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



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.



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.
Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands.
Reza
R
Haydarlou
Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands.
Annika
A
Jacobsen
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.
Nicola
N
Bonzanni
Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands.
K Anton
KA
Feenstra
Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands.
Sanne
S
Abeln
Centre for Integrative Bioinformatics (IBIVU) & Amsterdam Institute for Molecules Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1081, Amsterdam, The Netherlands.
Jaap
J
Heringa
D003198:Computer Simulation; D053263:Gene Regulatory Networks; D006801:Humans; D008954:Models, Biological; D011381:Programming Languages; D015398:Signal Transduction; D012984:Software