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Pathway Logic通路逻辑
Pathway Logic Symbolic Analysis of Biological Signaling Introduction Tremendous growth of genomic sequence information combined with technological advances in the analysis of gene expression has revolutionized research in biology and biomedicine Investigation of signaling and metabolic pathways would benefit greatly from the use of predictive models Although these pathways are complex, fundamental concepts that stemmed from contemporary research indicates that they are also amenable to analysis via computational methods. E.g. most signaling pathways involved hierarchical assembly in space and time of multi-protein complexes that regulate the flow of information via stimulation or inhibition Introduction Various models have been proposed that incorporates quantitative information such as rate and/or concentration information However they are limited due to the difficulty in obtaining the relevant parameters e.g. Michaelis constant etc. as well as stochastic features of signaling molecules Hence another way to look at such pathways is by the logic of signal, e.g. use of π-calculus to represent and forward simulate signaling pathway In this paper, we will look at the development of logical models based on the application of formal methods tools to mammalian signaling pathways Levels of Abstraction Continuous Abstraction Involves continuous mathematics such as differential equations and are analyzed using sophisticated numerical computational packages However the complexity of biological processes limits its accuracy and effective description Discrete Abstraction Natural processes are described by purely symbolic expressions Applicable to less predictable phenomena such as biological signaling processes (as we shall see later on) Pathway Logic Pathway Logic – an algebraic structure enabling the symbolic analysis of biological signaling pathways It uses rewriting theories to formalize the ‘informal’ models that biologists use to describe processes Advantages of u
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