  We describe a modular modelling approach permitting curation, updating, and
distributed development of modules through joined community effort overcoming
the problem of keeping a combinatorially exploding number of monolithic models
up to date. For this purpose, the effects of genes and their mutated alleles on
downstream components are modeled by composable, metadata-containing Petri net
models organized in a database with version control, accessible through a web
interface. Gene modules can be coupled to protein modules through mRNA modules
by specific interfaces designed for the automatic, database-assisted
composition. Automatically assembled executable models may then consider cell
type-specific gene expression patterns and the resulting protein
concentrations. Gene modules and allelic interference modules may represent
effects of gene mutation and predict their pleiotropic consequences or uncover
complex genotype/phenotype relationships. Forward and reverse engineered
modules are fully compatible.
