Modeling biological complexity using Biology System Description Language (BiSDL)

  title={Modeling biological complexity using Biology System Description Language (BiSDL)},
  author={F. Muggianu and A. Benso and Roberta Bardini and E. Hu and G. Politano and S. Carlo},
  journal={2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
  • F. Muggianu, A. Benso, +3 authors S. Carlo
  • Published 2018
  • Computer Science
  • 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  • 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… CONTINUE READING
    3 Citations
    Growth factor regulatory system: a new system for not truly recognized organisms


    LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2
    • 73
    • PDF
    Multi-level and hybrid modelling approaches for systems biology
    • 20
    • PDF
    NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail
    • 271
    • PDF
    The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology
    • 201
    • PDF
    Synthetic Biology Open Language (SBOL) Version 2.2.0
    • 25
    SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
    • 104
    • PDF
    CellML: its future, present and past.
    • 521
    • PDF
    SNAKES: A Flexible High-Level Petri Nets Library (Tool Paper)
    • 26
    • PDF
    Object Petri Nets: Using the Nets-within-Nets Paradigm
    • R. Valk
    • Computer Science
    • Lectures on Concurrency and Petri Nets
    • 2003
    • 132
    • PDF
    Using multi-level Petri nets models to simulate microbiota resistance to antibiotics
    • 4