Automated Workflow Compilation for Shared Instrument Scheduling
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Solution Overview
Problem
Current methods for synthesizing transcription activator-like effector nuclease (TALEN) pairs are inefficient, requiring separate vectors or lengthy subcloning procedures, limiting high-throughput construction and scalability in biological foundries.
Innovation Solution
A fully automated platform using a P2A self-cleavage sequence for one-step assembly of TALEN monomers onto a single vector, enabling the synthesis of 400 pairs of TALENs with over 96.2% success rate at a low material cost, facilitating genome-wide studies.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If separate vectors or subcloning procedures are used for synthesizing TALEN pairs, then traditional methods can be employed, but the synthesis process becomes inefficient and time-consuming
Solution Approach 1:
The patent combines the synthesis of both TALEN monomers into a single vector system. The first and second TALEN monomers are synthesized in the same biological foundry using the same set of instruments and reagents, eliminating the need for separate vectors and subcloning procedures. This merging of synthesis operations directly improves productivity and reduces the time required to generate TALEN pairs.
Solution Approach 2:
The patent performs preliminary synthesis of TALEN monomer libraries before final assembly. The biological foundry pre-synthesizes multiple TALEN monomers with different specificities and stores them as ready-to-use components. When a TALEN pair is needed, the system simply retrieves and combines pre-synthesized monomers rather than synthesizing them de novo, significantly reducing synthesis time.
2Productivity
If multiple processes share the same instrument in a biological foundry, then instrument utilization increases, but scheduling conflicts arise
Solution Approach 1:
The patent segments the TALEN synthesis process into distinct modular operations that can be scheduled independently. The biological foundry divides the synthesis of first and second TALEN monomers into separate workflow instances that can be executed in parallel or sequentially based on instrument availability. This segmentation allows the scheduling system to manage multiple processes sharing the same instruments without conflicts.
Solution Approach 2:
The patent creates a universal biological foundry platform that can execute multiple different TALEN synthesis workflows using the same set of instruments and reagents. The system is designed to handle diverse synthesis protocols (e.g., Golden Gate assembly, Gibson assembly) on the same equipment, maximizing instrument utilization while maintaining flexibility in scheduling different process types.
3Extent of automation
If traditional TALEN synthesis methods are used, then established protocols can be followed, but the process requires significant human intervention and is not scalable
Solution Approach 1:
The patent implements self-service automation where the biological foundry system automatically manages the entire TALEN synthesis process without human intervention. The system autonomously selects appropriate TALEN monomers from libraries, schedules synthesis operations across multiple instruments, monitors progress, and assembles final TALEN pairs. The workflow includes automatic error handling and quality control, making the process fully scalable while maintaining simplicity through standardized automated protocols.
Data Source
AI summary
Systems and methods for automated workflow include assigning a set of first targets to an uncompiled first workflow. The uncompiled first workflow specifies a first set of process modules. Each such module is associated with a subset of unit operations. Each unit operation includes a time interval and specifies an instrument. For each target in the set of first targets, the uncompiled workflow is translated into an instance of a compiled first workflow that includes a linear temporal order of unit operations. This translating resolves a logical condition of the uncompiled first workflow.