Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.
复制标题
DOI：
10.1515/jib-2020-0015
复制
发表时间：
2020-07-06
影响因子：
1.9
通讯作者：
Meier-Schellersheim M
中科院分区：
文献类型：
--
作者：
Zhang F;Smith LP;Blinov ML;Faeder J;Hlavacek WS;Juan Tapia J;Keating SM;Rodriguez N;Dräger A;Harris LA;Finney A;Hu B;Hucka M;Meier-Schellersheim M
基于规则的建模是一种允许根据分子相互作用和转化规则的规范构建反应网络的方法。这些规则可以包括诸如相互作用的亚分子结构域以及所涉及的组分的状态和结合状态等细节。从概念上讲，还可以提供诸如位置之类的细粒度空间信息。通过代表组分状态的"通配符"，共享某些性质的分子复合物的整个家族可以被指定为模式。这可以大大简化模型的定义，涉及多组分，多状态和多隔间的物种。系统生物学标记语言（SBML）第3级多包版本1扩展了SBML第3级版本1的核心，在Species和Combination类中引入了“类型”概念。因此，反应规则可以包含可以是模式并且存在于多个位置的种类。Simmune和BioNetGen等多种软件工具支持这一标准，因此也成为交换基于规则的模型的媒介。本文档提供了SBML Level 3 Multi包版本1的第2版的规范。在版本1和版本2之间，未对模型描述进行设计变更;变更仅限于更正勘误表和添加说明。
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.