蛋白质和膜相互作用的框架
A framework for protein and membrane interactions
摘要：
我们介绍了BioBeta框架，这是一个活细胞蛋白质水平和膜水平相互作用的元模型。这种形式主义旨在提供一种形式化的设置，在该设置中，在不同的抽象级别上对模型进行编码、比较和合并;特别地，可以根据低级别（即，蛋白质）相互作用。BioBeta规范提供了一个蛋白质签名，以及一组蛋白质反应，本着卡帕演算的精神。此外，该说明书描述了蛋白质构型何时触发仅有的两种允许的膜相互作用之一，即“夹持”和“融合”。本文定义了BioBeta的语法和语义，分析了它的性质，将其解释为生物传记反应系统，并通过与卡帕演算的比较和对重要实例的建模来讨论它的表达能力。值得注意的是，BioBeta是基于相同目的的双图元模型设计的。因此，演算的每个实例对应于一个双图反应系统，反之亦然（几乎）。因此，我们可以继承双图的丰富理论，如标记迁移系统和行为同余的自动构造。
英文摘要：
We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction levels; in particular, higher-level (e.g. membrane) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. A BioBeta specification provides a protein signature together a set of protein reactions, in the spirit of the kappa-calculus. Moreover, the specification describes when a protein configuration triggers one of the only two membrane interaction allowed, that is "pinch" and "fuse". In this paper we define the syntax and semantics of BioBeta, analyse its properties, give it an interpretation as biobigraphical reactive systems, and discuss its expressivity by comparing with kappa-calculus and modelling significant examples. Notably, BioBeta has been designed after a bigraphical metamodel for the same purposes. Hence, each instance of the calculus corresponds to a bigraphical reactive system, and vice versa (almost). Therefore, we can inherith the rich theory of bigraphs, such as the automatic construction of labelled transition systems and behavioural congruences.
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