Syntrack 2: A Scalable, Automated DNA Assembly Production Workflow Management

The management of DNA production assembly processes is an important contributor to the operation of an effective DNA biofoundry. Due to the multi-step complex process, there is a necessity to integrate various inputs and outputs including DNA synthesis outcomes, instructions for automation equipment, and various QC/QA results to optimize the production of the final deliverables in the context of variable workflows that include re-work steps. We present a highly scalable, DNA assembly tracking system (SynTrack 2) for integrating all the necessary information, from design to end-product verification in a single software platform.

Syntrack 2 is a workflow-driven DNA construct management system that controls the DNA assembly processes. All assembly operations enforced by the design specification rules that define the hierarchical relationships of the DNA fragments and assembly strategies are modeled in our pre-built workflow paths. With composed user-friendly interfaces, SynTrack 2 divides the routine DNA construction tasks into pre-assembly and assembly workflows respectively. The system can help manage the ordering and completion of synthetic fragments and allows for subsets to be selected for different pre-assembly workflows.

Under the pre-assembly workflow, DNA receiving date, quantity, plate map location, and vendor information are tracked closely. Synthetic or PCR fragments can then be re-arrayed in a customized fashion through automatically generated instructions. Fragments can then be cleaned up, and quantified as part as the QC workflow before the assembly process can begin.

One or more instance of assembly workflows can be created based on previously finished single or merged pre-assembly workflows. Typical assembly workflows will include, assembly set-up (Chewback, Golden gate, yeast, etc), transformation, plating, colony picking, colony screens and sequencing, and Syntrack 2 will generate instructions for all the automation system, integrate the QA/QC information from each step and manage re-work in a construct specific manner.

Implemented in Django web framework with an embedded workflow engine, SynTrack 2 stores data in PostgreSQL database with table attributes representing objects that are defined within XML based rulesets for workflow configurations. All DNA assembly data tracking have been condensed into secure tabular formatted web interfaces with the ability to monitor and update the status of DNA constructs with time stamps. For altering DNA assembly, the workflow task supplies a flexible method based QA/QC to move the workflow backwards or forwards as required. We show that SynTrack 2 supports ad hoc component and modular design that can be adapted for rapid customization, enhancing productivity by close integration with laboratory automation and user-friendly interface.