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CloneCoordinate: Open-Source Software for Collaborative DNA Construction.

Ethan Jeon1, Ziyang Shen1, Santiago Christ1

  • 1Williams College, Williamstown, Massachusetts 01267, United States.

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|November 18, 2025
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Summary
This summary is machine-generated.

Researchers can now manage molecular cloning more effectively with CloneCoordinate, a free electronic lab notebook in Google Sheets. This tool streamlines DNA construct design and troubleshooting, improving cloning efficiency for scientific teams.

Keywords:
CloneCoordinateDNA constructionautomationcloningplasmid construction

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Laboratory Management

Background:

  • Molecular cloning is crucial in life sciences, with researchers spending significant time on DNA construct design.
  • Existing computer-aided design tools lack robust support for managing the cloning process and documenting experimental workflows.
  • Inefficiencies in managing cloning projects lead to setbacks and reduced research productivity.

Purpose of the Study:

  • To develop a dedicated electronic laboratory notebook (ELN) for molecular cloning.
  • To provide researchers with a tool for better management and documentation of DNA construct assembly.
  • To enhance troubleshooting capabilities and improve overall cloning efficiency.

Main Methods:

  • Developed CloneCoordinate, a free, open-source ELN implemented entirely in Google Sheets.
  • Integrated features for real-time task prioritization, physical sample inventory management, and standardized data structures.
  • Utilized captured data for troubleshooting DNA assembly issues and analyzing cloning efficiency.

Main Results:

  • CloneCoordinate facilitates productive and collaborative cloning for individuals and teams.
  • The system enables data-driven insights into cloning efficiency and troubleshooting of assembly problems.
  • Information captured by CloneCoordinate can inform future improvements and potentially lead to automated recommendations.

Conclusions:

  • CloneCoordinate offers an accessible solution for managing and documenting molecular cloning workflows.
  • The ELN improves the efficiency and reproducibility of DNA assembly processes.
  • This approach sets a foundation for data-driven optimization of real-world cloning experiments.