Automated Workflow Compilation for Shared Lab Instrument Scheduling
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Solution Overview
Problem
Biological foundries face challenges in efficient scheduling and automation, leading to conflicts and underutilization, with manual handling of samples and instruments resulting in inefficiencies and contamination risks, particularly in synthesizing transcription activator-like effector nucleases (TALENs) for genome editing.
Innovation Solution
A fully automated platform using a single-step assembly scheme with a P2A self-cleavage sequence to synthesize TALEN pairs on a single vector, implemented on a robotic system like iBioFAB, enabling high-throughput synthesis of TALENs with over 96.2% success rate and minimal human intervention.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Object-affected harmful factors
If manual handling of samples and instruments is used, then flexibility in operation is maintained, but contamination risk and inefficiency increase
Solution Approach 1:
The system employs automated liquid handling robots and instrument controllers that perform sample processing, weighing, and instrument operation without human intervention. The robotic system autonomously executes workflows, manages sample tracking, and controls instruments, eliminating manual handling entirely and thus preventing contamination while maintaining operational flexibility through programmable automation
Solution Approach 2:
Manual mechanical operations are replaced with automated robotic systems equipped with precision liquid handlers, automated pipettes, and robotically controlled instruments. The system substitutes human-operated mechanical processes with computer-controlled automated mechanisms, eliminating contamination risks associated with manual handling while preserving operational adaptability through software control
2Productivity
If multiple processes share the same instrument without scheduling, then instrument utilization increases, but scheduling conflicts arise
Solution Approach 1:
The system implements a centralized scheduling software that continuously monitors instrument status, workflow progress, and resource availability. The scheduler receives real-time feedback from connected instruments and workflows, dynamically adjusts scheduling to prevent conflicts, and optimizes instrument utilization by allocating resources based on current system state and predicted future demands
Solution Approach 2:
The scheduling system serves multiple functions simultaneously: it acts as a conflict detection mechanism, a resource allocation optimizer, a workflow coordinator, and a system monitoring tool. This multi-functional approach manages the complexity of coordinating multiple processes across shared instruments while maximizing overall system productivity through integrated control
3Productivity
If TALEN synthesis is performed manually, then process flexibility is maintained, but synthesis efficiency and success rate decrease
Solution Approach 1:
The TALEN synthesis process is fully automated through robotic systems that perform DNA assembly, transformation, and vector construction without human intervention. The system autonomously executes multi-step synthesis protocols, manages reagent dispensing, and tracks synthesis progress, achieving high throughput and improved success rates while eliminating the inefficiencies of manual laboratory operations
Solution Approach 2:
The automated synthesis system operates continuously without interruption, executing TALEN synthesis workflows in an unbroken sequence. The robotic system maintains continuous operation through automated sample transfer, reagent replenishment, and instrument coordination, eliminating the start-stop nature of manual processes and thereby increasing synthesis throughput and consistency
4Ease of operation
If research scientists manually operate instruments, then adaptability to unexpected situations is improved, but time consumption and inefficiency increase
Solution Approach 1:
The system employs automated robotic workflows that independently execute instrument operations, sample processing, and data collection without requiring scientist intervention. Pre-programmed workflows autonomously manage complex multi-step procedures, dramatically reducing the time required per workflow while maintaining operational efficiency through optimized automated sequences and eliminating repetitive manual tasks
Data Source
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.