Linking Visual Formalisms and Specification Calculi for Biological Modeling

系统生物学家描述生物系统的方式，支持这些系统的调查，由计算机。他们需要语言来写他们的描述，这些语言必须既易于使用，又适合计算机解释。一个复杂的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）。目前有多种语言在使用。一种这样的语言是Statecharts，一种用于描述软件和其他计算机化系统的图形媒体。这种语言已被证明在生物学中用于建模细胞间行为的各种项目中非常有用。进程代数，例如CCS、通信系统演算和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。我们希望将两者的优势联合收割机结合起来，利用来自进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有用，例如，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.