A calculus of mobile processes, I
Information and Computation
BioAmbients: an abstraction for biological compartments
Theoretical Computer Science - Special issue: Computational systems biology
Modelling Intracellular Fate of FGF Receptors With BioAmbients
Electronic Notes in Theoretical Computer Science (ENTCS)
Communications of the ACM - Security in the Browser
An automated translation from a narrative language for biological modelling into process algebra
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Transactions on Computational Systems Biology VII
Proving stabilization of biological systems
VMCAI'11 Proceedings of the 12th international conference on Verification, model checking, and abstract interpretation
Model-Checking signal transduction networks through decreasing reachability sets
CAV'13 Proceedings of the 25th international conference on Computer Aided Verification
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A major challenge in computational systems biology is the articulation of a biological process in a form which can be understood by the biologist yet is amenable to computational execution. Process calculi have proved to especially powerful computational tools for modelling and reasoning about biological processes and we have previously described, and implemented, a Narrative approach to describing biological models which is a biologically intuitive high level language that can be translated into executable process calculus programs. Here we discuss an extension to the narrative approach which attempts to directly link biological data with Narrative primitives by suggesting an equivalence relationship between a string (the amino acid sequence) and a process. We outline future challenges in applying this approach more generally.