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Authors: Rafael S. Costa 1 ; Daniel Machado 2 ; A. R. Neves 3 and Susana Vinga 4

Affiliations: 1 University of Minho, Instituto de Engenharia de Sistemas e Computadores and Investigac¸ ˜ao e Desenvolvimento (INESC-ID), Portugal ; 2 University of Minho, Portugal ; 3 ITQB/UNL, Portugal ; 4 Instituto de Engenharia de Sistemas e Computadores, Investigac¸ ˜ao e Desenvolvimento (INESC-ID) and FCM-UNL, Portugal

Keyword(s): Systems biology, Integrated dynamic modelling, Hybrid Petri net, Approximate rate laws, Streptococcus pneumoniae.

Related Ontology Subjects/Areas/Topics: Agents ; Artificial Intelligence ; Bioinformatics ; Biomedical Engineering ; Enterprise Information Systems ; Genomics and Proteomics ; Information Systems Analysis and Specification ; Methodologies and Technologies ; Model Design and Evaluation ; Operational Research ; Simulation ; Systems Biology ; Transcriptomics

Abstract: The recent progress in the high-throughput experimental technologies allows the reconstruction of many biological networks and to evaluate changes in proteins, genes and metabolites levels in different conditions. On the other hand, computational models, when complemented with regulatory information, can be used to predict the phenotype of an organism under different genetic and environmental conditions. These computational methods can be used for example to identify molecular targets capable of inactivating a bacterium and to understand its virulence factors. This work proposes a hybrid metabolic-regulatory Petri net approach that is based on the combination of approximate enzyme-kinetic rate laws and Petri nets. A prototypic network model is used as a test-case to illustrate the application of these concepts in Systems Biology.

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Paper citation in several formats:
S. Costa, R.; Machado, D.; R. Neves, A. and Vinga, S. (2012). MULTI-LEVEL DYNAMIC MODELING IN BIOLOGICAL SYSTEMS - Application of Hybrid Petri Nets to Network Simulation. In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS; ISBN 978-989-8425-90-4; ISSN 2184-4305, SciTePress, pages 317-321. DOI: 10.5220/0003785503170321

@conference{bioinformatics12,
author={Rafael {S. Costa}. and Daniel Machado. and A. {R. Neves}. and Susana Vinga.},
title={MULTI-LEVEL DYNAMIC MODELING IN BIOLOGICAL SYSTEMS - Application of Hybrid Petri Nets to Network Simulation},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS},
year={2012},
pages={317-321},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003785503170321},
isbn={978-989-8425-90-4},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOSTEC 2012) - BIOINFORMATICS
TI - MULTI-LEVEL DYNAMIC MODELING IN BIOLOGICAL SYSTEMS - Application of Hybrid Petri Nets to Network Simulation
SN - 978-989-8425-90-4
IS - 2184-4305
AU - S. Costa, R.
AU - Machado, D.
AU - R. Neves, A.
AU - Vinga, S.
PY - 2012
SP - 317
EP - 321
DO - 10.5220/0003785503170321
PB - SciTePress

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