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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
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.
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.
