Modeling biological complexity using Biology System Description Language (BiSDL)

The Nets-within-Nets formalism (NWN) allows to model complex biological systems expressing hierarchy, encapsulation, selective communication, spatiality, quantitative mechanisms, and stochasticity. To make NWN usable by life science researchers as well as systems biologists, we introduce a new human-readable description language able to express these same NWN model properties, at different levels of abstraction. BiSDL (Biology Systems Description Language) is derived from the VHDL specification, a standard description language for hardware systems. In this paper we chose a simple signaling pathway example to show how BiSDL enables modeling complex biological systems by separating the behavioral model from the architectural details.

[1]  Zhen Zhang,et al.  Synthetic Biology Open Language (SBOL) Version 2.2.0 , 2018, J. Integr. Bioinform..

[2]  Rüdiger Valk,et al.  Object Petri Nets: Using the Nets-within-Nets Paradigm , 2003, Lectures on Concurrency and Petri Nets.

[3]  Steffen Klamt,et al.  SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools , 2013, BMC Systems Biology.

[4]  Gary D Bader,et al.  BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.

[5]  Pascale Gaudet,et al.  The Gene Ontology , 2019, Encyclopedia of Bioinformatics and Computational Biology.

[6]  Robert C. Cannon,et al.  LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2 , 2014, Front. Neuroinform..

[7]  Allan Kuchinsky,et al.  The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology , 2014, Nature Biotechnology.

[8]  Michael L. Hines,et al.  NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail , 2010, PLoS Comput. Biol..

[9]  Douglas L. Perry.  VHDL (2nd ed.) , 1993 .

[10]  Catherine M Lloyd,et al.  CellML: its future, present and past. , 2004, Progress in biophysics and molecular biology.

[11]  A. Benso,et al.  Multi-level and hybrid modelling approaches for systems biology , 2017, Computational and structural biotechnology journal.

[12]  Alfredo Benso,et al.  Using multi-level Petri nets models to simulate microbiota resistance to antibiotics , 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

[13]  Alfredo Benso,et al.  Using Nets-Within-Nets for Modeling Differentiating Cells in the Epigenetic Landscape , 2016, IWBBIO.

[14]  Franck Pommereau,et al.  SNAKES: A Flexible High-Level Petri Nets Library (Tool Paper) , 2015, Petri Nets.