BioASF: A framework for automatically generating executable pathway models specified in BioPAX

Reza Haydarlou, Annika Jacobsen, Nicola Bonzanni, K. Anton Feenstra, Sanne Abeln, Jaap Heringa

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

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.
Original languageEnglish
Pages (from-to)60-69
JournalBioinformatics
Volume32
Issue number12
DOIs
Publication statusPublished - 15 Jun 2016

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Pathway
Research Personnel
Catenins
Biological Models
Wnt Signaling Pathway
Network Modeling
Gene Regulatory Networks
Hematopoietic Stem Cells
Computational Biology
Multi agent systems
Documentation
Multi-agent Systems
Cell Biology
Signal Transduction
Language
Software
Cytology
Model
Signal transduction
Hierarchical Systems

Cite this

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title = "BioASF: A framework for automatically generating executable pathway models specified in BioPAX",
abstract = "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.",
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BioASF : A framework for automatically generating executable pathway models specified in BioPAX. / Haydarlou, Reza; Jacobsen, Annika; Bonzanni, Nicola; Feenstra, K. Anton; Abeln, Sanne; Heringa, Jaap.

In: Bioinformatics, Vol. 32, No. 12, 15.06.2016, p. 60-69.

Research output: Contribution to JournalArticleAcademicpeer-review

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