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Modelers of molecular signaling networks must cope with the combinatorial explosion of protein states generated by posttranslational modifications and complex formation. Rule-based models provide a powerful alternative to approaches that require explicit enumeration of all possible molecular species of a system. Such models consist of formal rules(More)
Many proteins are composed of structural and chemical features—“sites” for short—defined by definite interaction capabilities, such as non-covalent binding or covalent modification of other proteins. This modularity allows for varying degrees of independence, as the behavior of a site might be controlled by the state of some but not all sites of the ambient(More)
Game semantics, in its “modern” form, arose in the early 90s in the wake of sequential algorithms, process calculus and the geometry of interaction. The historical context of game semantics revolved around the long-standing problem of “full abstraction for PCF”, PCF being an idealized functional language. After Plotkin’s domain model (which he showed to be(More)
The general question of what constitutes bio-curation for rule-based modelling of cellular signalling is posed. A general approach to the problem is presented, based on rewriting in hierarchies of graphs, together with a specific instantiation of the methodology that addresses our particular bio-curation problem. The current state of the ongoing development(More)
Many proteins are composed of structural and chemical features--"sites" for short--characterized by definite interaction capabilities, such as noncovalent binding or covalent modification of other proteins. This modularity allows for varying degrees of independence, as the behavior of a site might be controlled by the state of some but not all sites of the(More)
This volume contains the papers presented at the Tenth International Workshop on Developments in Computational Models (DCM) held in Vienna, Austria on 13th July 2014, as part of the Vienna Summer of Logic. Several new models of computation have emerged in the last years, and many developments of traditional computational models have been proposed with the(More)
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