• BioASF: a framework for automa...

Treffer: BioASF: a framework for automatically generating executable pathway models specified in BioPAX.

Title:
BioASF: a framework for automatically generating executable pathway models specified in BioPAX.
Authors:
Haydarlou R; Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands., Jacobsen A; Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands., Bonzanni N; Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands NKI-AVL, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands., Feenstra KA; Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands., Abeln S; Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands., Heringa J; Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands.
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2016 Jun 15; Vol. 32 (12), pp. i60-i69.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Gene Regulatory Networks* , Models, Biological* , Signal Transduction* , Software*, Computer Simulation ; Humans ; Programming Languages
References:
Nat Biotechnol. 2010 Sep;28(9):935-42. (PMID: 20829833)
Nucleic Acids Res. 2009 Jan;37(Database issue):D674-9. (PMID: 18832364)
Nucleic Acids Res. 2000 Jan 1;28(1):27-30. (PMID: 10592173)
PLoS One. 2016 May 24;11(5):e0155743. (PMID: 27218469)
Bioinformatics. 2013 Jul 1;29(13):i80-8. (PMID: 23813012)
Bioinformatics. 2014 Jan 1;30(1):139-40. (PMID: 24045775)
Nucleic Acids Res. 2014 Jan;42(Database issue):D472-7. (PMID: 24243840)
Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90. (PMID: 21071392)
PLoS One. 2008 Feb 27;3(2):e1672. (PMID: 18301750)
Genome Biol. 2010 Jan 12;11(1):R3. (PMID: 20067622)
Bioinformatics. 2003 Mar 1;19(4):524-31. (PMID: 12611808)
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D504-6. (PMID: 16381921)
J Theor Biol. 2003 Jul 7;223(1):1-18. (PMID: 12782112)
Bioinformatics. 2008 Sep 1;24(17):1917-25. (PMID: 18614585)
PLoS Comput Biol. 2013;9(9):e1003194. (PMID: 24068901)
Nucleic Acids Res. 2012 Jan;40(Database issue):D1301-7. (PMID: 22096230)
Bioinformatics. 2013 Oct 15;29(20):2659-60. (PMID: 23918249)
Bioinformatics. 2010 Feb 1;26(3):429-31. (PMID: 20007251)
Bioinformatics. 2009 Aug 15;25(16):2049-56. (PMID: 19515963)
Nat Biotechnol. 2009 Aug;27(8):735-41. (PMID: 19668183)
Entry Date(s):
Date Created: 20160617 Date Completed: 20170823 Latest Revision: 20181202
Update Code:
20250114
PubMed Central ID:
PMC4908334
DOI:
10.1093/bioinformatics/btw250
PMID:
27307645
Database:
MEDLINE

Weitere Informationen

Motivation: Biological pathways play a key role in most cellular functions. To better understand these functions, diverse computational and cell biology researchers use biological pathway data for various analysis and modeling purposes. For specifying these biological pathways, a community of researchers has defined BioPAX and provided various tools for creating, validating and visualizing BioPAX models. However, a generic software framework for simulating BioPAX models is missing. Here, we attempt to fill this gap by introducing a generic simulation framework for BioPAX. The framework explicitly separates the execution model from the model structure as provided by BioPAX, with the advantage that the modelling process becomes more reproducible and intrinsically more modular; this ensures natural biological constraints are satisfied upon execution. The framework is based on the principles of discrete event systems and multi-agent systems, and is capable of automatically generating a hierarchical multi-agent system for a given BioPAX model.
Results: To demonstrate the applicability of the framework, we simulated two types of biological network models: a gene regulatory network modeling the haematopoietic stem cell regulators and a signal transduction network modeling the Wnt/β-catenin signaling pathway. We observed that the results of the simulations performed using our framework were entirely consistent with the simulation results reported by the researchers who developed the original models in a proprietary language.
Availability and Implementation: The framework, implemented in Java, is open source and its source code, documentation and tutorial are available at http://www.ibi.vu.nl/programs/BioASF CONTACT: j.heringa@vu.nl.
(© The Author 2016. Published by Oxford University Press.)