Linking Visual Formalisms and Specification Calculi for Biological Modeling
Lead Research Organisation:
University of Edinburgh
Department Name: Lab. for Foundations of Computer Science
Abstract
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.
Organisations
Publications
Amir-Kroll H
(2008)
GemCell: A generic platform for modeling multi-cellular biological systems
in Theoretical Computer Science
Harel D
(2008)
Can Programming Be Liberated, Period?
in Computer
Keller EF
(2007)
Beyond the gene.
in PloS one
Robertson S
(2007)
Postsecondary Education & Autism: Developing an Online Community
Y Atir
(2007)
Using lscs for scenario authoring in tactical simulators