Contact

  • Academic
    University - Student Department: ICME Operations Position: Graduate

All Publications

  • OpenEvo: An Open-Source Platform for Automated Evolution and Analysis. bioRxiv : the preprint server for biology Cocioba, S. S., Huang, P. C., Mallon, J., Chan, Z., Geremew, A. W., Bisson, A., Kyriakakis, P. 2026

    Abstract

    Here we introduce OpenEvo, a fully open-source, low-cost turbidostat platform for automated continuous culture and directed evolution experiments. Existing tools are expensive, complex, or lack open-source hardware; OpenEvo addresses this gap with a complete, fully automated evolution platform with detailed, illustrated construction instructions for beginners, open-source software and firmware, priced around $300. An optional PC-based interface offers enhanced functionality, including remote access, programmable evolution cycles, programmable LED stimulation, and a data visualization tool. OpenEvo can cycle through three types of media for positive, negative, and neutral selection conditions, supporting a wide range of experimental designs. We validate the use of OpenEvo by evolving Haloferax volcanii to grow from 15% to 12% salt over ~150 cycles, ~1,000 hours. Evolved cells grew 55% faster than wild-type at 12% salt. Whole-genome sequencing of adapted cells found SNPs and large deletions. We also demonstrate positive and negative selection using the OpenEvo LEDs to drive optogenetics via a Phytochrome B-based optogenetic tool, with light as the selection stimulus during over 4000 hours of growth. OpenEvo lowers the technical and cost barriers for continuous evolution experiments, serves as a teaching tool, and is designed to grow an open community of users who share modifications.

    View details for DOI 10.64898/2026.07.06.735356

    View details for PubMedID 42465385

    View details for PubMedCentralID PMC13370392