Smart Wrapper Bioinformatics Pipeline Error Correction
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Solution Overview
Problem
Current bioinformatics pipelines require users to have extensive knowledge of various tools and file formats, leading to errors and inconsistencies that can result in incorrect genetic analysis outcomes due to format mismatches and tool inefficiencies.
Innovation Solution
The implementation of smart wrappers within bioinformatics pipelines that can detect inconsistencies and errors, automatically adjust input data formats, and select alternative tools or resources to ensure correct analysis, thereby preventing errors and improving efficiency.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If users manually configure bioinformatics pipelines with multiple tools and file formats, then the pipeline can perform complex genomic analysis tasks, but the complexity of operation increases significantly and errors occur due to format mismatches and tool inconsistencies
Solution Approach 1:
The patent introduces smart wrappers as intermediary components between the user and the underlying bioinformatics tools. These wrappers automatically detect inconsistencies in file formats, data types, and tool parameters, and perform corrective actions without user intervention. This mediator layer shields users from the complexity of managing multiple tools and formats while maintaining full pipeline functionality.
Solution Approach 2:
The smart wrappers implement self-service mechanisms by autonomously detecting errors and inconsistencies in the pipeline configuration and data flow. The system automatically corrects format mismatches, selects appropriate tools based on data characteristics, and recovers from errors without requiring user expertise or manual intervention, thereby simplifying operation while preserving versatility.
2Measurement precision
If users select appropriate tools for each analysis step, then the analysis accuracy improves, but the likelihood of format inconsistencies and tool incompatibilities increases
Solution Approach 1:
The smart wrappers incorporate feedback mechanisms that continuously monitor the data flow between tools, detecting inconsistencies in file formats, data types, and parameters. When inconsistencies are detected, the wrappers automatically adjust the data or tool configuration to ensure compatibility, thereby maintaining both analysis accuracy through appropriate tool selection and execution reliability through automatic error correction.
Solution Approach 2:
The system implements beforehand cushioning by proactively detecting potential incompatibilities between tools and data formats before they cause pipeline failure. The smart wrappers prepare corrective actions in advance, such as converting file formats or adjusting parameters, to prevent errors from occurring during pipeline execution, thus maintaining both accuracy and reliability.
3Reliability
If the pipeline includes comprehensive error checking and correction mechanisms, then the pipeline reliability improves, but the processing time and computational resources increase
Solution Approach 1:
The smart wrappers perform preliminary actions by detecting and correcting potential errors at the beginning of each tool execution, rather than allowing the pipeline to fail later. This early detection and correction approach ensures high reliability while minimizing the time penalty, as the wrappers are designed to perform quick automated corrections without requiring extensive reprocessing or user intervention.
Data Source
AI summary
The invention relates to bioinformatics pipelines and wrapper scripts that call executables in those pipelines and that also identify beneficial changes to the pipelines. A tool in a pipeline has a smart wrapper that can cause the tool to analyze the sequence data it receives but that can also select a change to the pipeline when circumstances warrant. In certain aspects, the invention provides a system for genomic analysis. The system includes a processor coupled to a non-transitory memory. The system is operable to present to a user a plurality of genomic tools organized into a pipeline. At least a first one of the tools comprises an executable and a wrapper script. The system can receive instructions from the user and sequence data—instructions that call for the sequence data to be analyzed by the pipeline—and select, using the wrapper script, a change to the pipeline.