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Communicating Structure and Function in Synthetic Biology Diagrams.

Jacob Beal1,2, Tramy Nguyen3, Thomas E Gorochowski4

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|July 27, 2019
PubMed
Summary
This summary is machine-generated.

Synthetic biologists use diagrams to represent engineered DNA structures and functions. The Synthetic Biology Open Language Visual (SBOL Visual) standard version 2 enhances this visual language with new features for improved communication and representation.

Keywords:
Synthetic Biology Open Languagediagramssynthetic biologyvisualization

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Area of Science:

  • Synthetic Biology
  • Molecular Engineering
  • Bioinformatics

Background:

  • Biological engineers utilize diagrams for communicating engineered nucleic acid structures and functional relationships.
  • Emerging conventions in synthetic biology necessitate a standardized visual language.
  • The Synthetic Biology Open Language Visual (SBOL Visual) aims to organize and systematize these visual conventions.

Purpose of the Study:

  • To describe SBOL Visual version 2, an updated standard for biological diagrams.
  • To detail the enhancements in SBOL Visual 2, including new functional interactions and molecular species categories.
  • To outline the expanded capabilities for representing modular structures and system element mappings.

Main Methods:

  • Development and specification of SBOL Visual version 2.
  • Expansion of the glyph collection for genetic features.
  • Clarification of requirements and best practices for visual language application.
  • Demonstration of applicability with general and bespoke software tools.

Main Results:

  • SBOL Visual 2 introduces new glyphs and features for functional interactions and molecular species.
  • The standard now supports families of glyph variants and indicates modular structure.
  • Enhanced capabilities for mapping elements within a system are included.
  • SBOL Visual 2 provides clarified best practices and an expanded glyph set.

Conclusions:

  • SBOL Visual 2 significantly advances the standardization of visual communication in synthetic biology.
  • The updated standard facilitates clearer representation of complex biological designs and interactions.
  • SBOL Visual 2 is designed for broad applicability across various software tools, promoting wider adoption.