Automated Workflow Translation for Multi-Instrument Foundry Scheduling
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Solution Overview
Problem
Existing biological foundries face challenges in efficiently scheduling multiple processes, leading to conflicts and underutilization, particularly in the synthesis of transcription activator-like effector nucleases (TALENs) due to the need for separate vector synthesis and subcloning, which limits high-throughput genetic screening and scalability.
Innovation Solution
A fully automated platform using a P2A self-cleavage sequence to synthesize TALEN pairs in a single transcript format, implemented on a versatile biological foundry like iBioFAB, enabling one-step assembly of TALENs with high fidelity and reduced material cost, allowing for large-scale genome-wide studies.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If separate vector synthesis and subcloning methods are used for TALEN production, then traditional workflows can be maintained, but throughput is limited and genetic screening efficiency is reduced
Solution Approach 1:
The patent combines multiple separate steps (vector synthesis, subcloning, and TALEN production) into a single integrated workflow using Golden Gate assembly. This merging of operations allows all TALEN pairs required for genome-wide screening to be synthesized simultaneously in one reaction, dramatically increasing throughput while reducing workflow complexity.
Solution Approach 2:
The patent segments the TALEN synthesis process into modular components that can be assembled through Golden Gate cloning. By designing the system with standardized modules (promoters, TALEN pairs, terminators) that can be independently synthesized and then assembled, the workflow achieves both high throughput and ease of implementation.
2Productivity
If multiple processes share the same instrument in a biological foundry, then instrument utilization improves, but scheduling conflicts arise without proper coordination
Solution Approach 1:
The patent implements a scheduling system that monitors instrument availability and workflow progress in real-time. The system provides feedback to adjust scheduling decisions, allowing multiple processes to share instruments efficiently while preventing conflicts. The scheduler can dynamically allocate resources based on current system state and predicted future needs.
Solution Approach 2:
The scheduling system is designed to be dynamic rather than static, allowing it to adapt to changing conditions in the biological foundry. The scheduler can modify process timing and resource allocation based on actual instrument availability, process progress, and emerging conflicts, ensuring high utilization without sacrificing reliability.
3Stability of the object's composition
If a biological foundry processes tasks at the lowest common denominator, then system stability is maintained, but overall efficiency and productivity are reduced
Solution Approach 1:
The patent changes key parameters of the TALEN synthesis process by implementing Golden Gate assembly with optimized reaction conditions, standardized modules, and automated workflows. These parameter changes enable the system to operate at higher speeds and efficiencies while maintaining stability through rigorous validation and quality control measures.
Solution Approach 2:
The patent performs preliminary actions by pre-designing and validating standardized modular components before implementing the full workflow. Promoters, TALEN pairs, and terminators are pre-characterized and tested, allowing the system to maintain stability while achieving high productivity through standardized, pre-validated operations.
Data Source
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AI summary
Systems and methods for automated workflow comprise 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 comprising a linear temporal order of unit operations, each including execution instructions for an addressed instrument. A set of second targets is obtained and assigned a second uncompiled workflow. Compilation of the second uncompiled workflow for each second target produces a different instance of a compiled second workflow. Each second compiled workflow comprises a linear temporal order of unit operations, with each unit operation including execution instructions for an addressed instrument and specifying a time interval.