Overview

TeselaGen's BUILD module provides many of the functions of a traditional LIMS system, allowing users to manage inventory, valuable biosamples, and chain common laboratory actions into workflows that can be tracked and monitored. The BUILD module also plays a crucial role in capturing the computed design from the DESIGN module and turning into actionable instructions for automation. Finally, the BUILD module represents the best way to track down systematic errors that can destroy projects and make all the automation and AI in the world just about useless. Without control of systematic errors, machine learning approaches to data-driven product development become much harder.
 
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. The BUILD module starts from the premise that protocols are generated automatically and are (for the most part) handed off from the DESIGN module. This preserves the continuity of the DESIGN/BUILD connection and helps preserve provenance and process tracking, as well as enforcing discipline about the 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 researchers). 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 for automation.

Workflow design and execution

The BUILD module works because there are fundamental 'atomic' level actions or steps that are the same for any laboratory no matter what sort of science or engineering is underway. We call these fundamental actions 'Steps' which we build using our set of 'Tools', into complete 'Workflows'. By knitting the right set of fundamental steps together we can express just about any workflow imaginable. Our workflows follow a dataflow execution model where any acyclic directed workflow graph is accommodated. The list of "Tools" we have built continues to grow and are documented later on in the BUILD module help articles. An example of a workflow run in progress is shown in Figure 1.

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.

Biosample Management

We have extended the idea of strain management to accommodate biomaterials in general; DNA, Oligos, Strains, Proteins, Enzymes and Reagents, and other configurable domain-specific biomaterial types. In the case of 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 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. A microbial material database entry is shown in Figure 2.

Figure 2: Microbial material entries are linked to physical aliquotes as well as their canonical strain information.

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. A manufacturability check is shown in Figure 3.

Figure 3: Checking DNA material for manufacturability and price in BioShop.

This quick outline only scratches the surface of what the BUILD module provides. In the following set of Help Articles, we hope to explain many of the nice features the team here at TeselaGen has developed in collaboration with our customers in order to bring a high degree of functionality and a lot of value to your laboratory operations!

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