Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems

Background The Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology. It allows synthetic biologists to represent spatiality and multi-level cellular dynamics inherent to multicellular designs, filling a gap in the state...

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Vydáno v:BMC bioinformatics Ročník 25; číslo 1; s. 166 - 33
Hlavní autoři: Giannantoni, Leonardo, Bardini, Roberta, Savino, Alessandro, Di Carlo, Stefano
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 25.04.2024
BioMed Central Ltd
Springer Nature B.V
BMC
Témata:
Accessibility
Algorithms
Analysis
Bioinformatics
Biological effects
Biology
Biomedical and Life Sciences
Collaboration
Computational biology
Computational Biology/Bioinformatics
Computational linguistics
Computer Appl. in Life Sciences
Computer applications
Conceptual design
Data exchange
Data mining
Design
Domain-specific languages
Evaluation
Genetic engineering
Information management
Interoperability
Language
Language processing
Life Sciences
Microarrays
Modelling
Models, Biological
Morphogenesis
Natural language interfaces
Ordinary differential equations
Programming Languages
R&D
Research & development
Semantics
Simulation
Software
Specification and description languages
Syntax
Synthetic biology
Synthetic Biology - methods
System effectiveness
Systems biology
Systems Biology - methods
Italy
Synthetic biology
Domain-specific languages
Systems biology
Computational biology
ISSN:1471-2105, 1471-2105
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Popis
Shrnutí:Background The Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology. It allows synthetic biologists to represent spatiality and multi-level cellular dynamics inherent to multicellular designs, filling a gap in the state of the art. Developed for designing and simulating spatial, multicellular synthetic biological systems, BiSDL integrates high-level conceptual design with detailed low-level modeling, fostering collaboration in the Design-Build-Test-Learn cycle. BiSDL descriptions directly compile into Nets-Within-Nets (NWNs) models, offering a unique approach to spatial and hierarchical modeling in biological systems. Results BiSDL’s effectiveness is showcased through three case studies on complex multicellular systems: a bacterial consortium, a synthetic morphogen system and a conjugative plasmid transfer process. These studies highlight the BiSDL proficiency in representing spatial interactions and multi-level cellular dynamics. The language facilitates the compilation of conceptual designs into detailed, simulatable models, leveraging the NWNs formalism. This enables intuitive modeling of complex biological systems, making advanced computational tools more accessible to a broader range of researchers. Conclusions BiSDL represents a significant step forward in computational languages for synthetic biology, providing a sophisticated yet user-friendly tool for designing and simulating complex biological systems with an emphasis on spatiality and cellular dynamics. Its introduction has the potential to transform research and development in synthetic biology, allowing for deeper insights and novel applications in understanding and manipulating multicellular systems.
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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-024-05782-x