GReg : a domain specific language for the modeling of genetic regulatory mechanisms

ContributorsSedlmajer, Nicolas
DirectorsBuchs, Didier
Defense date2012

This document describes an approach to the modeling and analysis of genetic regulatory mechanisms involved in a cells protein production, based on formal modeling and reasoning and was developed following the Model-Driven Engineering (MDE) methodology. Most available tools propose simulation frameworks to explore biological pathways. Simulation only explores a few of the most probable pathways in the system. On the contrary, techniques such as model checking, explore all the possible behaviors of the modeled systems, thus helping to identify the most relevant pathways. A main drawback of most model checking tools in the life sciences domain is that they take as input a language designed for computer scientists, that is not easily understood by non-expert users. We propose Genetic Regulation language (GReg), a Domain Specific Language (DSL), to provide a comprehensible language to describe the system, while allowing the use of complex and powerful underlying model checking techniques. Algebraic Petri nets Analyzer (AlPiNA) is a powerful model checker handling very large state spaces. AlPiNA was also developed using Eclipse Modeling Project (EMP) approach. This allows us to use Model To Model (M2M) or Model To Text (M2T) transformations. GReg is thus fully integrated in the Eclipse/EMP framework.

  • Genetic Regulatory Mechanisms
  • Domain Specific Languages
  • Eclipse Modeling Framework
  • Model Checking
  • Algebraic Petri Nets
  • AlPiNA
Citation (ISO format)
SEDLMAJER, Nicolas. GReg : a domain specific language for the modeling of genetic regulatory mechanisms. 2012.
Main files (1)
Master thesis
  • PID : unige:18792

Technical informations

Creation03/12/2012 5:33:00 PM
First validation03/12/2012 5:33:00 PM
Update time03/14/2023 5:09:37 PM
Status update03/14/2023 5:09:37 PM
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