Modeling biological complexity using Biology System Description Language (BiSDL)

@article{Muggianu2018ModelingBC,
  title={Modeling biological complexity using Biology System Description Language (BiSDL)},
  author={F. Muggianu and Alfredo Benso and Roberta Bardini and E. Hu and Gianfranco Politano and Stefano Di Carlo},
  journal={2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
  year={2018},
  pages={713-717}
}
  • F. Muggianu, A. Benso, +3 authors S. Carlo
  • Published 1 December 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… Expand
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References

SHOWING 1-10 OF 17 REFERENCES
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2
TLDR
LEMS and NeuroML 2 provide a new, comprehensive framework for defining computational models of neuronal and other biological systems in a machine readable format, making them more reproducible and increasing the transparency and accessibility of their underlying structure and properties. Expand
Multi-level and hybrid modelling approaches for systems biology
TLDR
Models which are both multi-level and hybrid satisfy both accuracy and capability for making a good knowledge base, making a very useful tool in computational systems biology. Expand
NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail
TLDR
The development of NeuroML as a common description language for biophysically detailed neuronal and network models enables interoperability across multiple simulation environments, thereby improving model transparency, accessibility and reuse in computational neuroscience. Expand
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology
TLDR
The Synthetic Biology Open Language (SBOL) is described, a proposed data standard for exchanging designs within the synthetic biology community that represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. Expand
Synthetic Biology Open Language (SBOL) Version 2.2.0
TLDR
version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year’s JIB special issue includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model. Expand
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
TLDR
The collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models. Expand
CellML: its future, present and past.
TLDR
The structure of CellML is summarized, its current applications (including biological pathway and electrophysiological models), and its future development--in particular, the development of toolsets and the integration of ontologies are summarized. Expand
SNAKES: A Flexible High-Level Petri Nets Library (Tool Paper)
TLDR
This paper describes SNAKES’ structure and features and describes the companion tool Neco that compiles a Petri net into an optimised library allowing to compute efficiently its state space or perform LTL model-checking thanks to library SPOT. Expand
Object Petri Nets: Using the Nets-within-Nets Paradigm
  • R. Valk
  • Computer Science
  • Lectures on Concurrency and Petri Nets
  • 2003
TLDR
This introduction into the field of object Petri nets starts with small examples and proceeds by giving formal examples, some of which are modelled within the formalism of the Renew tool. Expand
Using multi-level Petri nets models to simulate microbiota resistance to antibiotics
TLDR
This work model the relation between different antibiotic administration protocols and resistance spread dynamics both at the human population and at the single microbiota level using the Nets-within-nets formalism. Expand
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