Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Synthetic Biology02:55

Synthetic Biology

4.9K
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.
Golden rice
Golden rice is a genetically modified...
4.9K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

19.0K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
19.0K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A Framework for a Standard-Enabled FAIR Data Management Workflow for Synthetic Biology.

ACS synthetic biology·2026
Same author

A Decade of SBOL Visual: Growing Adoption of a Diagram Standard for Engineering Biology.

ACS synthetic biology·2025
Same author

The need for adaptability in detection, characterization, and attribution of biosecurity threats.

Nature communications·2024
Same author

Evaluating the Contribution of Model Complexity in Predicting Robustness in Synthetic Genetic Circuits.

ACS synthetic biology·2024
Same author

SeqImprove: Machine-Learning-Assisted Curation of Genetic Circuit Sequence Information.

ACS synthetic biology·2024
Same author

Investigating and Modeling the Factors That Affect Genetic Circuit Performance.

ACS synthetic biology·2023

Related Experiment Video

Updated: Aug 7, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.1K

SynBioSuite: A Tool for Improving the Workflow for Genetic Design and Modeling.

Zachary Sents1, Thomas E Stoughton2, Lukas Buecherl3

  • 1Department of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States.

ACS Synthetic Biology
|March 8, 2023
PubMed
Summary

Synthetic biology software tools like SBOLCanvas and iBioSim aid genetic circuit design but lack integration. SynBioSuite offers a cloud-based solution, automating data transfer and simulation for improved design-build-test-learn workflows.

Keywords:
APISBOLCanvasgenetic design automationiBioSimsynthetic biologyweb server

More Related Videos

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

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

Published on: February 8, 2017

17.7K
Automated Robotic Liquid Handling Assembly of Modular DNA Devices
11:22

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Published on: December 1, 2017

12.5K

Related Experiment Videos

Last Updated: Aug 7, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.1K
A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

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

Published on: February 8, 2017

17.7K
Automated Robotic Liquid Handling Assembly of Modular DNA Devices
11:22

Automated Robotic Liquid Handling Assembly of Modular DNA Devices

Published on: December 1, 2017

12.5K

Area of Science:

  • Synthetic Biology
  • Computational Biology
  • Bioengineering

Background:

  • Numerous software tools exist for synthetic biology, including SBOLCanvas, iBioSim, and SynBioHub, facilitating genetic circuit design and simulation.
  • Current tools support the design-build-test-learn cycle but often require manual, error-prone data transfer between applications.
  • Lack of integration hinders efficient workflow and increases the potential for design errors in synthetic biology research.

Purpose of the Study:

  • To address the integration challenges in synthetic biology software tools.
  • To develop a unified platform that automates the process of genetic circuit design and simulation.
  • To improve the efficiency and reduce errors in the design-build-test-learn workflow.

Main Methods:

  • Development of SynBioSuite, a cloud-based platform.
  • Implementation of an application programming interface (API) for automated data exchange.
  • Integration of existing tools (e.g., SBOLCanvas, iBioSim) within the SynBioSuite framework.

Main Results:

  • SynBioSuite automates the setup and retrieval of simulation results for designed genetic circuits.
  • The platform streamlines the transfer of information between disparate synthetic biology software tools.
  • Reduced manual effort and potential for errors in the genetic circuit design and simulation process.

Conclusions:

  • SynBioSuite enhances the synthetic biology design-build-test-learn process through automation and integration.
  • The cloud-based tool offers a more efficient and reliable approach to genetic circuit design and simulation.
  • Automating inter-tool communication is crucial for advancing synthetic biology research and development.