Linking Visual Formalisms and Specification Calculi for Biological Modeling

系统生物学家用一种支持计算机对这些系统进行调查的方式来描述生物系统。他们需要语言来写他们的描述，这些语言必须易于使用，并适合计算机的解释。复杂生物系统的行为包括细胞间效应和细胞内效应（如基因和蛋白质信号）。目前，使用的语言多种多样。Statecharts就是这样一种语言，它是一种描述软件和其他计算机系统的图形化媒介。这种语言已被证明在生物学中模拟细胞间行为的各种项目中是有用的。过程代数，如CCS、通信系统演算和圆周率演算，都是用符号书写的，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化社区的见解，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，尽管我们的见解也被期望更广泛地有用，例如，对软件设计师。

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.