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About DT4DDS

Digital Twin For DNA Data Storage (DT4DDS) is a customizable, digital representation of widely-used DNA data storage workflows, enabling data-driven experimental design and rational design of redundancy.

DT4DDS is offered both as a web-based service and a Python package providing a digital representation of DNA data storage workflows involving array synthesis, PCR, Aging, and Sequencing-By-Synthesis. By modelling each part of such user-defined workflows with fully customizable experimental parameters, it supports experimental design and aids in the design of redundancy for error-correction coding. DT4DDS also includes a pipeline for comprehensively analyzing errors in sequencing data, both from experiments and simulation.

DT4DDS is based on the following publications:

Gimpel, A.L., Stark, W.J., Heckel, R., Grass R.N. A digital twin for DNA data storage based on comprehensive quantification of errors and biases. Nat Commun 14, 6026 (2023). DOI:10.1038/s41467-023-41729-1

Gimpel, A.L., Stark, W.J., Heckel, R., Grass R.N. Challenges for error-correction coding in DNA data storage: photolithographic synthesis and DNA decay. bioRxiv 2024.07.04.602085 (2024). DOI:10.1101/2024.07.04.602085

Digital Twin

By combining a thorough quantification of the error sources with a customizable process model and analysis pipeline, DT4DDS can reproduce and predict experimental results. For more details on the error quantification and the approach, please refer to the manuscript.

Python Package

Running DT4DDS locally allows for custom workflows and full control over experimental parameters. For the full code and more information on how to use DT4DDS in Python, please visit the GitHub repository.