A critical review on modelling formalisms and simulation tools in computational biosystems

Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Abstract

Integration of different kinds of biological processes is an ultimate goal for whole-cell modelling. We briefly review modelling formalisms that have been used in Systems Biology and identify the criteria that must be addressed by an integrating framework capable of modelling, analysing and simulating different biological networks. Aware that no formalism can fit all purposes we realize Petri nets as a suitable model for Metabolic Engineering and take a deeper perspective on the role of this formalism as an integrating framework for regulatory and metabolic networks. © 2009 Springer Berlin Heidelberg.
Original languageEnglish
Title of host publicationDistributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living : 10th International Work-Conference on Artificial Neural Networks, IWANN 2009 Workshops, Salamanca, Spain, June 10-12, 2009. Proceedings
Volume2
PublisherSpringer
Publication date2009
Pages1063-1070
ISBN (Print)978-3-642-02480-1
ISBN (Electronic)978-3-642-02481-8
DOIs
Publication statusPublished - 2009
Externally publishedYes
Event10th International Work-Conference on Artificial Neural Networks (IWANN 2009) - Salamanca, Spain
Duration: 9 Jun 200912 Jun 2009
Conference number: 10

Conference

Conference10th International Work-Conference on Artificial Neural Networks (IWANN 2009)
Number10
CountrySpain
CitySalamanca
Period09/06/200912/06/2009
SeriesLecture Notes in Computer Science
Volume5518
ISSN0302-9743

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