持平均节点度不变。这些网络根据其多边形结构和 assortativities(局部有序性的一种度量)进行表征。分析了广泛的实验图像,并以类似方式对基础网络进行量化。讨论了获取网络结构的局限性。根据基础度量构建了实验观察和模拟网络的“网络景观”。增强的键切换算法能够生成涵盖所有实验观察范围的网络。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6cc/9057274/9048ae02a860/d0ra06205g-f1.jpg

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