Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments
Transactions on Computational Systems Biology XI
Petri nets for systems and synthetic biology
SFM'08 Proceedings of the Formal methods for the design of computer, communication, and software systems 8th international conference on Formal methods for computational systems biology
Snoopy --- a unifying petri net tool
PETRI NETS'12 Proceedings of the 33rd international conference on Application and Theory of Petri Nets
A module-based approach to biomodel engineering with Petri nets
Proceedings of the Winter Simulation Conference
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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 (www.biomodelkit.org). 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.