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CMSB
2011
Springer
12 years 6 months ago
Coloured stochastic multilevel multiset rewriting
From the phosphorylation state of a molecule to the volume of a cell, parameters are ubiquitous in systems biology. At the same time, most models involve static or dynamic compart...
Nicolas Oury, Gordon D. Plotkin
FM
2009
Springer
138views Formal Methods» more  FM 2009»
14 years 1 months ago
What Can Formal Methods Bring to Systems Biology?
This position paper argues that the operational modelling approaches from the formal methods community can be applied fruitfully within the systems biology domain. The results can ...
Nicola Bonzanni, K. Anton Feenstra, Wan Fokkink, E...
WWW
2002
ACM
14 years 7 months ago
Simulation, verification and automated composition of web services
Web services -- Web-accessible programs and devices ? are a key application area for the Semantic Web. With the proliferation of Web services and the evolution towards the Semanti...
Srini Narayanan, Sheila A. McIlraith
EDBTW
2010
Springer
14 years 1 months ago
Biochemical network matching and composition
Graph composition has applications in a variety of practical applications. In drug development, for instance, in order to understand possible drug interactions, one has to merge k...
Martin Hugh Goodfellow, John Wilson, Ela Hunt
BIBE
2007
IEEE
149views Bioinformatics» more  BIBE 2007»
13 years 11 months ago
XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes
Multi-state molecules and multi-component complexes are commonly involved in cellular signaling. Accounting for molecules that have multiple potential states, such as a protein tha...
Michael L. Blinov, Ion I. Moraru