Syntrack: Streamline Complex DNA Assembly Processes
Synthetic Biology Engineering Evolution Design SEED
2016
2016 Synthetic Biology: Engineering, Evolution & Design (SEED)
Poster Session
Accepted Posters
The assembly of multiple DNA fragments into final constructs is a complex multi-step process that requires close integration with laboratory automation systems and needs to incorporate QC/QA outcomes at multiple steps. In addition when dealing with large batches of DNA parts, which result in many different deliverable constructs, assembly steps often require re-work. Hence, tracking the required laboratory steps, QA/QC inputs, the location of the intermediates, and the status of the deliverables is a complex process.
To facilitate all critical DNA construction operations we have developed the SynTrack system at JGI. Syntrack is a dynamic, workflow-driven data management system that tracks the DNA build process starting from a standardized design file that defines the final construct deliverables to the hierarchical relationships of the DNA parts and intermediate fragments. Syntrack first generates DNA ordering forms, tracks when DNA parts are received, and then proceeds through all the subsequent PCR, assembly and cloning steps. The system captures QC outcomes, defines location in plates, and creates interactive plate maps that operators can query. Driven by DNA assembly workflows, the system leverages all construct design and production operations, and integrates with laboratory automation equipment throughout the DNA construction process. For example, it first generates instructions for setting up assembly and cloning reactions with the Labcyte ECHO. Then, it integrates outputs from plate readers, colony pickers, and nextgen sequencers. The system supplies a flexible method to allow for changes in the assembly process and the addition of re-work at any stage, allowing the ability to move backwards and forwards throughout the workflow. During all assembly steps, the status of the hierarchal DNA fragment structures is closely monitored and updated accurately with a date/time stamp of every fragment status change or action.
The source code is written in Django web framework. The code is open, modular, and optimized for rapid data entry with CSV or Excel inputs. The complex requirements of all DNA assembly data tracking have been condensed into more simple, secure interfaces that provide laboratory operators with the ability to see the status of their DNA constructs, anywhere in the process. The application integrates data from multiple sources within the assembly line with automated generation of plate map and well instructions. It handles DNA Assembly requests at a variety of levels, from an individual fragment to a batch of constructs. SynTrack also presents visual warnings or can deny access, when proper event sequence is not followed. We show that SynTrack supports ad hoc and modular application design. Without significant efforts, Syntrack produces a superior maintainable application that can adapted to changes in the workflow as technology evolves. Syntrack creates productivity enhancements and better process visibility to support a scalable DNA foundry operation.