CN107239675A - Biological information analysis system based on cloud platform - Google Patents
Biological information analysis system based on cloud platform Download PDFInfo
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- CN107239675A CN107239675A CN201710598332.8A CN201710598332A CN107239675A CN 107239675 A CN107239675 A CN 107239675A CN 201710598332 A CN201710598332 A CN 201710598332A CN 107239675 A CN107239675 A CN 107239675A
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B99/00—Subject matter not provided for in other groups of this subclass
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- H—ELECTRICITY
- H04—ELECTRIC COMMUNICATION TECHNIQUE
- H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
- H04L67/00—Network arrangements or protocols for supporting network services or applications
- H04L67/01—Protocols
- H04L67/02—Protocols based on web technology, e.g. hypertext transfer protocol [HTTP]
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- H—ELECTRICITY
- H04—ELECTRIC COMMUNICATION TECHNIQUE
- H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
- H04L67/00—Network arrangements or protocols for supporting network services or applications
- H04L67/01—Protocols
- H04L67/12—Protocols specially adapted for proprietary or special-purpose networking environments, e.g. medical networks, sensor networks, networks in vehicles or remote metering networks
Abstract
The invention discloses a kind of biological information analysis system based on cloud platform, including cloud platform client, cloud platform web server and cloud platform computing system, received and sent messages between cloud platform client and cloud platform web server by network, cloud platform web server and cloud platform computing system exchange data by Nginx web page servers；Cloud platform web server includes analysis of biological information request interface, and cloud platform computing system includes analysis of biological information application interface, analysis of biological information component, storage server, Mysql databases and Mongo databases；Analysis of biological information request interface is connected to analysis of biological information application interface by Nginx web page servers, and the output end of analysis of biological information application interface is connected to analysis of biological information component by work-flow process administrative unit.The analysis program modularization of the present invention, can be combined multiplexing, and analysis efficiency is greatly improved, and deployment is convenient.
Description
Technical field
The present invention relates to a kind of biological information analysis system based on cloud platform, belong to bioinformatic analysis technology neck
Domain.
Background technology
With the fast development of sequencing technologies, gene studies mechanism, medical research mechanism and company generate the life of magnanimity
Thing sequencing data.It is well known that, the initial data that experiment sequencing is obtained can not directly provide valuable science and grind
The related information of information or disease therapeuticing medicine is studied carefully, it is necessary to carry out calculating digging to these data using bioinformatic analysis technology
Pick, so as to provide object information that is clear and being easy to export conclusion.Bioinformatics is with calculating in the research of life science
Machine is that main research tool is stored and calculated analysis to biological data, in face of the magnanimity number produced by high-flux sequence
According to, increasing researcher or company be based on high-performance computer cluster by install various analysis of biological information softwares come
Carry out calculating analysis.Analysis of biological information process is also that many softwares and program are interrelated, at different step methods
Final analysis result is obtained after reason data, because bioinformatics software layer goes out continuous, renewal iteration, each analysis program ginseng
Number, file format, the method for operation are different, and researcher will constantly go to study new software approach and on computer or cluster
Installation and deployment all become sufficiently complex.Shared storage, calculating and the transmission of mass data are also that researchers quickly access and divided
Analyse the difficult point in data.So a kind of biological information cloud computing system for automating favorable expandability of design construction is very necessary.
The content of the invention
Present invention aim to address current analysis of biological information software a great variety, analysis efficiency is low, automatic extension
Property it is poor, large-scale data is difficult to the shared and diversified software program of storage and builds the complicated technical problem of deployment analysis flow.
To realize above goal of the invention, on the one hand, the present invention provides a kind of biological information analysis system based on cloud platform,
Including cloud platform client, cloud platform web server and cloud platform computing system；
Received and sent messages between the cloud platform client and the cloud platform web server by network, the cloud platform
Data are exchanged by Nginx web page servers between web server and the cloud platform computing system；
The cloud platform web server includes analysis of biological information request interface；
The cloud platform computing system includes analysis of biological information application interface, analysis of biological information component, storage service
Device, Mysql databases and Mongo databases；
The cloud platform computing system also includes some calculate nodes, for carrying out analysis calculating to biological information；
The analysis of biological information request interface is connected to the analysis of biological information by the Nginx web page servers
Application interface, the output end of the analysis of biological information application interface is connected to the biology by work-flow process administrative unit
The input of information analysis component, the output end of the analysis of biological information component be respectively connecting to the storage server,
Mysql databases and Mongo databases；
The analysis of biological information request interface sends analysis of biological information to the analysis of biological information application interface please
Ask and send parameter；
The storage server is used to store analysis result data, and the Mysql databases are used to store analysis record, shape
State and log information, the Mongo databases are used to store the chart data shown for the cloud platform client.
Further, the analysis of biological information component is instant pattern analysis component or submits pattern analysis component.
Further, the submission pattern analysis component includes work-flow process administrative unit, analysis module and file group
Part；
The analysis module includes some analysis tools, and each analysis tool passes through corresponding tool agent and the work
Thread management unit is flowed into be communicated；
The work-flow process administrative unit is used to being scheduled to different analysis tasks into the different analysis modules；
The file components are used to make analysis result form general biological data form.
Further, the work-flow process administrative unit carries out task scheduling by slurm systems.
On the other hand, the present invention provides a kind of analysis of biological information method based on cloud platform, comprises the following steps：
The parameter for analysis is inputted in client and sends analysis request message to web server；
Analysis of biological information application interface, analytic parameter are forwarded to after receiving request message by Nginx web page servers；
Parameter described in interpretation is that instant computing type still delivers calculation type；
If instant computing type, then analysis of biological information workflow is directly run on special instant computing server；
If delivering calculation type, then parameter is transferred to operation analysis of biological information workflow on calculate node server；
The result data of generation is uploaded to the storage server and mongo databases of cloud platform；
The running status of analysis of biological information workflow is stored in Mysql databases in real time；
Returned to web server and analyze successful message, web server obtains result from mongo databases and is supplied to visitor
Family end.
Further, the analysis workflow for delivering calculation type is as follows：
After work-flow process administrative unit gets parms, according to the pre-defined logical relation in inside, parameter is delivered to
Each analysis module of analysis of biological information component, is triggered between the operation of each analysis module, each analysis module by assisting journey to monitor
There is the running status of the analysis module of dependence mutually, using each analysis tool in each analysis module as minimal level analysis group
Part, is delivered to calculate node by slurm by each analysis tool and starts to calculate analysis, while constantly monitoring and receiving the shape of analysis
State.
Compared with prior art, the beneficial effects of the invention are as follows：
The present invention analysis program modularization, can be combined multiplexing, with favorable expandability with automatically working stream run
System framework, solves large-scale data and is difficult to the complicated skill of the shared and diversified software program structure deployment analysis flow of storage
Art problem, analysis efficiency is greatly improved, and deployment is convenient.
Brief description of the drawings
Fig. 1 is the theory diagram of present system；
Fig. 2 is one embodiment theory diagram of analysis of biological information component；
Fig. 3 is the flow chart of the inventive method.
In figure, cloud platform client 1；Cloud platform web server 2；Analysis of biological information request interface 21；Cloud platform is calculated
System 3；Analysis of biological information application interface 31；Analysis of biological information component 32；Analysis module 322；Tool agent 3221；Analysis
Instrument 3222；File components 323；Storage server 33；Mysql databases 34；Mongo databases 35；Work-flow process is managed
Unit 36；Calculate node 3701,3702 ...；Nginx web page servers 4.
Embodiment
The invention will be further described with specific embodiment below in conjunction with the accompanying drawings.
Embodiment 1
As shown in figure 1, the biological information analysis system based on cloud platform of the present invention, including cloud platform client 1, Yun Ping
Platform web server 2 and cloud platform computing system 3；
Received and sent messages between cloud platform client 1 and the cloud platform web server 2 by network, cloud platform web services
Data are exchanged by Nginx web page servers 4 between device 2 and the cloud platform computing system 3；
Cloud platform web server 2 includes analysis of biological information request interface 21；
Cloud platform computing system 3 includes analysis of biological information application interface 31, analysis of biological information component 32, storage service
Device 33, Mysql databases 34 and Mongo databases 35；
Cloud platform computing system 3 also includes some calculate nodes 3701,3702 etc., for carrying out analysis meter to biological information
Calculate；Cloud platform computing system 3 includes the large-scale calculations node for analyzing various different biological informations, different analytic unit quilts
It is delivered to calculate node and analysis calculating is carried out to biological information；
Analysis of biological information request interface 21 is connected to analysis of biological information application interface by Nginx web page servers 4
31, the output end of analysis of biological information application interface 31 is connected to biological information by work-flow process administrative unit (WPM) 36
The input of analytic unit 32, the output end of analysis of biological information component 32 is respectively connecting to storage server 33, Mysql data
The output end of storehouse 34 and Mongo databases 35, Mysql databases 34 and Mongo databases 35 is taken by Nginx webpages respectively
Business device 4 is connected to cloud platform web server 2；
Analysis of biological information request interface 21 sends analysis of biological information request simultaneously to analysis of biological information application interface 31
Send parameter；
Storage server 33 is used to store analysis result data, Mysql databases 34 be used to storing analysis record, state and
Log information, Mongo databases 35 are used to store the chart data for the displaying of cloud platform client 1.
Preferably, analysis of biological information component 32 is instant pattern analysis component or submits pattern analysis component.
Preferably, as shown in Fig. 2 submitting pattern analysis component 32 to include analysis module 322 and file components 323；
Analysis module 322 includes some analysis tools 3222, and each analysis tool 3222 passes through corresponding tool agent 3221
Communicated with work-flow process administrative unit 36；Different analysis of biological information tasks is thrown by the analysis tool of difference in functionality
It is delivered to single or multiple calculate nodes and completes analysis calculating；
Work-flow process administrative unit 36 is used to being scheduled to different analysis tasks into different analysis modules 222；
File components 323 are used to making analysis result form general biological data form going forward side by side row format inspection.
Preferably, work-flow process administrative unit 36 carries out task scheduling by slurm systems.
Embodiment 2
As shown in figure 3, the analysis of biological information method based on cloud platform of the present invention, comprises the following steps：
S100：Analysis request message is sent to web server and input parameter for analysis in client；
S110：Analysis of biological information application interface is forwarded to after receiving request message by Nginx web page servers, is parsed
Parameter；
S120：Interpretation parameter is that instant computing type still delivers calculation type；
S125：If instant computing type, then analysis of biological information work is directly run on special instant computing server
Stream；
S126：If delivering calculation type, then parameter is transferred to operation analysis of biological information work on calculate node server
Flow；
S130：The result data of generation is uploaded to the storage server and mongo databases of cloud platform；
S140：The running status of analysis of biological information workflow is stored in Mysql databases in real time；
S150：Returned to web server and analyze successful message, web server obtains result from mongo databases and provided
To client.
Preferably, the analysis workflow for delivering calculation type is as follows：
After work-flow process administrative unit gets parms, according to the pre-defined logical relation in inside, parameter is delivered to
Each analysis module of analysis of biological information component, is triggered between the operation of each analysis module, each analysis module by assisting journey to monitor
There is the running status of the analysis module of dependence mutually, using each analysis tool in each analysis module as minimal level analysis group
Part, is delivered to calculate node by slurm by each analysis tool and starts to calculate analysis, while constantly monitoring and receiving the shape of analysis
State.
The system is built in High-Performance Computing Cluster, is the Back end data store and analysis computing system of cloud platform, and is passed through
The network-side of Nginx web page servers and cloud platform carries out data communication, including receives analysis task ID and parameter, sends and divides
Analyse calculating state.
System uses the expansible parallel file system data storage files of Lustre, and unified life is provided for All Clients
The name space, supports extensive high-flux sequence data acquisition storage, analysis intermediate file and destination file storage to access, Yi Ji great
The storage of biomolecule information database is measured, all analysis of biological information program softwares can unify installation and deployment and specific environment is matched somebody with somebody
Put, data and program can support the unification of all calculate nodes to access and call.
Core is divided into automation Computational frame, including following part in system：
The information that Nginx web page servers are carried out using uwsgi protocol interfaces between client and web frame applications is handed over
Change, respond to create using web.py network frames in the request of cloud platform page end, the system and write analysis of biological information meter
Calculate application interface.Calculation workflow is analyzed according to the mode combinations of analysis of biological information component, realizes Back end data in high-performance
Automation computing on cluster.
Analysis of biological information component, including flow (Workflow), module (Moudule), instrument and its agency (Tool,
ToolAgent), and define biological data form file components (File).
Instrument is the analysis of biological information component of a simple function, can call one or more analysis softwares or make by oneself
Adopted program bag, can be reused, and realize an analytic function.It is all to be existed by instrument for least unit that analysis of biological information, which is calculated,
Completed in calculate node.Because calculate node belongs to remote server, thus a tool agent is needed to be responsible for carrying out with instrument
Communication, instrument is corresponded with tool agent, and information mutual communication is realized by network service.
Analysis module completes the combination for including multiple instruments in a specific more complicated analytic function, analysis module,
A specific analytic function is realized by the operation logic between defined analysis instrument.
Flow completes a complete raw letter analysis process, by defining operation logic, calls a series of module of combination
A set of analysis process scheme is realized with instrument.Instrument and module can be multiplexed in different streams according to the analysis design of user
Cheng Zhong, so as to realize purpose of the analysis using Reusability of once packing.
A kind of general biological data form of document definition, includes data attribute and universal process method function, work
By being set in parameter at the file object transmission data of input, output, row format of going forward side by side checking and file between tool, module
Manage calling for universal method.
WPM work-flow process administrative units, the automatic operation that system passes through WPM administrative analysis workflows.WPM is monitored
Received task asks sum of parameters, opens a process operation workflow component, and parameter is passed into corresponding workflow
According to the logical relation of definition in component, flow component, Transfer Parameters to module therein and instrument trigger the fortune of sub-component
OK, and instrument is delivered into calculate node to start to calculate analysis, while constantly monitoring and receiving the state of operation.
The task run scheduling of calculate node employs Slurm systems to manage toward calculating in Slurm task schedulings, system
The task of node is delivered, and slurm is a kind of fault-tolerant cluster manager dual system of telescopic in height available for mass computing node cluster
And job scheduling system.
The state for analyzing operation is stored in Mysql databases in real time in Database Systems, system, by analysis result number
Mongo databases are stored according to by the data structure pre-defined, fast and effectively obtains and inquires about for page end server, it is real
The client user of existing cloud platform quickly directly accesses data.
In order to improve the interactive efficiency and experience that user is quick with data, access immediately, the system realizes two kinds of analyses
Computation schema, a kind of is to use submission pattern for the time-consuming longer task of large-scale data analytic operation, and user is without waiting
Client, clicks in client and submits, and operation can check the progress of operation at any time before completing.One kind is for small-sized data
Or processed rear tables of data, when carrying out time-consuming shorter analysis, system automatic decision simultaneously uses instant pattern, is delivered without task,
Directly calculating, and quick returning result are run in multiple calculate nodes of special configuration.
System operation step is as follows：
1. high in the clouds Web server is by way of client browser is supplied to subscriber network access plateform system, user
Analysis of biological information application is selected in browser cloud platform website, is filled in after parameter submission, client passes through the data of submission
The network transmission protocol is sent to web server, and message is received by Nginx web page servers, and Nginx is a performance oriented design
HTTP server, support high concurrent and high-performance supported equilibrium, can receive request of data parallel, processing request and returning rings
Should.
2.Nginx servers are received after request message, and message and parameter are passed into web.py by uwsgi interfaces
The analysis of biological information application interface created is developed in framework in advance, message is handled by application interface, the parameter to transmission is entered
After row parsing and inspection, start to start biological data analysis calculation workflow；
The management of 3.WPM work-flow process starts and administrative analysis work flow operation, and WPM monitoring receptions to Application of Interface are initiated
Task requests and parameter, type is calculated by application type parameter discriminatory analysis, including two types, one kind is instant computing
Type, one kind is to deliver calculation type, while opening a process operation workflow api, and parameter is passed into corresponding workflow；
If 4. Application of Interface is instant computing type, calculating time-consuming shorter, workflow analysis component will be directly special
Run on instant computing server, the result data of generation can upload to platform storage server position, while displaying will be needed
Analysis of biological information mongo databases are stored in the chart data of client terminal website, obtains and shows for page end, be then back to and disappear
Cease to web server, web server shows client after obtaining result data from database.User can pass through net in real time
Network checks analysis result.
If 5. Application of Interface is to deliver to calculate type, biological data needs by the long period that (dozens of minutes is to several
Individual hour), after flow component gets parms, according to the pre-defined logical relation in inside, Transfer Parameters to mould therein
Block and instrument, trigger the operation of sub-component, between component by assisting journey to monitor the operation shape for the module for having dependence mutually
State, when being run to minimal level tool assembly, is delivered to calculate node by slurm by instrument and starts to calculate analysis, while not
The disconnected state monitored and receive operation.The running status of instrument exchanges number by tool agent with other assemblies in same workflow
According to, the central characteristic dynamic configuration computing resource understood according to each component itself of operation, and record running status and progress, report an error
Log information, if occurring connecting or running failure, system can judge whether that adjustment configuration is recalculated according to default situation,
Constantly operation progress status can be updated in database simultaneously, web server end utilizes real after timer acquisition state
When can track running situation at any time in page furbishing progress, user.Calculate after end of run, result data can upload to storage clothes
It is engaged in device position, while the data of needs are stored in into analysis of biological information mongo databases, returning message to web server end,
Web server returns to new results page, is checked for user.
Analysis of biological information component include flow (Workflow), module (Moudule), instrument and its agency (Tool,
ToolAgent), and define biological data form file components (File).Flow is according to tool by module and instrument
The analysis product operation logic of body is combined, and is had between module and instrument and is relied on incidence relation, module or tool assembly it
Between data, including input-output file parameter and field parameter are transmitted by parameter, input-output file parameter needs fixed in advance
The attribute and method of file can be defined in the file components of adopted this document form, file components, and to the tray of transmission
Formula is checked.What the input/output argument between component was transmitted is file components object.In task management node, a flow
In component include module and tool agent, task is delivered to calculate node by tool agent in startup optimization by slurm
Corresponding instrument is calculated, and by tool agent real-time exchange data, tool agent sends operating instruction and meter to instrument
Parameter needed for calculating, instrument returns to running status and daily record.If a component relies on the result of calculation of multiple components, need to wait for
The automatic activation operation after successfully terminating of multiple assembly operatings.Whole process is monitored and controlled by WPM workflow managements, so that
Realize the automatic operation of analysis system.
Using the above-mentioned desirable embodiment according to the present invention as enlightenment, by above-mentioned description, relevant staff is complete
Various changes and amendments can be carried out without departing from the scope of the technological thought of the present invention' entirely.The technology of this invention
Property scope is not limited to the content on specification, it is necessary to its technical scope is determined according to right.
Claims (6)
1. the biological information analysis system based on cloud platform, it is characterised in that including cloud platform client, cloud platform web services
Device and cloud platform computing system；
Received and sent messages between the cloud platform client and the cloud platform web server by network, the cloud platform web clothes
It is engaged between device and the cloud platform computing system exchanging data by Nginx web page servers；
The cloud platform web server includes analysis of biological information request interface；
The cloud platform computing system include analysis of biological information application interface, analysis of biological information component, storage server,
Mysql databases and Mongo databases；
The cloud platform computing system also includes some calculate nodes, for carrying out analysis calculating to biological information；
The analysis of biological information request interface is connected to the analysis of biological information application by the Nginx web page servers
Interface, the output end of the analysis of biological information application interface is connected to the biological information by work-flow process administrative unit
The input of analytic unit, the output end of the analysis of biological information component is respectively connecting to the storage server, Mysql numbers
According to storehouse and Mongo databases；
The analysis of biological information request interface sends analysis of biological information request simultaneously to the analysis of biological information application interface
Send parameter；
The storage server is used to store analysis result data, the Mysql databases be used to storing analysis record, state and
Log information, the Mongo databases are used to store the chart data shown for the cloud platform client.
2. the biological information analysis system as claimed in claim 1 based on cloud platform, it is characterised in that the biological information point
Component is analysed to be instant pattern analysis component or submit pattern analysis component.
3. the biological information analysis system as claimed in claim 2 based on cloud platform, it is characterised in that the submission pattern point
Analysing component includes work-flow process administrative unit, analysis module and file components；
The analysis module includes some analysis tools, and each analysis tool passes through corresponding tool agent and the workflow
Management of process unit is communicated；
The work-flow process administrative unit is used to being scheduled to different analysis tasks into the different analysis modules；
The file components are used to make analysis result form general biological data form.
4. the biological information analysis system as claimed in claim 3 based on cloud platform, it is characterised in that the work-flow process
Administrative unit carries out task scheduling by slurm systems.
5. the analysis of biological information method based on cloud platform, it is characterised in that comprise the following steps：
The parameter for analysis is inputted in client and sends analysis request message to web server；
Analysis of biological information application interface, analytic parameter are forwarded to after receiving request message by Nginx web page servers；
Parameter described in interpretation is that instant computing type still delivers calculation type；
If instant computing type, then analysis of biological information workflow is directly run on special instant computing server；
If delivering calculation type, then parameter is transferred to operation analysis of biological information workflow on calculate node server；
The result data of generation is uploaded to the storage server and mongo databases of cloud platform；
The running status of analysis of biological information workflow is stored in Mysql databases in real time；
Returned to web server and analyze successful message, web server obtains result from mongo databases and is supplied to client.
6. the analysis of biological information method as claimed in claim 5 based on cloud platform, it is characterised in that the delivery calculation type
Analysis workflow it is as follows：
After work-flow process administrative unit gets parms, according to the pre-defined logical relation in inside, parameter is delivered to biology
Each analysis module of information analysis component, triggers mutual by assisting journey to monitor between the operation of each analysis module, each analysis module
There is the running status of the analysis module of dependence, using each analysis tool in each analysis module as minimal level analytic unit,
Each analysis tool is delivered into calculate node by slurm to start to calculate analysis, while constantly monitoring and receiving the state of analysis.
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| CN201710598332.8A CN107239675A (en) | 2017-07-21 | 2017-07-21 | Biological information analysis system based on cloud platform |
| CN201810796979.6A CN109192248B (en) | 2017-07-21 | 2018-07-19 | Biological information analysis system and method based on cloud platform and cloud computing platform system |
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| CN109192248A (en) | 2019-01-11 |
| CN109192248B (en) | 2021-08-03 |
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