CN109326330A - The production method of analysis of biological information tool, device and can storage medium - Google Patents
The production method of analysis of biological information tool, device and can storage medium Download PDFInfo
- Publication number
- CN109326330A CN109326330A CN201811004190.9A CN201811004190A CN109326330A CN 109326330 A CN109326330 A CN 109326330A CN 201811004190 A CN201811004190 A CN 201811004190A CN 109326330 A CN109326330 A CN 109326330A
- Authority
- CN
- China
- Prior art keywords
- analysis
- biological information
- order
- analysis module
- output
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Granted
Links
- 238000004458 analytical method Methods 0.000 title claims abstract description 149
- 238000004519 manufacturing process Methods 0.000 title claims abstract description 13
- 238000000034 method Methods 0.000 claims abstract description 95
- 230000008569 process Effects 0.000 claims abstract description 85
- 230000002452 interceptive effect Effects 0.000 claims abstract description 19
- 241000208340 Araliaceae Species 0.000 claims description 5
- 235000005035 Panax pseudoginseng ssp. pseudoginseng Nutrition 0.000 claims description 5
- 235000003140 Panax quinquefolius Nutrition 0.000 claims description 5
- 235000008434 ginseng Nutrition 0.000 claims description 5
- 238000003908 quality control method Methods 0.000 description 4
- 238000012163 sequencing technique Methods 0.000 description 4
- 238000007405 data analysis Methods 0.000 description 3
- 230000008901 benefit Effects 0.000 description 2
- 238000011161 development Methods 0.000 description 2
- 238000005516 engineering process Methods 0.000 description 2
- 230000006870 function Effects 0.000 description 2
- 238000013507 mapping Methods 0.000 description 2
- 108020004999 messenger RNA Proteins 0.000 description 2
- 238000004364 calculation method Methods 0.000 description 1
- 230000008859 change Effects 0.000 description 1
- 238000010276 construction Methods 0.000 description 1
- 238000001514 detection method Methods 0.000 description 1
- 230000007613 environmental effect Effects 0.000 description 1
- 230000006872 improvement Effects 0.000 description 1
- 230000003993 interaction Effects 0.000 description 1
- 238000012423 maintenance Methods 0.000 description 1
- 238000012545 processing Methods 0.000 description 1
- 230000008439 repair process Effects 0.000 description 1
Landscapes
- Apparatus Associated With Microorganisms And Enzymes (AREA)
- Management, Administration, Business Operations System, And Electronic Commerce (AREA)
Abstract
The invention discloses a kind of production methods of analysis of biological information tool, device and can storage medium.Wherein method includes the analysis process for parsing a biological information, establishes the implementation order of at least two mutually independent analytical procedures and any analytical procedure；According to the input traffic of analytical procedure Allocation Analysis module and analysis module, output stream and Parameter File；The execution program of Allocation Analysis module implementation analytical procedure；Implementing between two analysis modules adjacent in order, the output stream for configuring the analysis module of first order and the input traffic of the analysis module in rear order have same interface standard, establish the interactive link of all analysis modules according to different interface standards and execute sequence.According to the execution program of analysis module, Parameter File, and interactive link, the execution sequentially built analysis of biological information tool of any analysis module.The present invention can fast, efficiently establish the modularization analysis of biological information tool with good reusability.
Description
Technical field
The present invention relates to biology information technology analysis fields, in particular to a kind of system of analysis of biological information tool
Make method, apparatus and can storage medium.
Background technique
With the development of sequencing technologies, related sequencing data is increased with the rate for surpassing More's law, service sequencing number
According to bioinformatics software be widely deployed.
Since sequencing data to be treated is more, the operation flow of current biological information software and the realization of source code are caused
It is second-rate；So, it is very heavy to provide the analysis of biological information tool with good readable, reusability and portability
It wants.
Summary of the invention
The embodiment of the present invention at least provides a kind of production method of analysis of biological information tool, can be according to different biologies
Information fast, efficient foundation have the analysis tool of good reusability.
The specific implementation of above-described embodiment, as described below.
The described method includes:
The analysis process for parsing a biological information establishes at least two mutually independent analytical procedures and any analysis
The implementation order of step；
According to the analytical procedure Allocation Analysis module and input traffic, output stream and the ginseng of the analysis module
Number file；
Configure the execution program that the analysis module implements the analytical procedure；
Between two analysis modules adjacent in the implementation order, the defeated of the analysis module of first order is configured
The input traffic of data flow and the analysis module in rear order has same interface standard out, according to the different interface marks
Standard establishes the interactive link of all analysis modules and executes sequence.
According to the execution program of the analysis module, Parameter File and all analysis modules interactive link, hold
Analysis of biological information tool described in row sequentially built.
Preferred version is to establish several independent implementations time respectively according to the analysis process in the present embodiment
Sequence.
Preferred version is that the input traffic includes at least initial data, sample names, connector letter in the present embodiment
One of breath and journal file are a variety of；
Preferred version is that the output stream includes at least outgoing route and/or cache path in the present embodiment.
Preferred version is that the Parameter File is to be stored in config interface in the analysis module in the present embodiment
Build one of library type, minimum length and sliding window size or a variety of.
Preferred version is in the present embodiment, which comprises
The analysis process for parsing a biological information establishes at least two mutually independent analytical procedures and any analysis
The implementation order of step；
According to the analytical procedure Allocation Analysis module and input traffic, output stream and the ginseng of the analysis module
Number file；
One workflow frame is established according to the implementation order between any analysis module using nextflow；
Match the process of different analysis modules respectively in the workflow frame；
Implement the nextflow shell script of the process according to analytical procedure configuration；
Parameter is implemented in config interface setting according to Parameter File in the process；
In the process according to input data stream configuration input, output is configured according to output data stream configuration,
Implement to configure the output of the process of first order and in rear order between two adjacent process of order
The input of process has same-interface standard；
The interactive link between process described in any two is established according to interface standard identical input and output
And execute sequence；
The execution program and implementation for the process, the process configuration for including according to the workflow frame
Analysis of biological information tool described in parameter, the interactive connection of any process and execution sequentially built.
The embodiment of the present invention separately disclose one kind can storage medium, for storing instruction, which is characterized in that described instruction is located
Reason device realizes above-mentioned steps when executing.
The embodiment of the present invention separately discloses a kind of producing device of analysis of biological information tool,
Described device includes:
Parsing module parses the analysis process of a biological information, establishes at least two mutually independent analytical procedures and appoints
The implementation order for the analytical procedure of anticipating；According to the analytical procedure Allocation Analysis module and the input data of the analysis module
Stream, output stream and Parameter File；
Module is made, one workflow is established according to the implementation order between any analysis module using nextflow
Frame；Match the process of different analysis modules respectively in the workflow frame；It is configured according to the analytical procedure real
Apply the nextflow shell script of the process；Config interface according to Parameter File in the process is arranged in fact
Apply parameter；In the process according to input data stream configuration input, output is configured according to output data stream configuration, in reality
It applies between two adjacent process of order, configures the output and the process in rear order of the process of first order
Input have same-interface standard；It is established described in any two according to interface standard identical input and output
Interactive link between process and execute sequence；
Package module, the execution of the process for including according to the workflow frame, the process configuration
Analysis of biological information tool described in program and implementation parameter, the interactive connection of any process and execution sequentially built.
For above scheme, the present invention is by being referring to the drawings described in detail disclosed exemplary embodiment, also
The other feature and its advantage for making the embodiment of the present invention understand.
Detailed description of the invention
In order to illustrate the technical solution of the embodiments of the present invention more clearly, below will be to needed in the embodiment attached
Figure is briefly described, it should be understood that the following drawings illustrates only certain embodiments of the present invention, therefore is not construed as pair
The restriction of range for those of ordinary skill in the art without creative efforts, can also be according to this
A little attached drawings obtain other relevant attached drawings.
Fig. 1 is the flow chart of embodiment method；
Fig. 2 is the structure chart of embodiment device.
Specific embodiment
In order to make the object, technical scheme and advantages of the embodiment of the invention clearer, below in conjunction with the embodiment of the present invention
In attached drawing, technical scheme in the embodiment of the invention is clearly and completely described, it is clear that described embodiment is
A part of the embodiment of the present invention, instead of all the embodiments.The present invention being usually described and illustrated herein in the accompanying drawings is implemented
The component of example can be arranged and be designed with a variety of different configurations.
Therefore, the detailed description of the embodiment of the present invention provided in the accompanying drawings is not intended to limit below claimed
The scope of the present invention, but be merely representative of selected embodiment of the invention.Based on the embodiments of the present invention, this field is common
Technical staff's every other embodiment obtained without creative efforts belongs to the model that the present invention protects
It encloses.
The present embodiment provides a kind of production methods of analysis of biological information tool.Method through this embodiment, this implementation
Example will decompose the analysis process of biological information, make the biggish execution program of a scale of construction in fact according to biological information
Analytical procedure be divided into several different analysis modules；It is relatively independent and have a single function between analysis module, it can be independent
Operation executes program, is easily managed and uses.Between different analysis modules, it is only necessary to application such as nextflow and binding analysis stream
Journey bonds different analysis modules by defining interface type, realizes the continuous of analysis module.
In order to realize above content, Fig. 1 is please referred to.The present embodiment makes modularization for carrying out data analysis to mRNA
Analysis of biological information tool, specifically include:
Step100, parsing are number Quality Control (QC), genome alignment to the mRNA analysis process for implementing data analysis
(Mapping), quantitative (Quantify), variance analysis (Diff), variable sheer (AS), variation detection (SNV) and function enrichment
(GO/KEGG) the implementation order between independent analytical procedure and analytical procedure such as.
Step210, according to above-mentioned analytical procedure respectively establish matching QC, Mapping, AS, Quantify, SNV, Diff and
The analysis module of the analytical procedures such as GO/KEGG.
Step220, input, processing and output according to analytical procedure to data configure config interface in analysis module
And abstract input traffic, output stream and other parameters.
For example, the corresponding input traffic of config interface of QC analysis module include at least initial data, sample names,
Joint information and journal file, output stream include at least outgoing route, cache path, and other parameters include at least and build library class
Type, minimum length and sliding window size etc..
Step310, a workflow frame is established using biological information process Customization Tool nextflow and in workflow
Independent process is established according to each analysis module in frame.
Nextflow is mainly the interface standard for passing through definition input and output, different implementation project, that is, process
It connects, to realize the analysis process for carrying out data analysis to biological information.
Step320, configuration realize the nextflow script of process, include at least actuator, environmental variance and process ginseng
Number etc..The language of nextflow script is preferably the superset of groovy language.
Step330, other above-mentioned ginsengs that each process corresponding with analysis module is respectively configured according to config interface
Number.
Step340, according to implement order process configuration meet above-mentioned input interface standard and with abstract input number
According to the corresponding input of stream；Configuration meets above-mentioned output interface standard and output corresponding with abstract output stream.
I.e. between adjacent two process for implementing order, upper one implements the output of order process and next reality
The interface standard for applying the input of order process is identical, realizes interactive link；
The interactive link that the present embodiment is formed by input between any two process and output is established all
Interaction between process and sequence is executed, and then establishes the analysis process of analysis of biological information tool.
Step350, in the analysis process of analysis of biological information tool and the interactive link of all process and sequence is executed
After the completion of foundation, that is, analysis of biological information tool can be used to execute nextflow_run order realization to the analysis work of biological information
Make.
Through the above scheme, the interface standard that the present embodiment application nextflow is defined quickly connects different process'
Input and output stream；Above-mentioned process can individually be developed under different language environment according to specific analytical procedure,
Simplify production process；Meanwhile the analysis of biological information tool of the present embodiment method production has reusability, effective solution
Development difficulty existing for current biological information analysis tool is big, reusability is poor and is difficult to problem difficult in maintenance.
Further, the present embodiment separately provide a kind of computer can storage medium, executed based on above-mentioned steps by storing
The instruction of calculation machine.
Referring to FIG. 2, the present embodiment separately discloses a kind of producing device of analysis of biological information tool, including parsing module,
Make module and package module.
Parsing module parses the analysis process of a biological information, establishes at least two mutually independent analytical procedures and any
The implementation order of analytical procedure；According to the input traffic of analytical procedure Allocation Analysis module and analysis module, output stream
And Parameter File.It makes module application nextflow and one workflow frame is established according to the implementation order between any analysis module
Frame；Match the process of different analysis modules respectively in workflow frame；Implemented according to analytical procedure configuration
The nextflow shell script of process；Parameter is implemented in config interface setting according to Parameter File in process；?
Process configures output according to input data stream configuration input, according to output data stream configuration, and implementing, order is adjacent
Between two process, the input for configuring the output and the process in rear order of the process of first order has phase
Same interface standard；According to interface standard identical input and output establish interactive link between any two process and
Execute sequence.Package module, the execution program for process, process configuration for including according to workflow frame and implementation are joined
The interactive connection and execution sequentially built analysis of biological information tool of several, any process.
The foregoing is only a preferred embodiment of the present invention, is not intended to restrict the invention, for the skill of this field
For art personnel, the invention may be variously modified and varied.All within the spirits and principles of the present invention, made any to repair
Change, equivalent replacement, improvement etc., should all be included in the protection scope of the present invention.
Claims (8)
1. a kind of production method of analysis of biological information tool, which is characterized in that
The described method includes:
The analysis process for parsing a biological information establishes at least two mutually independent analytical procedures and any analytical procedure
Implementation order；
According to the input traffic of the analytical procedure Allocation Analysis module and the analysis module, output stream and parameter text
Part；
Configure the execution program that the analysis module implements the analytical procedure；
Between two analysis modules adjacent in the implementation order, the output number of the analysis module of first order is configured
There is same interface standard according to stream and the input traffic of the analysis module in rear order, built according to the different interface standards
It founds the interactive link of all analysis modules and executes sequence.
It is suitable according to the execution program of the analysis module, the interactive link of Parameter File and all analysis modules, execution
Sequence makes the analysis of biological information tool.
2. the production method of analysis of biological information tool as described in claim 1, which is characterized in that
Several independent implementation order are established respectively according to the analysis process.
3. the production method of analysis of biological information tool as described in claim 1, which is characterized in that the input data is flow to
It less include one of initial data, sample names, joint information and journal file or a variety of.
4. the production method of analysis of biological information tool as described in claim 1, which is characterized in that the output data is flow to
It less include outgoing route and/or cache path.
5. the production method of analysis of biological information tool as described in claim 1, which is characterized in that the Parameter File is to deposit
Storage config interface in the analysis module builds one of library type, minimum length and sliding window size or a variety of.
6. the production method of analysis of biological information tool as described in claim 1, which is characterized in that the described method includes:
The analysis process for parsing a biological information establishes at least two mutually independent analytical procedures and any analytical procedure
Implementation order；
According to the input traffic of the analytical procedure Allocation Analysis module and the analysis module, output stream and parameter text
Part；
One workflow frame is established according to the implementation order between any analysis module using nextflow；
Match the process of different analysis modules respectively in the workflow frame；
Implement the nextflow shell script of the process according to analytical procedure configuration；
Parameter is implemented in config interface setting according to Parameter File in the process；
In the process according to input data stream configuration input, output is configured according to output data stream configuration, is being implemented
Between two adjacent process of order, the output of the process of first order is configured with the process's in rear order
Input has same-interface standard；
According to the interface standard identical input and output interactive link established between process described in any two and hold
Row sequence；
The execution program and implementation ginseng for the process, the process configuration for including according to the workflow frame
Analysis of biological information tool described in number, the interactive connection of any process and execution sequentially built.
7. one kind can storage medium, for storing instruction, which is characterized in that realize when described instruction is executed by processor such as right
It is required that the step of 1 to 6 any one the method.
8. a kind of producing device of analysis of biological information tool, which is characterized in that
Described device includes:
Parsing module parses the analysis process of a biological information, establishes at least two mutually independent analytical procedures and any institute
State the implementation order of analytical procedure；According to the input traffic of the analytical procedure Allocation Analysis module and the analysis module,
Output stream and Parameter File；
Module is made, one workflow frame is established according to the implementation order between any analysis module using nextflow
Frame；Match the process of different analysis modules respectively in the workflow frame；It is configured and is implemented according to the analytical procedure
The nextflow shell script of the process；It is arranged according to Parameter File in the config interface of the process and is implemented
Parameter；In the process according to input data stream configuration input, output is configured according to output data stream configuration, is being implemented
Between two adjacent process of order, the output of the process of first order is configured with the process's in rear order
Input has same-interface standard；Process described in any two is established according to interface standard identical input and output
Between interactive link and execute sequence；
Package module, the execution program of the process for including according to the workflow frame, the process configuration
And implements parameter, the interactive connection of any process and execute analysis of biological information tool described in sequentially built.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN201811004190.9A CN109326330B (en) | 2018-08-30 | 2018-08-30 | Method and device for manufacturing biological information analysis tool and storage medium |
Applications Claiming Priority (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN201811004190.9A CN109326330B (en) | 2018-08-30 | 2018-08-30 | Method and device for manufacturing biological information analysis tool and storage medium |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CN109326330A true CN109326330A (en) | 2019-02-12 |
| CN109326330B CN109326330B (en) | 2020-10-16 |
Family
ID=65264268
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CN201811004190.9A Active CN109326330B (en) | 2018-08-30 | 2018-08-30 | Method and device for manufacturing biological information analysis tool and storage medium |
Country Status (1)
| Country | Link |
|---|---|
| CN (1) | CN109326330B (en) |
Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110750362A (en) * | 2019-12-19 | 2020-02-04 | 深圳华大基因科技服务有限公司 | Analysis method, device and storage medium for biological information |
| CN115757520A (en) * | 2022-11-28 | 2023-03-07 | 北京元码医学检验实验室有限公司 | Flow control processing method and device, electronic equipment and storage medium |
Citations (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20020168664A1 (en) * | 1999-07-30 | 2002-11-14 | Joseph Murray | Automated pathway recognition system |
| CN107004069A (en) * | 2015-04-30 | 2017-08-01 | 株式会社Xcoo | Genome analysis device and genome visualization method |
| CN107122626A (en) * | 2017-03-13 | 2017-09-01 | 上海海云生物科技有限公司 | The method and system of the bioinformatic analysis of two generations sequencing DNA mutation detection |
| CN107563152A (en) * | 2017-08-03 | 2018-01-09 | 北京百迈客生物科技有限公司 | The data analysis application system that methylates based on biological cloud platform |
| CN107590365A (en) * | 2017-08-22 | 2018-01-16 | 武汉古奥基因科技有限公司 | Application of the Docker technologies in high-flux sequence data analysis |
| CN107657150A (en) * | 2017-09-07 | 2018-02-02 | 北京荣之联科技股份有限公司 | One kind visualization analysis of biological information instrument generation method and device |
-
2018
- 2018-08-30 CN CN201811004190.9A patent/CN109326330B/en active Active
Patent Citations (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20020168664A1 (en) * | 1999-07-30 | 2002-11-14 | Joseph Murray | Automated pathway recognition system |
| CN107004069A (en) * | 2015-04-30 | 2017-08-01 | 株式会社Xcoo | Genome analysis device and genome visualization method |
| CN107122626A (en) * | 2017-03-13 | 2017-09-01 | 上海海云生物科技有限公司 | The method and system of the bioinformatic analysis of two generations sequencing DNA mutation detection |
| CN107563152A (en) * | 2017-08-03 | 2018-01-09 | 北京百迈客生物科技有限公司 | The data analysis application system that methylates based on biological cloud platform |
| CN107590365A (en) * | 2017-08-22 | 2018-01-16 | 武汉古奥基因科技有限公司 | Application of the Docker technologies in high-flux sequence data analysis |
| CN107657150A (en) * | 2017-09-07 | 2018-02-02 | 北京荣之联科技股份有限公司 | One kind visualization analysis of biological information instrument generation method and device |
Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110750362A (en) * | 2019-12-19 | 2020-02-04 | 深圳华大基因科技服务有限公司 | Analysis method, device and storage medium for biological information |
| CN115757520A (en) * | 2022-11-28 | 2023-03-07 | 北京元码医学检验实验室有限公司 | Flow control processing method and device, electronic equipment and storage medium |
Also Published As
| Publication number | Publication date |
|---|---|
| CN109326330B (en) | 2020-10-16 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| Sim et al. | ChemOS 2.0: An orchestration architecture for chemical self-driving laboratories | |
| CN114424257A (en) | Automatic rendering and extraction of form data using machine learning | |
| Ahmad et al. | A framework for architecture-driven migration of legacy systems to cloud-enabled software | |
| JP2005521947A5 (en) | ||
| CN119558340B (en) | Methods and related devices for handling explicit result acquisition tasks based on multi-agent collaboration | |
| CN105653900A (en) | Reference-genome-free transcriptome analysis system and reference-genome-free transcriptome analysis method | |
| CN109522005A (en) | Cross-platform GRAPHICAL PROGRAMMING method | |
| CN107657150A (en) | One kind visualization analysis of biological information instrument generation method and device | |
| US20250252376A1 (en) | Workflow Optimization Leveraging Generative AI and Quantum Simulation | |
| Bates et al. | Unified modeling language code generation from diagram images using multimodal large language models | |
| CN109326330A (en) | The production method of analysis of biological information tool, device and can storage medium | |
| Petrakis et al. | Enhancing DevOps Practices in the IoT–Edge–Cloud Continuum: Architecture, Integration, and Software Orchestration Demonstrated in the COGNIFOG Framework | |
| Ko et al. | ModelCenter MBSE for OpenMBEE: MBSE analysis integration for distributed development | |
| Han | Bioworks: a workflow system for automation of bioinformatics analysis processes | |
| Prakash et al. | Systematic Analysis of Factors Influencing Modulith Architecture Adoption over Microservices | |
| CN114327580B (en) | Management method, system, device and storage medium based on software warehouse | |
| Lücke-Tieke et al. | Lowering the barrier for successful replication and evaluation | |
| CN118034672A (en) | Spark-based visual data processing analysis method and system | |
| JP2024132871A (en) | How to automatically optimize tasks in production and research facilities | |
| CN117762404A (en) | Configurable operator processing method and device for data mining | |
| Frolov et al. | Digital Transformation in the Biopharmaceutical Industry: Rebuilding the Way We Discover Complex Therapeutics | |
| Mileff | Design and development of a web-based graph editor and simulator application | |
| CN105956033A (en) | Plate form generation method and apparatus | |
| Maldonado et al. | Towards a Domain-Specific Language for Provisioning Multiple Cloud Testing Environments for Mobile Applications | |
| de Luz Palomino Valdivia et al. | Guided visual analysis of multivariate time series |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| PB01 | Publication | ||
| PB01 | Publication | ||
| SE01 | Entry into force of request for substantive examination | ||
| SE01 | Entry into force of request for substantive examination | ||
| GR01 | Patent grant | ||
| GR01 | Patent grant | ||
| TR01 | Transfer of patent right |
Effective date of registration: 20230406 Address after: No. 303, 3rd Floor, Building 9, Youyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya City, Hainan Province, 572025 Patentee after: Sanya Boruiyuan Technology Co.,Ltd. Address before: Room 3, 4th Floor, Building 6, Phase 1, Yinjiu Technology Industrial Park, No. 35 Guanggu Avenue, Donghu New Technology Development Zone, Wuhan City, Hubei Province, 430000 Patentee before: WUHAN GOOAL GENE TECHNOLOGY CO.,LTD. |
|
| TR01 | Transfer of patent right |