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Mathias John, Dagmar Köhn, and Robert Waltemath (2007)

The Pi Markup Language - A First Approach to Make Pi Exchangable

Poster, Computational Methods in Systems Biology 2007.

For the Pi-calculus, there exist many notations which hampers the model exchange and thus their reuse. We introduce a first approach for the Pi-calculus Markup Language (PiML) as a common notation-independent format for validating, storing, and exchanging Pi-models. PiML is a particular XML Schema with full Pi-syntax expressiveness. The PiML schema supports definitions of actions as well as definitions of nested parallel processes and summations. Actions can be defined globally and thus be reused within the PiML schema. Existing Pi-models can be automatically transformed into PiML representations and vice versa in a consistent manner. As PiML is notation-independent, it is now possible to store all models in a single data base. Models can as well be queried using a common query language and are comparable by using sophisticated matching algorithms. By defining PiML interfaces, tools can exchange models without considering different Pi-calculus notations. Additionally, model-related meta-information can be introduced allowing for more effective model reuse including data base querying. This first version of PiML covers all concepts of the basic Pi-syntax. Extensions of the Pi-calculus can be added by designing additional modules. For example, for PiML to entirely cover SpacePi models, a module is needed that introduces besides a wait()-action also numbers, vectors, variables, units of time and space, and movement functions. The example used throughout the poster is a SpacePi-model of Euglena's phototaxis which has been published in [John, M., Ewald, R., Uhrmacher, A., A Spatial Extension to the Pi-Calculus, Theor. Comput. Sci. (2007 to appear)].

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