Pose: phase I: creation of an open source ecosystem to repurpose DNA sequencers as an automation platform

The National Science Foundation (NSF) awarded $319,753 to the New York Genome Center, Inc. on July 15, 2025, under the NSF Technology, Innovation, and Partnerships program (CFDA 47.084) for a Phase I project to establish an open-source ecosystem enabling the repurposing of decommissioned DNA sequencers as flexible automation platforms. The project centers on expanding PySeq, an existing open-source toolkit for controlling DNA sequencer components, to transform obsolete sequencing instruments—originally valued at hundreds of thousands of dollars—into repurposed automation systems for modern biological research applications. By leveraging the advanced components inherent in decommissioned sequencers (including precision robotics, optics, temperature control, and microfluidic systems), the initiative addresses accessibility barriers in emerging fields such as spatial omics research by providing cost-effective alternatives to prohibitively expensive commercial automation platforms.

The project aims to deliver a comprehensive open-source ecosystem that unites researchers, engineers, and developers in advancing decommissioned sequencer repurposing capabilities for applications including cancer research, neurodegeneration studies, and immune response investigation. Through coordinated ecosystem development, the award supports improvements in research throughput, expanded laboratory accessibility to automation technologies, reduction in electronic waste, and greater standardization in biological research methodologies. The performance period extends through June 30, 2026, with work conducted at the awardee's location in New York, NY.

Abstract

As DNA sequencing technology rapidly evolves, once state-of-the-art equipment, originally priced in the hundreds of thousands of dollars, often becomes obsolete in less than a decade. Consequently, thousands of DNA sequencers are being decommissioned and, without a clear use, are either discarded or sold on secondary markets at a fraction of their original cost. Despite being outdated for sequencing, these instruments still contain highly valuable components including precision robotics, advanced optics, temperature control, and microfluidic systems. With the right software, engineering support, and experimental framework, these components could be repurposed into powerful platforms for automating a wide range of modern biological assays, thereby accelerating research and discovery. In particular, the emerging field of spatial omics offers transformative insights into important biological processes such as cancer, neurodegeneration, and immune response, but is currently hindered by its reliance on commercial automation platforms that remain prohibitively expensive to many laboratories. This project addresses this challenge by establishing an open-source ecosystem that unites researchers, engineers, and developers working towards the common goal of transforming decommissioned DNA sequencers into flexible automation platforms. This initiative will improve throughput, increase accessibility, reduce electronic waste, and promote greater standardization in biological research. This project builds upon pyseq, an open-source toolkit developed to control individual components within DNA sequencers, enabling their use in spatial omics and other biomedical research applications. The primary goal is to unlock the full potential of decommissioned DNA sequencers by creating an open-source ecosystem centered around pyseq, transforming these powerful but unused instruments into flexible platforms for laboratory automation. The project is realized through three main aims: (I) engage directly with current pyseq users to establish a core community of contributors focused on developing control tools, protocols, and documentation; (II) collaborate with users and developers to establish sustainable governance structures that support long-term community development and open-source philosophy; and (III) expand the user base by disseminating technological knowledge, procedures, best practices, and new perspectives to researchers utilizing laboratory automation. Through the exchange of protocols, hardware modifications, maintenance procedures, and software tools, the overarching goal is to build a self-sustained community that will launch pyseq OSE as a robust platform that transforms once-obsolete instruments into powerful, accessible tools for modern science. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the foundation's intellectual merit and broader impacts review criteria.- subawards are not planned for this award.