A4 Refereed article in a conference publication
An Excursion Through Quantitative Model Refinement
Authors: Sepinoud Azimi, Eugen Czeizler, Cristian Gratie, Diana-Elena Gratie, Bogdan Iancu, Nebiat Ibssa, Ion Petre, Vladimir Rogojin, Tolou Shadbahr, Fatemeh Shokri
Editors: Grzegorz Rozenberg,Arto Salomaa,José M.Sempere,Claudio Zandron
Conference name: International Conference on Membrane Computing
Publisher: Springer
Publication year: 2015
Book title : Membrane computing
Series title: Lecture Notes in Computer Science
Volume: 9504
First page : 25
Last page: 47
Number of pages: 23
ISBN: 978-3-319-28474-3
ISSN: 0302-9743
DOI: https://doi.org/10.1007/978-3-319-28475-0_3
There is growing interest in creating large-scale computational models for biological process. One of the challenges in such a project is to fit and validate larger and larger models, a process that requires more high-quality experimental data and more computational effort as the size of the model grows. Quantitative model refinement is a recently proposed model construction technique addressing this challenge. It proposes to create a model in an iterative fashion by adding details to its species, and to fix the numerical setup in a way that guarantees to preserve the fit and validation of the model. In this survey we make an excursion through quantitative model refinement – this includes introducing the concept of quantitative model refinement for reaction-based models, for rule-based models, for Petri nets and for guarded command language models, and to illustrate it on three case studies (the heat shock response, the ErbB signaling pathway, and the self-assembly of intermediate filaments).