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• W101885789 abstract "AbstractThis paper introduces Protein Calculus, a special modeling language designed for en-coding and calculating the behaviors of compartmentilized biological systems. The for-malism combines, in a unified framework, two successful computational paradigms - pro-cess algebras and membrane systems. The goal of Protein Calculus is to provide a formaltool for transforming collected information from in vivo experiments into coded definitionof the different types of proteins, complexes of proteins, and membrane-organized systemsof such entities. Using this encoded information as input, our calculus computes, in silico,the possible behaviors of a living system. 1 The computational challenge in Systems Biology Many of the activities of the biological cells are regulated by proteins which carry signals thatmodify the expression of different genes at a given time, but how these signals do so is notknown. The use of Systems Biology is therefore essential if we are ever to make sense of thebiological complexity, as intuitive ’conceptual’models.Systems Biology is a multi-disciplinary approach that studies the relationships and inter-actions of various cellular mechanisms and cellular components. It encompases the growingnumber of mechanistic but largely isolated insights and increasingly, high-throughput ’omics’data sets which tends to be semi-quantitative and specific to its experimental system and inte-grates them into a conceptual modelling framework that is holistic, quantitative and predictive.By abstracting biological systems on the level of their behaviours, models are obtained shar-ing many characteristics with computational systems. Consequently, on all levels of organisa-tion (i.e. from the atomic to full organisms) concurrent behaviours - be it event-driven, causal,time-dependent or distributed - is attained. Owing to these similarities, modelling (reverse-engineering, simulating and analysing) a biological system has been considered in a similarway to the engineering of complex artificial systems [2, 4]. This has resulted in questions suchas - Is the structure of a cell much more complex than the structure of a jet plane? - to beraised. In answering the question, the challenge therefore is to construct, in silico, reliable‘copies’ of biological systems that would allow the simulation of various experiments, which1" @default.
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• W101885789 date "2007-01-01" @default.
• W101885789 modified "2023-09-27" @default.
• W101885789 title "A Process Algebraical Approach to Modelling Compartmentalized Biological Systems" @default.
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