Bioprocess Workflow Interfaces for ELN-Linked Step Execution
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Solution Overview
Problem
The bioprocess development cycle is highly manual and disorganized, prone to errors due to the involvement of multiple scientists across different facilities, making it difficult to monitor and memorialize small deviations from the bioprocess plan during execution.
Innovation Solution
A cloud-based bioinformatics platform that provides automatic or semi-automatic bioprocess design, execution, and analysis, utilizing a recipe data model with unit operations, electronic laboratory notebook objects, and worksheet interfaces for flexible data entry and modification, allowing for the generation and maintenance of analysis-ready records.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If manual processes are used for bioprocess development, then flexibility in handling diverse experiments is maintained, but organization and error-proneness increase significantly
Solution Approach 1:
The bioprocess development cycle is divided into discrete unit operations (e.g., media preparation, inoculation, fermentation, harvesting) that can be independently configured and executed. Each unit operation is defined as a separate module with its own parameters and procedures, allowing flexible combination while maintaining systematic organization through the workflow engine.
Solution Approach 2:
A workflow engine serves as an intermediary system that coordinates between multiple scientists and facilities. The system provides standardized templates and configurations that mediate the manual processes, ensuring consistent organization and reducing errors while allowing adaptability through configurable parameters.
2Adaptability or versatility
If multiple scientists across different facilities collaborate manually, then diverse expertise is leveraged, but monitoring and memorializing deviations becomes difficult
Solution Approach 1:
The system implements automated feedback mechanisms that track actual execution parameters against planned bioprocess parameters. Deviations are automatically detected, recorded, and memorialized in the electronic laboratory notebook, providing continuous monitoring across all facilities and scientists involved in the collaboration.
Solution Approach 2:
Electronic copies of all bioprocess parameters, execution data, and deviations are maintained in a centralized database. The electronic laboratory notebook creates persistent records that replicate the entire bioprocess history, ensuring that information is preserved and accessible regardless of which scientist or facility is accessing the data.
3Manufacturing precision
If form-based step-by-step execution is used, then structured data capture is enforced, but flexibility to enter new information in different formats is reduced
Solution Approach 1:
The data entry system transitions from static forms to dynamic interfaces that can adapt to different data types and formats. The system maintains structured templates for consistent data capture while allowing users to input new information in various formats (text, numbers, units) and automatically converts or validates the data as needed.
Solution Approach 2:
The system allows parameters to be configured with flexible data types and validation rules. Users can define custom parameter formats, units, and validation criteria, enabling the system to accommodate diverse data entry requirements while maintaining structural integrity through configurable parameter schemas.
Data Source
AI summary
Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for automatic or semi-automatic bioprocess design, execution, and analysis. In one aspect, a system comprises receiving a request to execute a sequence of unit operations specified by a recipe representing a bioprocess, wherein each unit operation defines one or more steps to be performed, generating, for each step of each unit operation, a worksheet representing laboratory effects of performing the step and having a worksheet interface for displaying bioprocess data and receiving execution data, including initializing, for each worksheet, a corresponding electronic laboratory notebook object in an underlying electronic laboratory notebook subsystem, receiving execution data entered into the worksheet interface for a particular step of a first unit operation, and updating, in the electronic laboratory notebook subsystem, the corresponding electronic laboratory notebook object using the execution data.