CloneCoordinate: Open-source software for collaborative DNA construction

Jeon, E.; Shen, Z.; Christ, S.; Qi, E.; Fan, I.; Lee, N.; Morgan, O.; Ohl, M.; Millson, D.; Laker, M.; Pierson, A.; Villegas Garcia, E.; Zhang, Y.; Choi, A.; Iyengar, A.; Kim, R.; Lee, J.; Niedeck, L.; Oeien, V.; Rashid, M.; Seetharaman, N.; Singh, A.; Soble, D.; Yu, J.; Yu, K.; Berdy, S.; Chang, E.; Kitazono, R.; Ortiz, S.; Taylor, D.; Thuronyi, B. W.

doi:10.1101/2025.07.04.663221

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bioRxiv · 10.1101/2025.07.04.663221

CloneCoordinate: Open-source software for collaborative DNA construction

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Abstract

Custom DNA constructs have never been more common or important in the life sciences. Many researchers therefore devote substantial time and effort to molecular cloning, aided by abundant computer-aided design tools. However, support for managing and documenting the construction process, and for effectively handling and reducing the frequency of setbacks, is lacking. To address this need, we developed CloneCoordinate, a free, open-source electronic laboratory notebook specifically designed for cloning and fully implemented in Google Sheets. By maintaining a real-time, automatically prioritized task list, a uniform physical sample inventory, and standardized data structures, CloneCoordinate enables productive, collaborative cloning for individuals or teams. We demonstrate how the information captured by CloneCoordinate can be leveraged to troubleshoot assembly problems and provide data-driven insights into cloning efficiency. CloneCoordinate offers a new and uniquely accessible model for how to carry out, and iteratively improve on, real-world DNA assembly.

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Jeon, E., Shen, Z., Christ, S., Qi, E., Fan, I., Lee, N., Morgan, O., Ohl, M., Millson, D., Laker, M., Pierson, A., Villegas Garcia, E., Zhang, Y., Choi, A., Iyengar, A., Kim, R., Lee, J., Niedeck, L., Oeien, V., Rashid, M., Seetharaman, N., Singh, A., Soble, D., Yu, J., Yu, K., Berdy, S., Chang, E., Kitazono, R., Ortiz, S., Taylor, D., Thuronyi, B. W.. 2025-07-06. CloneCoordinate: Open-source software for collaborative DNA construction. https://doi.org/10.1101/2025.07.04.663221

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