NIAID/NIH, Bethesda, USA.
University of Washington, Seattle, USA.
J Integr Bioinform. 2020 Jul 6;17(2-3):20200015. doi: 10.1515/jib-2020-0015.
Rule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains and the states and binding status of the involved components. Conceptually, fine-grained spatial information such as locations can also be provided. Through "wildcards" representing component states, entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states, and multiple compartments. The systems biology markup language (SBML) Level 3 Multi Package Version 1 extends the SBML Level 3 Version 1 core with the "type" concept in the Species and Compartment classes. Therefore, reaction rules may contain species that can be patterns and exist in multiple locations. Multiple software tools such as Simmune and BioNetGen support this standard that thus also becomes a medium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level 3 Multi package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications.
基于规则的建模是一种方法，允许根据分子相互作用和转化的规则来构建反应网络。这些规则可以包括相互作用的亚分子域以及涉及的组件的状态和结合状态等细节。从概念上讲，也可以提供精细的空间信息，如位置。通过代表组件状态的“通配符”，可以将具有某些属性的整个分子复合物家族指定为模式。这可以大大简化涉及具有多个组件、多个状态和多个隔室的物种的模型的定义。系统生物学标记语言 (SBML) Level 3 Multi Package Version 1 通过在“Species”和“Compartment”类中引入“type”概念，扩展了 SBML Level 3 Version 1 核心。因此，反应规则可以包含可以是模式并存在于多个位置的物种。多个软件工具，如 Simmune 和 BioNetGen，支持此标准，因此也成为了基于规则模型的交换媒介。本文档提供了 SBML Level 3 Multi package 版本 1 的第 2 次发布的规范。在版本 1 的第 1 次发布和第 2 次发布之间，模型的描述没有设计更改；更改仅限于纠正勘误表并添加澄清。
