Abstract
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.
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Blätke, M.A., Heiner, M., Marwan, W. (2012). Predicting Phenotype from Genotype through Automatically Composed Petri Nets. In: Gilbert, D., Heiner, M. (eds) Computational Methods in Systems Biology. CMSB 2012. Lecture Notes in Computer Science(), vol 7605. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33636-2_7
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DOI: https://doi.org/10.1007/978-3-642-33636-2_7
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