Linking Visual Formalisms and Specification Calculi for Biological Modeling

将视觉形式主义和规范计算联系起来进行生物建模

• 批准号: EP/E031161/1
• 负责人: Gordon Plotkin
• 金额: $ 10万
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2007
• 资助国家: 英国
• 起止时间: 2007 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FE031161%2F1
• 关键词: Linking; Visual; Formalisms; Specification; Calculi

Systems biologists describe biological systems in a way that supportsthe investigation of those systems by computer. They need languages inwhich to write their descriptions, and these languages have to be botheasy to use and suitable for interpretation by a computer. The behaviorof a complex biological system consists of inter-cellular effects, and intra-cellular ones (such as gene and protein signalling). Currently, a variety of languages are in use. One such language is Statecharts, a diagrammatic medium for describing software and other computerized system. This language has proved useful in a variety of projects for modeling inter-cellular behavior in biology. Process algebras, such as CCS, the Calculus of Communicating Systems, and the pi calculus, are written in symbols, and have mechanismssuitable for describing intra-cellular behavior. We want to combine theadvantages of both, using insights from the process algebra and visual formalisms communities, to build a combined language that would be able to deal with entire biological systems. Our initial target group of users isthat of systems biologists, although our insights are also expected to be useful more widely, for example, to software designers.

系统生物学家以支持计算机研究这些系统的方式描述生物系统。他们需要用语言来编写描述，而这些语言必须既易于使用又适合计算机解释。复杂生物系统的行为由细胞间效应和细胞内效应（例如基因和蛋白质信号传导）组成。目前，有多种语言在使用。其中一种语言是状态图，它是一种用于描述软件和其他计算机化系统的图形媒体。事实证明，这种语言在生物学中细胞间行为建模的各种项目中非常有用。过程代数，例如 CCS、通信系统微积分和 pi 演算，都是用符号编写的，并且具有适合描述细胞内行为的机制。我们希望结合两者的优势，利用过程代数和视觉形式主义社区的见解，构建一种能够处理整个生物系统的组合语言。我们最初的目标用户群是系统生物学家，尽管我们的见解也有望更广泛地发挥作用，例如对软件设计师而言。

项目成果

Beyond the gene.

• DOI: 10.1371/journal.pone.0001231
• 发表时间: 2007-11-28
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Keller EF;Harel D
• 通讯作者: Harel D

Using lscs for scenario authoring in tactical simulators

使用 LSC 在战术模拟器中进行场景创作

• 发表时间: 2007
• 作者: Y Atir