Our work “Modeling biological complexity using Biology System Description Language (BiSDL)” has been accepted as a short paper for oral presentation and publication in the proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018) taking place in Madrid Dec 3rd-6th 2018.
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.
This paper describes part of the master thesis work by Flavia Muggianu and part of the research internship work by Eileen Hu. The undersigned contributed to team coordination and as a tester of the prototypes. Stefano, Alfredo and Gianfranco coordinated the project towards completion of the identified objectives 😉
Please find below some rare pictures of the three BioSysters in the wild showing typical behavioural patterns.
BiSDL is part of a larger project, encompassing the complete flow from an experimentalist-friendly interface to a custom simulator for NWN models of complex biological systems. Be prepared for much other news on the topic…
Stay tuned!
[“Modeling biological complexity using Biology System Description Language (BiSDL)“, F. Muggianu, A. Benso, R.Bardini, E. Hu, G. Politano, S. Di Carlo, accepted for publication in the Proceedings of the 2018 IEEE International
Conference on Bioinformatics and Biomedicine (BIBM2018), Madrid, Spain, Dec 3-6, 2108]
Roberta Bardini