Three-dimensional genome visualization synchronization method and device, electronic equipment and storage medium

Abstract

The application provides a three-dimensional genome visualization synchronization method and device, electronic equipment and storage medium, including in response to the user on the target terminal initiated visualization operation, obtain visualization parameters; based on three-dimensional genome dataset name, query three-dimensional genome dataset matched with target species and genome location from database; and pretreat three-dimensional genome dataset; based on the pretreated three-dimensional genome dataset, render genome view according to the visualization mode of target terminal, and write visualization parameters and rendering state into shared configuration file; read shared configuration file on another terminal, and synchronize rendering genome view according to its corresponding visualization mode. The application introduces shared configuration file in multi-terminal visualization system, realizes real-time synchronization of two-dimensional linear view and three-dimensional immersive view. Significantly improve the efficiency and experience of cross-platform collaborative analysis.

Description

Technical Field

[0001] This invention relates to the field of technology, and more specifically, to a three-dimensional genome visualization synchronization method, apparatus, electronic device, and storage medium. Background Technology

[0002] Chromosomes are not arranged linearly in space, but rather folded in a specific organizational structure. This spatial organization of chromosomes allows two functional elements that are far apart to be brought close together, thus enabling them to interact and influence the transcriptional regulation of genes. Visualizing chromosomes can reveal the relationships between gene data.

[0003] However, existing tools such as 3D Genome Browser are mostly based on two-dimensional planar display. Projecting three-dimensional conformations onto two dimensions will result in the loss of depth information. At the same time, their limited visualization range and spatial data visualization effects will exacerbate the occlusion problem, limiting the visualization of the complex physical structure of the 3D genome, the interactions between physical structures, and the correlations with other omics data. Summary of the Invention

[0004] In view of this, the purpose of the present invention is to provide a three-dimensional genome visualization synchronization method, device, electronic device and storage medium to accurately present the three-dimensional information of the genome and the relationships between them.

[0005] Firstly, a method for synchronizing genome visualization is provided, applied to a multi-terminal visualization system. The multi-terminal visualization system includes a first terminal for two-dimensional genome visualization and a second terminal for three-dimensional genome visualization; including: In response to a user's visualization operation on the target terminal, obtain visualization parameters; the visualization parameters include at least the target species, genome location, and the name of the 3D genome dataset; Based on the name of the 3D genome dataset, query the database for 3D genome datasets that match the target species and genomic location; and preprocess the 3D genome datasets. Based on the preprocessed 3D genome dataset, the genome view is rendered according to the visualization method of the target terminal, and the visualization parameters and rendering status are written to the shared configuration file. The shared configuration file is read on another terminal, and the genome view is rendered synchronously according to its corresponding visualization method; the other terminal is a terminal with a different visualization method than the target terminal.

[0006] Optionally, based on the name of the 3D genome dataset, query the database for 3D genome datasets that match the target species and genomic location; and preprocess the 3D genome datasets, including: Call the external data processing interface corresponding to the target terminal so that the external data processing interface can parse the name of the three-dimensional genome dataset and extract the data identification information contained therein; Based on the data identification information, find the storage path of the corresponding three-dimensional genome dataset in the metadata index table; Based on the storage path, obtain a three-dimensional genome dataset that matches the target species and genome location; The three-dimensional genome dataset is preprocessed to adapt to the data format of the target terminal; Receives a preprocessed 3D genome dataset returned by an external data processing interface.

[0007] Optionally, the 3D genome dataset includes 3D spatial coordinate files and gene annotation files, and visualization parameters also include Hi-C data resolution; when the target terminal is a second terminal, the genome view is rendered according to the visualization method of the target terminal, including: A chromatin ball-and-stick structure model was constructed based on a three-dimensional spatial coordinate file. Each ball in the ball-and-stick structure model represents a genome segment, the length of which is determined by the Hi-C data resolution, and the sticks represent the sequence continuity connections between adjacent genome segments. Based on the genomic location information in the gene annotation file, the gene annotations in the gene annotation file are mapped to the corresponding balls in the ball-and-stick structure model; Immersive 3D rendering of the ball stick structure model and its mapped gene annotations.

[0008] Optionally, the three-dimensional genome dataset is a knowledge graph with nodes and relational topology; when the target terminal is a second terminal, the genome view is rendered according to the visualization method of the target terminal, including: Based on the nodes and their relationship information in the knowledge graph, a three-dimensional node and relationship network model is constructed in the world coordinate system of the augmented reality scene; where each node represents a genome and each relationship line represents the association between two genomes; In the 3D node and relationship network model, preset visual styles are used to distinguish and render different types of nodes and relationships.

[0009] Optionally, when the other terminal is the first terminal, the genome view is synchronously rendered according to its corresponding visualization method, including: Read the shared configuration file to obtain the target species, genome location, and current visualization rendering layer; Based on the target species and genomic location, load the corresponding linear genome sequence from the database; Two-dimensional visualization rendering is performed based on linear genome sequences to form a linear view synchronized with the current visualization rendering layer in the second terminal.

[0010] Optionally, the method also includes: In response to a user's visual action on the target terminal, a unique visual session identifier is generated; Name the shared configuration file with a unique visual session identifier; Correspondingly, reading the shared configuration file includes: Read the shared configuration file based on a unique visual session identifier.

[0011] Optionally, the method also includes: In response to an update operation performed by a user on any terminal, the shared configuration file is updated; update operations include adding a data layer, deleting a data layer, or highlighting a specified genome location; The shared configuration file is polled at preset time intervals; In response to the detection that the shared configuration file has been updated, the corresponding genome data is reloaded based on the updated shared configuration file, and the genome view is re-rendered according to the visualization method of each terminal.

[0012] Secondly, a genome visualization synchronization device is provided for use in a multi-terminal visualization system, the multi-terminal visualization system comprising a first terminal for two-dimensional genome visualization and a second terminal for three-dimensional genome visualization; including: The acquisition unit is used to acquire visualization parameters in response to a visualization operation initiated by the user on the target terminal; the visualization parameters include at least the target species, genome location, and the name of the three-dimensional genome dataset; The query and preprocessing unit is used to query the database for three-dimensional genome datasets that match the target species and genomic location based on the name of the three-dimensional genome dataset; and to preprocess the three-dimensional genome datasets. The first rendering unit is used to render the genome view based on the preprocessed three-dimensional genome dataset in a visualization manner according to the target terminal, and write the visualization parameters and rendering status into the shared configuration file. The second rendering unit is used to read the shared configuration file on another terminal and synchronously render the genome view according to its corresponding visualization method; the other terminal is a terminal with a different visualization method than the target terminal.

[0013] Thirdly, an electronic device is provided, including a processor, a communication interface, a memory, and a communication bus, wherein the processor, the communication interface, and the memory communicate with each other through the communication bus; Memory, used to store computer programs; A processor, when executing a program stored in memory, implements any of the methods of the first aspect.

[0014] Fourthly, a computer-readable storage medium is provided, wherein a computer program is stored therein, and when the computer program is executed by a processor, it implements any of the methods of the first aspect.

[0015] This invention provides a method, apparatus, electronic device, and storage medium for synchronizing genome visualization. It acquires visualization parameters in response to a user's visualization operation initiated on a target terminal; queries a database for a 3D genome dataset matching the target species and genomic location based on the dataset name; preprocesses the 3D genome dataset; renders the genome view according to the visualization mode of the target terminal based on the preprocessed 3D genome dataset, and writes the visualization parameters and rendering status to a shared configuration file; and reads the shared configuration file on another terminal and synchronously renders the genome view according to its corresponding visualization mode. This invention achieves real-time synchronization between two-dimensional linear views and three-dimensional immersive views by introducing a shared configuration file into a multi-terminal visualization system. After a user initiates a visualization operation on any terminal, another terminal can automatically load the same genomic regions and annotation content, accurately presenting the three-dimensional information of the genome and their interrelationships, significantly improving the efficiency and experience of cross-platform collaborative analysis.

[0016] To make the above-mentioned objects, features and advantages of the present invention more apparent and understandable, preferred embodiments are described below in detail with reference to the accompanying drawings. Attached Figure Description

[0017] To more clearly illustrate the technical solutions of the embodiments of the present invention, the accompanying drawings used in the embodiments will be briefly introduced below. It should be understood that the following drawings only show some embodiments of the present invention and should not be regarded as a limitation on the scope. For those skilled in the art, other related drawings can be obtained based on these drawings without creative effort.

[0018] Figure 1 A flowchart of a genome visualization synchronization method provided by an embodiment of the present invention is shown; Figure 2 A schematic diagram of an immersive three-dimensional view provided by an embodiment of the present invention is shown; Figure 3 A schematic diagram of a two-dimensional linear view provided by an embodiment of the present invention is shown; Figure 4 A schematic diagram of the structure of a genome visualization synchronization device provided in an embodiment of the present invention is shown; Figure 5A schematic diagram of the structure of an electronic device provided in an embodiment of the present invention is shown. Detailed Implementation

[0019] To make the objectives, technical solutions, and advantages of the embodiments of the present invention clearer, the technical solutions of the embodiments of the present invention will be clearly and completely described below with reference to the accompanying drawings. Obviously, the described embodiments are only some embodiments of the present invention, and not all embodiments. The components of the embodiments of the present invention described and shown in the accompanying drawings can generally be arranged and designed in various different configurations. Therefore, the following detailed description of the embodiments of the present invention provided in the accompanying drawings is not intended to limit the scope of the claimed invention, but merely to illustrate selected embodiments of the invention. All other embodiments obtained by those skilled in the art based on the embodiments of the present invention without inventive effort are within the scope of protection of the present invention.

[0020] This invention provides a method for synchronizing genome visualization, applied to a multi-terminal visualization system. This system includes a first terminal (such as a computer, tablet, etc.) for two-dimensional genome visualization and a second terminal (such as HoloLens, MetaQuest, or other augmented reality or virtual reality devices) for three-dimensional genome visualization. Figure 1 As shown, the method includes the following steps: Step S101: In response to the visualization operation initiated by the user on the target terminal, obtain the visualization parameters.

[0021] In this embodiment of the invention, visualization operation refers to the behavior of a user explicitly specifying the genome content to be viewed through interface interaction, such as selecting a dataset from a drop-down menu and entering a chromosome region in an AR device, or clicking on a gene on a PC to trigger a jump.

[0022] This operation generates a set of structured parameters. For example, visualization parameters include at least the target species (e.g., hg19), genomic location (e.g., chr1:2000-5000), and the name of the 3D genome dataset (e.g., MOGEN_GSE63525_K562_combined(hg19)). These parameters collectively define the context for subsequent data loading and rendering.

[0023] Step S102: Based on the name of the three-dimensional genome dataset, query the database for three-dimensional genome datasets that match the target species and genome location; and preprocess the three-dimensional genome datasets.

[0024] Specifically, based on the metadata associated with the dataset name, the corresponding Hi-C derived 3D coordinate file and accompanying annotation file are located in the backend database, and only the sub-region data that matches the current genome location are read.

[0025] Preprocessing includes format conversion, coordinate normalization, and lightweight compression to adapt to terminal rendering capabilities. For example, the original MOGEN output TXT file is converted to JSON format, retaining only the coordinates and track labels of specified areas to reduce transmission load.

[0026] Step S103: Based on the preprocessed 3D genome dataset, render the genome view according to the visualization method of the target terminal, and write the visualization parameters and rendering status into the shared configuration file.

[0027] Continuing from the previous example, if the target terminal is a second terminal (such as an augmented reality device), an immersive 3D view is rendered; if the target terminal is a first terminal (such as a PC), a 2D view such as gene structure and epigenetic modification signals is rendered in a linear coordinate system.

[0028] After rendering is complete, the key state information of the current session is serialized into structured data (such as JSON format) and written to a shared configuration file on the server. This configuration file serves as the core carrier for multi-terminal synchronization, ensuring the consistency of views across different terminals.

[0029] Specifically, when a user initiates a visualization operation for the first time, a globally unique visualization session identifier (e.g., sessionId: "b5f3a1c8") is generated. This session identifier is used to name the corresponding shared configuration file (e.g., session_b5f3a1c8.json) and serves as the entry credential for multi-user collaborative access.

[0030] For example, the information recorded in the shared configuration file includes, but is not limited to: session ID (e.g., sessionId:123456), track name in the current view (e.g., 3dmodel:MOGEN_GSE63525_K562_combined), species (e.g., organism:hg19), and genome position (e.g., position:chr1:2000-5000).

[0031] It should be noted that the Track name will be accumulated based on the type of event occurring in the current view (such as the addTrack event, removeTrack event, highlightPos event, etc.). For example, if the current view's Track name is Track1, a new Track2 will be generated when one Track event is added.

[0032] Step S104: Read the shared configuration file on another terminal and synchronously render the genome view according to its corresponding visualization method; the other terminal is a terminal with a different visualization method than the target terminal.

[0033] In this step, the shared configuration file is read based on a unique visual session identifier. Continuing the previous example, entering b5f3a1c8 on the PC will read the session file for the first time.

[0034] It should be noted that this embodiment supports bidirectional synchronization: when a second terminal (such as an AR device) creates a view, the PC can join and view the linear view of the same area; and vice versa. For example, if a user locates the HBB gene region in an AR application, the PC will automatically jump to chr11:5.2Mb and load the gene, ChIP-seq, etc., to achieve linked analysis of structure and function. This mechanism effectively bridges the gap between immersive exploration and traditional linear browsing.

[0035] This embodiment achieves real-time synchronization between two-dimensional linear views and three-dimensional immersive views by introducing a shared configuration file into a multi-terminal visualization system. After a user initiates a visualization operation on one terminal, the other terminal can automatically load the same genomic region and annotation content, accurately presenting the three-dimensional information of the genome and the relationships between them, significantly improving the efficiency and experience of cross-platform collaborative analysis.

[0036] Based on the above embodiments, the database is queried for 3D genome datasets that match the target species and genomic location, based on the name of the 3D genome dataset; and the 3D genome dataset is preprocessed, including: Step S102A: Call the external data processing interface corresponding to the target terminal to parse the name of the three-dimensional genome dataset and extract the data identification information contained therein.

[0037] This parsing is performed on the server side, avoiding the need for the target terminal to handle complex string processing.

[0038] Step S102B: Based on the data identification information, find the storage path of the corresponding three-dimensional genome dataset in the metadata index table.

[0039] In this embodiment of the invention, a metadata index table (such as SQLite or Redis) is maintained to record the mapping relationship between the unique identifier of each dataset and its physical storage path (such as S3 bucket address or local NAS path). This identification information enables rapid retrieval, improving query efficiency.

[0040] Step S102C: Based on the storage path, obtain a three-dimensional genome dataset that matches the target species and genome location.

[0041] Specifically, the interface extracts the corresponding genome's three-dimensional spatial coordinates and gene annotation files from the original .bigWig or .hic files based on the storage path. This process is completed on the server side, offloading the computational burden from the target terminal.

[0042] Step S102D: Perform format conversion preprocessing on the three-dimensional genome dataset to adapt it to the data format of the target terminal.

[0043] For example, convert TXT files to JSON format that Unity3D can directly instantiate, and convert Track annotations to arrays with type labels.

[0044] Step S102E: Receive the preprocessed three-dimensional genome dataset returned by the external data processing interface.

[0045] In this embodiment of the invention, the target terminal (such as AR glasses or a PC client) receives the processed lightweight data from an external data processing interface deployed on the server via HTTP or WebSocket protocols.

[0046] Based on the above embodiments, the visualization parameters also include Hi-C (High-throughput Chromosome Conformation Capture) data resolution. When the target terminal is a second terminal, rendering the genome view according to the visualization method of the target terminal includes: Step S103A1: Construct a chromatin ball-and-stick structure model based on a three-dimensional spatial coordinate file.

[0047] In this embodiment of the invention, each sphere corresponds to a genomic fragment (bin), the length of which is determined by the Hi-C data resolution (e.g., 5kb resolution, each bin = 5000bp). For example, in the chr11:5,225,000–5,230,000 interval, if the resolution is 5kb, a sphere is generated, and its center coordinates are calculated by the Hi-C modeling algorithm. Sticks connect adjacent bins, representing linear sequence continuity rather than spatial interaction.

[0048] Step S103A2: Based on the genomic location information in the gene annotation file, map the gene annotations in the gene annotation file to the corresponding balls in the ball-and-stick structure model.

[0049] For example, the HBB gene is located at chr11:5,225,464–5,227,071, falling within the aforementioned 5kbbin. Therefore, its track elements (such as exon structures) are anchored to the three-dimensional coordinates of this sphere. If the gene spans multiple bins, it is split and mapped to multiple spheres to ensure spatial accuracy.

[0050] Step S103A3: Immersive 3D rendering of the ball stick structure model and the mapped gene annotations.

[0051] The data types in the 3D genome dataset are divided into physical structure, label data, quality data, and region data. The physical structure is rendered using a ball-and-stick model. Specifically, the Unity3D engine can be used for 3D rendering. The Unity3D engine instantiates a ball and a stick in the AR world coordinate system and floats the symbol labels of the corresponding gene fragments around the outer perimeter of the ball.

[0052] Tag data is rendered using text labels, quality data is rendered using rings of different colors, and region data is rendered using consecutive highlighted regions of alternating colors. Figure 2 As shown, an immersive 3D rendering of the genome is presented. Users can use gestures to zoom and rotate the model to visually observe the spatial proximity of the HBB gene and its distal enhancers.

[0053] Based on the above embodiments, the three-dimensional genome dataset is a knowledge graph with nodes and relational topology; when the target terminal is a second terminal, rendering the genome view according to the visualization method of the target terminal includes: Step S103B1: Based on the nodes and their relationship information in the knowledge graph, construct a three-dimensional node and relationship network model in the world coordinate system of the augmented reality scene.

[0054] In this embodiment of the invention, the three-dimensional genome dataset is generalized into a knowledge graph with a node-relationship topology, where the genome segments that originally represented chromatin bins correspond to entity nodes in the knowledge graph, and the functional associations implied by linear adjacency on chromosomes correspond to semantic relationships in the knowledge graph.

[0055] The structure of the knowledge graph is mapped to a three-dimensional space: each node (such as a gene or regulatory element) is assigned a three-dimensional coordinate, and each relationship (such as regulation, association, or location) connects two nodes with a line. This mapping uses graph layout algorithms (such as force-directed layout or graph neural network embedding) to generate a spatial arrangement that brings semantically similar nodes close to each other in three-dimensional space, thereby preserving the core characteristic of spatial proximity of distant elements in the original genome's three-dimensional conformation.

[0056] Step S103B2: In the 3D node and relationship network model, use a preset visual style to distinguish and render different types of nodes and relationships.

[0057] Specifically, different geometric shapes and colors are assigned according to node type; relation edges are colored according to semantic type, such as green for regulation and orange for co-expression.

[0058] This visual encoding mechanism adopts the design concept of functional annotation differentiation in the genome track, transferring the logic of hierarchical display of different omics data in a linear genome to the multidimensional semantic space of a knowledge graph. This allows users to intuitively identify complex biomedical associations in an immersive environment. Through this technology, the visualization framework originally used to analyze chromatin spatial folding can be effectively reused in knowledge-driven multi-omics integration analysis scenarios.

[0059] Based on the above embodiments, when the other terminal is the first terminal, synchronously rendering the genome view according to its corresponding visualization method includes: Step S104A: Read the shared configuration file to obtain the target species, genome location, and current visualization rendering layer.

[0060] For example, the PC client uses Ajax to poll the JSON shared configuration file on the server to obtain the chr11:5.2Mb area of ​​the current session ID and the layer name Track of the current view.

[0061] Step S104B: Based on the target species and genomic location, load the corresponding linear genome sequence into the database.

[0062] In this step, the PC-side data processing interface is called to obtain the reference sequence fragment of hg19chr11, which is used as the coordinate reference for rendering.

[0063] It should be noted that the first terminal and the second terminal can share the same database, or they can each build their own independent database.

[0064] Step S104C: Perform two-dimensional visualization rendering based on the linear genome sequence to form a linear view synchronized with the current visualization rendering layer in the second terminal.

[0065] In this embodiment of the invention, the first terminal uses a web-based genome browser framework (such as IGV.js or a customized Delta browser) to render a two-dimensional linear view. This framework uses JavaScript to call data visualization libraries such as D3.js to convert the linear genome sequence and its annotation information loaded from the database into an interactive graphical interface.

[0066] Specifically, based on the genomic location (e.g., chr11:11.1–11.3Mb) and track list (e.g., “gene”) in the shared configuration file, sequence fragments of the corresponding interval are obtained from the reference genome database, and their associated gene annotation files (e.g., GTF format) are loaded. Subsequently, the physical location of the genome is represented by a horizontal coordinate axis, and different types of tracks are arranged hierarchically in the vertical direction.

[0067] exist Figure 3The linear view shown renders a track named "LCR_Gene" that contains information on multiple genes. Each gene is represented by a line segment with an arrow, the direction of which indicates the transcription direction (forward or backward).

[0068] For example, “HBB”, “HBG1”, “HBG2” and “HBE1” are all members of the globin gene family located on chromosome 11. Their coding regions are represented by rectangles, and exons are connected by short horizontal lines to represent introns.

[0069] These genes are spatially clustered together to form a typical gene cluster, with their regulatory elements (such as LCRs) also located nearby, reflecting a complex cis-regulatory network.

[0070] In addition, the Selecttracks button at the top of the view allows users to dynamically add or remove tracks, while the zoom controls above (such as 10,000,000) are used to adjust the display resolution, supporting multi-scale browsing from macro to micro.

[0071] When a gene is highlighted on the AR device, the corresponding transcript can be highlighted on the PC device through an event listening mechanism, enabling cross-terminal collaborative analysis.

[0072] Through the aforementioned technical means, the two-dimensional linear view not only provides precise annotation of genome structure, but also supports real-time synchronization with the three-dimensional immersive view, enabling researchers to deeply interpret gene function and regulatory relationships in traditional analysis modes.

[0073] Based on the above embodiments, the method further includes: Step S105: In response to an update operation performed by the user on any terminal, update the shared configuration file.

[0074] Update operations include adding data layers, deleting data layers, or highlighting specific genome locations.

[0075] For example, after adding the track "H3K4me3" to the AR client, a new trackName field is added to the configuration file.

[0076] Step S106: Poll the shared configuration file at preset time intervals.

[0077] For example, both ends send GET requests to the server at 1-second intervals to check if the file's last modified timestamp has changed.

[0078] Step S107: In response to the detection that the shared configuration file has been updated, the corresponding genome data is reloaded based on the updated shared configuration file, and the genome view is re-rendered according to the visualization method of each terminal.

[0079] In this embodiment of the invention, when a user actively changes the genome coordinate position on a first terminal such as a PC (e.g., from chr1:2000-5000 to chr1:3000-4000), the shared configuration file will be updated.

[0080] This update operation will immediately trigger the data synchronization service on the second terminal. After the second terminal (such as an AR device) detects the configuration file change, it reads and parses the above JSON content, and recalculates the number of genome bins to be displayed based on the new genome location chr1:3000-4000 and the resolution binsize=1000.

[0081] Since the region is 1000bp long, which corresponds exactly to a Hi-C bin, the second terminal updates the ballstick model to contain only one sphere and positions it at the corresponding spatial coordinates generated by the 3D modeling algorithm. At the same time, the gene's symbol tag is mapped onto the sphere to complete the precise synchronization of the view.

[0082] Through this synchronization mechanism, interactive operations on any terminal can drive the dynamic response of another terminal by sharing a configuration file, achieving a collaborative visual experience that is cross-platform, low-latency, and consistent in state.

[0083] Based on the same inventive concept, embodiments of the present invention provide a genome visualization synchronization device applied to a multi-terminal visualization system. The multi-terminal visualization system includes a first terminal for two-dimensional genome visualization and a second terminal for three-dimensional genome visualization. Figure 4 As shown, it includes: The acquisition unit 401 is used to acquire visualization parameters in response to a visualization operation initiated by the user on the target terminal.

[0084] Visualization parameters should include at least the target species, genomic location, and the name of the 3D genome dataset.

[0085] The query and preprocessing unit 402 is used to query the database for three-dimensional genome datasets that match the target species and genome location based on the name of the three-dimensional genome dataset; and to preprocess the three-dimensional genome datasets.

[0086] The first rendering unit 403 is used to render a genome view based on the preprocessed three-dimensional genome dataset in a visualization manner according to the target terminal, and write the visualization parameters and rendering status into a shared configuration file.

[0087] The second rendering unit 404 is used to read the shared configuration file on another terminal and synchronously render the genome view according to its corresponding visualization method; the other terminal is a terminal with a different visualization method than the target terminal.

[0088] Based on the same technical concept, embodiments of the present invention also provide an electronic device, such as... Figure 5 As shown, it includes a processor 501, a communication interface 502, a memory 503, and a communication bus 504, wherein the processor 501, the communication interface 502, and the memory 503 communicate with each other through the communication bus 504.

[0089] Memory 503 is used to store computer programs; The processor 501 is used to implement the steps of the genome visualization synchronization method when executing the program stored in the memory 503.

[0090] The communication bus mentioned in the above electronic devices can be a Peripheral Component Interconnect (PCI) bus or an Extended Industry Standard Architecture (EISA) bus, etc. This communication bus can be divided into address bus, data bus, control bus, etc. For ease of illustration, only one thick line is used to represent it in the diagram, but this does not mean that there is only one bus or one type of bus.

[0091] The communication interface is used for communication between the aforementioned electronic devices and other devices.

[0092] The memory may include random access memory (RAM) or non-volatile memory (NVM), such as at least one disk storage device. Optionally, the memory may also be at least one storage device located remotely from the aforementioned processor.

[0093] The processors mentioned above can be general-purpose processors, including central processing units (CPUs), network processors (NPs), etc.; they can also be digital signal processors (DSPs), application-specific integrated circuits (ASICs), field-programmable gate arrays (FPGAs), or other programmable logic devices, discrete gate or transistor logic devices, or discrete hardware components.

[0094] In another embodiment of the present invention, a computer-readable storage medium is also provided, which stores a computer program that, when executed by a processor, implements the steps of any of the above-described genome visualization synchronization methods. Specific implementation details can be found in the method embodiments and will not be repeated here.

[0095] The genome visualization synchronization device provided in this embodiment of the invention can be specific hardware on a device or software or firmware installed on the device. The implementation principle and technical effects of the device provided in this embodiment of the invention are the same as those in the foregoing method embodiments. For the sake of brevity, any parts not mentioned in the device embodiments can be referred to the corresponding content in the foregoing method embodiments. Those skilled in the art will clearly understand that, for the sake of convenience and brevity, the specific working processes of the systems, devices, and units described above can all be referred to the corresponding processes in the above method embodiments, and will not be repeated here.

[0096] In the embodiments provided by this invention, it should be understood that the disclosed apparatus and method can be implemented in other ways. The apparatus embodiments described above are merely illustrative. For example, the division of units is only a logical functional division, and in actual implementation, there may be other division methods. Furthermore, multiple units or components may be combined or integrated into another system, or some features may be ignored or not executed. Additionally, the displayed or discussed mutual couplings, direct couplings, or communication connections may be through some communication interfaces; indirect couplings or communication connections between devices or units may be electrical, mechanical, or other forms.

[0097] The units described as separate components may or may not be physically separate. The components shown as units may or may not be physical units; that is, they may be located in one place or distributed across multiple network units. Some or all of the units can be selected to achieve the purpose of this embodiment according to actual needs.

[0098] In addition, the functional units in the embodiments provided by the present invention can be integrated into one processing unit, or each unit can exist physically separately, or two or more units can be integrated into one unit.

[0099] If the aforementioned functions are implemented as software functional units and sold or used as independent products, they can be stored in a computer-readable storage medium. Based on this understanding, the technical solution of this invention, essentially, or the part that contributes to the prior art, or a portion of the technical solution, can be embodied in the form of a software product. This computer software product is stored in a storage medium and includes several instructions to cause a computer device (which may be a personal computer, server, or network device, etc.) to execute all or part of the steps of the methods described in the various embodiments of this invention. The aforementioned storage medium includes various media capable of storing program code, such as USB flash drives, portable hard drives, read-only memory (ROM), random access memory (RAM), magnetic disks, or optical disks.

[0100] It should be noted that similar labels and letters in the following figures indicate similar items. Therefore, once an item is defined in one figure, it does not need to be further defined and explained in subsequent figures. In addition, the terms "first", "second", "third", etc. are used only to distinguish descriptions and should not be construed as indicating or implying relative importance.

[0101] Finally, it should be noted that the above-described embodiments are merely specific implementations of the present invention, used to illustrate the technical solutions of the present invention, and not to limit it. The scope of protection of the present invention is not limited thereto. Although the present invention has been described in detail with reference to the foregoing embodiments, those skilled in the art should understand that any person skilled in the art can still modify or easily conceive of changes to the technical solutions described in the foregoing embodiments within the technical scope disclosed in the present invention, or make equivalent substitutions for some of the technical features; and these modifications, changes, or substitutions do not cause the essence of the corresponding technical solutions to deviate from the spirit and scope of the technical solutions of the embodiments of the present invention. All should be covered within the scope of protection of the present invention. Therefore, the scope of protection of the present invention should be determined by the scope of the claims.

Claims

1. A method for synchronizing three-dimensional genome visualization, characterized in that, This is applied to a multi-terminal visualization system, which includes a first terminal for two-dimensional genome visualization and a second terminal for three-dimensional immersive genome visualization; comprising: In response to a user's visualization operation initiated on the target terminal, visualization parameters are obtained; the visualization parameters include at least the target species, genome location, and the name of the three-dimensional genome dataset; Based on the name of the three-dimensional genome dataset, query the database for three-dimensional genome datasets that match the target species and genome location; and preprocess the three-dimensional genome datasets. Based on the preprocessed 3D genome dataset, the genome view is rendered according to the visualization method of the target terminal, and the visualization parameters and rendering status are written into the shared configuration file; The shared configuration file is read on another terminal, and the genome view is rendered synchronously according to its corresponding visualization method; the other terminal is a terminal with a different visualization method than the target terminal.

2. The method according to claim 1, characterized in that, The process involves querying a database for a 3D genome dataset that matches the target species and its genomic location, based on the name of the 3D genome dataset. The preprocessing of the three-dimensional genome dataset includes: The external data processing interface corresponding to the target terminal is invoked so that the external data processing interface can parse the name of the three-dimensional genome dataset and extract the data identification information contained therein; Based on the data identification information, the storage path of the corresponding three-dimensional genome dataset is found in the metadata index table; Based on the storage path, obtain a three-dimensional genome dataset that matches the target species and genome location; The three-dimensional genome dataset is preprocessed to adapt to the data format of the target terminal; Receive the preprocessed three-dimensional genome dataset returned by the external data processing interface.

3. The method according to claim 1, characterized in that, The three-dimensional genome dataset includes a three-dimensional spatial coordinate file and a gene annotation file. The visualization parameters also include Hi-C data resolution. When the target terminal is a second terminal, rendering the genome view according to the visualization method of the target terminal includes: A chromatin ball-and-stick structure model is constructed based on the three-dimensional spatial coordinate file, wherein each ball in the ball-and-stick structure model represents a genome segment, the length of the genome segment is determined by the Hi-C data resolution, and the stick represents the sequence continuity connection between adjacent genome segments; Based on the genomic location information in the gene annotation file, the gene annotations in the gene annotation file are mapped to the corresponding balls in the ball-and-stick structure model; The ball-and-stick structure model and the mapped gene annotations were then subjected to immersive 3D rendering.

4. The method according to claim 1, characterized in that, The three-dimensional genome dataset is a knowledge graph with nodes and relational topology; When the target terminal is a second terminal, rendering the genome view according to the visualization method of the target terminal includes: Based on the nodes and their relationship information in the knowledge graph, a three-dimensional node and relationship network model is constructed in the world coordinate system of the augmented reality scene; wherein, each node represents a genome, and each relationship line represents the association between two genomes; In the three-dimensional node and relationship network model, a preset visual style is used to distinguish and render different types of nodes and relationships.

5. The method according to claim 1, characterized in that, When the other terminal is the first terminal, synchronously rendering the genome view according to its corresponding visualization method includes: Read the shared configuration file to obtain the target species, genome location, and current visualization rendering layer; Based on the target species and genomic location, the corresponding linear genome sequence is loaded into the database; Two-dimensional visualization rendering is performed based on the linear genome sequence to form a linear view synchronized with the current visualization rendering layer in the second terminal.

6. The method according to claim 5, characterized in that, The method further includes: In response to a user's visual action on the target terminal, a unique visual session identifier is generated; The shared configuration file is named with the unique visual session identifier; Correspondingly, reading the shared configuration file includes: The shared configuration file is read based on the unique visual session identifier.

7. The method according to claim 1, characterized in that, The method further includes: In response to an update operation performed by a user on any terminal, the shared configuration file is updated; the update operation includes adding a data layer, deleting a data layer, or highlighting a specified genome location; The shared configuration file is polled at preset time intervals; In response to the detection that the shared configuration file has been updated, the corresponding genomic data is reloaded based on the updated shared configuration file, and the genomic view is re-rendered according to the visualization method of each terminal.

8. A three-dimensional genome visualization synchronization device, characterized in that, This is applied to a multi-terminal visualization system, which includes a first terminal for two-dimensional genome visualization and a second terminal for three-dimensional genome visualization; it includes: The acquisition unit is used to acquire visualization parameters in response to a visualization operation initiated by a user on a target terminal; the visualization parameters include at least the target species, genome location, and the name of the three-dimensional genome dataset. The query and preprocessing unit is used to query the database for three-dimensional genome datasets that match the target species and genomic location based on the name of the three-dimensional genome dataset; and to preprocess the three-dimensional genome datasets. The first rendering unit is used to render a genome view based on the preprocessed three-dimensional genome dataset according to the visualization method of the target terminal, and write the visualization parameters and rendering status into a shared configuration file. The second rendering unit is used to read the shared configuration file on another terminal and synchronously render the genome view according to its corresponding visualization method; the other terminal is a terminal with a different visualization method than the target terminal.

9. An electronic device, characterized in that, It includes a processor, a communication interface, a memory, and a communication bus, wherein the processor, the communication interface, and the memory communicate with each other through the communication bus; The memory is used to store computer programs; When the processor executes the program stored in the memory, it implements the method described in any one of claims 1-7.

10. A computer-readable storage medium, characterized in that, The computer-readable storage medium stores a computer program that, when executed by a processor, implements the method described in any one of claims 1-7.

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