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Synthetic Biology

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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Related Experiment Video

Updated: Mar 26, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

VisBOL: Web-Based Tools for Synthetic Biology Design Visualization.

James Alastair McLaughlin¹, Matthew Pocock², Göksel Mısırlı¹

¹School of Computing Science, Newcastle University , Tyne and Wear, NE1 7RU, U.K.

ACS Synthetic Biology

|January 26, 2016

Summary

VisBOL renders genetic circuit designs into the visual format of the Synthetic Biology Open Language (SBOL). This tool aids synthetic biologists by exporting designs as images for publications and embedding diagrams in other software.

Keywords:

SBOL Visual Synthetic Biology Open Language genetic circuits synthetic biology visualization

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Last Updated: Mar 26, 2026

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Area of Science:

Synthetic Biology
Bioinformatics Visualization

Background:

Synthetic biologists need standardized methods for designing and communicating genetic circuits.
Current tools may lack interoperability or user-friendly visualization capabilities.

Purpose of the Study:

To introduce VisBOL, a web-based application for rendering genetic circuit designs.
To facilitate the visual communication of synthetic biology designs in SBOL visual format.

Main Methods:

VisBOL processes designs specified in Synthetic Biology Open Language (SBOL) version 2.0.
It supports input from various bioinformatics formats like GenBank and Pigeoncad notation.
Visualizations are generated and can be exported as PNG and SVG images.

Main Results:

VisBOL provides a user-accessible website for rendering genetic circuit designs.
Designs can be exported in standard image formats for integration into various media.
The tool functions as an open-source JavaScript library for embedding diagrams.

Conclusions:

VisBOL enhances the visual communication of genetic circuit designs for synthetic biologists.
The application promotes interoperability by supporting multiple input formats.
Its availability as a web tool and library increases accessibility and usability.