Genome Analysis Device Parallel Processing
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Solution Overview
Problem
Current genome visualization tools, such as Web browser-based viewers, face challenges in seamless visualization due to the need for recalculating and transmitting large amounts of data, leading to slow performance when changing display ranges, and require high-specification devices or additional software for standalone viewers.
Innovation Solution
A genome analysis device and method that utilizes a cloud-based or on-premises server system, functioning as both an application and Web server, performs parallel distributed processing to preprocess and analyze genome data, allowing for efficient generation and transmission of output data, enabling seamless visualization within a Web browser without the need for recalculation.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If Web browser type viewers recalculate display data based on large number of read sequences when display range changes, then visualization accuracy is maintained, but time required for updating display range increases significantly
Solution Approach 1:
The patent applies preliminary action by pre-calculating and storing analysis results of read sequences in a database before visualization is needed. When a user requests genome visualization, the system retrieves pre-computed data instead of calculating it in real-time, enabling fast display range changes while maintaining visualization accuracy.
Solution Approach 2:
The patent segments the large-scale genome data processing into multiple steps: (1) pre-processing and analysis of read sequences to generate intermediate results, (2) storage of these results in a database, and (3) retrieval and rendering of specific portions based on user-defined display ranges. This segmentation allows the system to maintain accuracy while reducing real-time computational burden.
2Ease of operation
If standalone viewers are used to achieve seamless visualization, then visualization smoothness is improved, but requirement for high specifications of computer device increases
Solution Approach 1:
The patent introduces a server as an intermediary between the user's Web browser and the genome analysis system. The server performs the computationally intensive tasks of data processing and analysis, while the client device only handles data retrieval and rendering. This intermediary approach enables seamless visualization in Web browsers without requiring high-specification client devices.
Solution Approach 2:
The patent replaces the traditional client-side computational mechanism with a server-side computational mechanism. Instead of requiring the user's computer to perform heavy calculations, the system substitutes this with remote server processing accessed through standard Web browser protocols, thereby reducing device complexity requirements while maintaining visualization quality.
3Measurement precision
If recalculation of display data is performed for each display range change, then data accuracy is maintained, but productivity of data transmission and processing decreases
Solution Approach 1:
The system performs preliminary calculation and analysis of genome data in advance, storing the results in a database. When users change display ranges, the system retrieves pre-computed data rather than recalculating it, thereby maintaining data accuracy while significantly improving processing productivity and reducing transmission time.
Data Source
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AI summary
There is provided a genome analysis device (2) configured to analyze genome data including a large quantity of fragmented genome base sequences, and transmit output data concerning the genome data in response to an output request from a client device (3) connected via a network (4), the genome analysis device (2) including: a storage unit (209) for storing data for visualization of multiple different layers, for the genome data; a request receiving unit (203) for receiving an output request from the client device (3); and an output data generating unit (207) for selecting data for visualization of a layer corresponding to the output request from the storage (209) when the request receiving unit (203) receives the output request, and generating output data based on the data for visualization of the selected layer.