A petri net application to model metabolic processes
Systems Analysis Modelling Simulation
Petri Net Representations in Metabolic Pathways
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology
Mathematical Models in Biology
Mathematical Models in Biology
A new approach to flux coupling analysis of metabolic networks
CompLife'06 Proceedings of the Second international conference on Computational Life Sciences
Petri nets for modelling metabolic pathways: a survey
Natural Computing: an international journal
Model verification framework with application to molecular biology (Work-in-Progress)
Proceedings of the 2011 Symposium on Theory of Modeling & Simulation: DEVS Integrative M&S Symposium
Survey: Computational challenges in systems biology
Computer Science Review
Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets
Journal of Biomedical Informatics
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The investigation of spliceosomal processes is currently a topic of intense research in molecular biology. In the molecular mechanism of alternative splicing, a multi-protein-RNA complex - the spliceosome - plays a crucial role. To understand the biological processes of alternative splicing, it is essential to comprehend the biogenesis of the spliceosome. In this paper, we propose the first abstract model of the regulatory assembly pathway of the human spliceosomal subunit U1. Using Petri nets, we describe its highly ordered assembly that takes place in a stepwise manner. Petri net theory represents a mathematical formalism to model and analyze systems with concurrent processes at different abstraction levels with the possibility to combine them into a uniform description language. There exist many approaches to determine static and dynamic properties of Petri nets, which can be applied to analyze biochemical systems. In addition, Petri net tools usually provide intuitively understandable graphical network representations, which facilitate the dialog between experimentalists and theoreticians. Our Petri net model covers binding, transport, signaling, and covalent modification processes. Through the computation of structural and behavioral Petri net properties and their interpretation in biological terms, we validate our model and use it to get a better understanding of the complex processes of the assembly pathway. We can explain the basic network behavior, using minimal T-invariants which represent special pathways through the network. We find linear as well as cyclic pathways. We determine the P-invariants that represent conserved moieties in a network. The simulation of the net demonstrates the importance of the stability of complexes during the maturation pathway. We can show that complexes that dissociate too fast, hinder the formation of the complete U1 snRNP.