TeselaGen's BUILD module provides many of the functions of a traditional LIMS system, allowing users to manage inventory, bio samples, and chain common laboratory actions into workflows that can be tracked and monitored. The BUILD module also plays the crucial role of capturing the computed design from the DESIGN module and turning into actionable instructions for subsequent automation.
Experience with synthetic biology workflows has shown that creating seamless handoffs between the design of complex DNA libraries and their “in-practice” construction speeds research and benefits reproducibility. With our BUILD module we have started from the premise that protocols are generated automatically and are (for the most part) handed off from a DESIGN module. This preserves the continuity of the DESIGN/BUILD connection and helps preserve provenance and process tracking, as well as enforcing discipline about design of experiments and replicates.
Important features of the BUILD module:
- Design to build information translation
- Complex workflow design, execution, and monitoring
- Biological material management and sourcing
- Interfacing with suppliers of reagents and services
Integration with DESIGN module
An important role of the BUILD module is the seamless transformation of computed design information and automatically generated protocols into actionable instructions for automation (and/or laboratory workers). The BUILD module has many of the same functional features as a traditional LIMS (Laboratory Information Management System) but is unique in its ability to translate computed designs to worklists.
Workflow design and execution
Experience has shown that, although the fundamental sciences is common to all workflows, users can be very heterogeneous in their workflow goals and approaches. Rather than locking the BUILD platform into a particular approach or methodology, we have chosen to make the platform modular, following a dataflow execution model. Currently, acyclic directed workflow graphs are accommodated. A number of pre-programmed macros have been built including:
- PCR Prep and Execution
- Assembly Reaction Prep and Execution
- Clonal Transformation
- DNA Ordering
- Plate Registration, Barcoding, Reformatting, Rehydration, Replication, Consolidation, Combination
- Colony Plating
- Reaction Mapping
We have extended the idea of strain management to accommodate bio materials in general; DNA, Oligos, Strains, Proteins, Enzymes and Reagents and other configurable domain specific bio material types. In the case of a microbial material, the notion of a strain has been enhanced to include information about the individual plasmids the strain may have been modified to carry, information about physical aliquotes such as location, volume and concentration. Physical strains resulting from a synthetic biology workflow have built in provenance for the parent strain and the DNA design used to generate them. The system is also accommodates inventory management tasks such as recording and displaying locations and contents for samples contained in plates/wells, tubes and trays as well as laboratory equipment.
Interfacing with Suppliers
Automatic protocol generation raises the possibility of optimizing protocols against just-in-time availability of reagents and services. The DESIGN module performs this function, but actual fulfillment tasks are handed off to the BUILD module. In the BUILD module, actual orders to our early partners such as Twist and IDT are possible.
Figure 1: The Build module uses a macro style workflow execution paradigm. Distinct macro blocks are listed from top to bottom at left, their associated data and internal logic at right.
Figure 2: Microbial material entries are linked to physical aliquotes as well as their canonical strain information.