On deducing causality in metabolic networks

Background: Metabolic networks present a complex interconnected structure, whose understanding is in general a non-trivial task. Several formal approaches have been developed to support the investigation of such networks. One of the relevant problems in this context is the comprehension of causality dependencies amongst the molecules involved in the metabolic process. Results: We apply techniques from formal methods and computational logic to develop an qualitative model of metabolic networks in order to determine possible causal dependencies. Keeping in mind both expressiveness and ease of use, we aimed at providing: i) a minimal notation to represent causality in biochemical interactions, and ii) an automated tool allowing human experts to easily vary conditions of in silico experiments. We exploit a reading of chemical reactions in terms of logical implications: starting from a description of a metabolic network in terms of reaction rules and initial conditions, chains of reactions...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Chiara Bodei, Andrea Bracciali, Davide Chiarugi
• Keywords: BMCBI 2008, Computational Logic, Metabolic Network, Several Formal Approaches