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Biofoundry Palette: Planning-Assistant Software for Liquid Handler-Based Experimentation and Operation in the

Sung Cheon Ko1,2, Mingu Cho1, Hyun Jeong Lee1,2

  • 1Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea.

ACS Synthetic Biology
|September 29, 2022
PubMed
Summary

Biofoundry Palette software streamlines synthetic biology by automating pre-experiment planning for liquid handler workflows. This tool enhances biofoundry operations, reducing errors in gene cloning and genome engineering.

Keywords:
biofoundryhuman errorslab automationreproducibilityworkflow

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Area of Science:

  • Synthetic biology
  • Biofoundry automation
  • Bioinformatics software development

Background:

  • Lab automation and biofoundry facilities enable high-throughput synthetic biology experiments.
  • Pre-experiment procedures in biofoundry workflows remain underdetermined, posing challenges for consistent execution.
  • Automated gene cloning and genome engineering require precise planning and management.

Purpose of the Study:

  • To develop a Python-based planning assistant software, Biofoundry Palette, for biofoundry liquid handler operations.
  • To provide precise, project-specific information for pre-experiment units within biofoundry workflow modules.
  • To address the underdetermined nature of before-experiment procedures in automated synthetic biology.

Main Methods:

  • Development of a Python-based software tool named Biofoundry Palette.
  • Integration of Biofoundry Palette into the biofoundry workflow for liquid handler-based experimentation.
  • Generation of unique information sets for pre-experiment units based on synthetic biology project requirements.

Main Results:

  • Biofoundry Palette successfully generated over 200 unique information sets for automated experiments.
  • Demonstrated application in automated gene cloning and pathway construction.
  • The software provides precise planning and management information for biofoundry operations.

Conclusions:

  • Biofoundry Palette facilitates the faithful execution of biofoundry workflows by securing before-experiment units.
  • The software has the potential to lower human error rates in synthetic biology applications.
  • Successful biofoundry operations for synthetic biology are enhanced through automated planning and management.