  We describe a molecule-oriented modelling approach based on a collection of
Petri net models organized in the form of modules into a prototype database
accessible through a web interface. The JAK/STAT signalling pathway with the
extensive cross-talk of its components is selected as case study. Each Petri
net module represents the reactions of an individual protein with its specific
interaction partners. These Petri net modules are graphically displayed, can be
executed individually, and allow the automatic composition into coherent models
containing an arbitrary number of molecular species chosen ad hoc by the user.
Each module contains metadata for documentation purposes and can be extended to
a wiki-like minireview. The database can manage multiple versions of each
module. It supports the curation, documentation, version control, and update of
individual modules and the subsequent automatic composition of complex models,
without requiring mathematical skills. Modules can be (semi-) automatically
recombined according to user defined scenarios e.g. gene expression patterns in
given cell types, under certain physiological conditions, or states of disease.
Adding a localisation component to the module database would allow to simulate
models with spatial resolution in the form of coloured Petri nets. As synthetic
biology application we propose the fully automated generation of synthetic or
synthetically rewired network models by composition of metadata-guided
automatically modified modules representing altered protein binding sites.
Petri nets composed from modules can be executed as ODE system, stochastic,
hybrid, or merely qualitative models and exported in SMBL format.
