CN102982409A - Informationalized management design method for information biology high-performance computing platform - Google Patents
Informationalized management design method for information biology high-performance computing platform Download PDFInfo
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Abstract
The invention provides an informationalized management design method for an information biology high-performance computing platform. Various experiment procedures, namely a plurality of links such as deoxyribonucleic acid (DNA) library construction, genomic sequencing, data processing, result analyzing, result producing and data sharing are generally involved in information biology, different skilled persons take part in all the links, and therefore the problems such as information loss and low efficiency in passing-on or taking-over of all the links can occur. An integrated set of method for systematically linking the whole links together does not exist so far, and a specialized tool for managing the biological information platform does not exist either. The management method aims at information of a high-performance computing laboratory of the information biology, and the purposes are standardizing procedure management in the stages of experimentation and computing in the information biology and improving work efficiency.
Description
Technical field
The present invention relates to the Computer Applied Technology field, specifically a kind of information system management method for designing of bioinformatics high-performance calculation platform.
Background technology
Along with the fast development of life science experimental technique, robotization, the intelligent level of scientific instrument improve day by day, and the data output capacity has had qualitative leap.Simultaneously, life science has all proposed higher standard and the request to the requirement of analytical test at aspects such as sample size, analytical cycle, analysis project and data accuracies, and the information of biology laboratory output increases by geometric progression.In traditional biology laboratory, because data type is various, form differs, the preservation of data, exchange, inquiry, analysis, maintenance are all very inconvenient, and the information that has seriously hindered between the researchist is submitted to.Especially the order-checking in bioinformatics, the high-performance calculation link, specialty order-checking laboratory need to be accepted a large amount of order-checking order projects, arrange order-checking to test, in time process the sequencing result of high speed output.Growing order-checking demand and the data of high speed output have brought huge challenge for the data management in order-checking laboratory.For the data of such high speed output, it is very difficult only managing with computer file system.Electrical form and paper document save data are generally adopted in the order-checking laboratory.Exist and these modes all are the forms of disperseing, be difficult to put together unified management.In the data collection process, how to cooperate and follow the trail of each experimental data.It is the challenge that laboratory management faces.Therefore need to set up normalized software systems, can preserve the related data of all seminars, can collect again, store, integrate, related, analyze different experiments sample and result, realize unified management.And information system management demand in the bioinformatics, we have proposed a cover biological information high-performance calculation platform laboratory information management method.
Summary of the invention
Purpose of the present invention designs high-performance calculation platform information management design method in a kind of bioinformatics.
The objective of the invention is to realize in the following manner, set up a Standardized Design platform, this design platform is divided into 4 design modules: project management design module, sample managing design module, experiment management design module, personal management design module; Can realize customer information, project data, project achievement; The sample warehouse-in, storage, inquiry; Experiment flow, without the experimental phase; The laboratory worker management, the data exchanges such as role assignments, project is followed the trail of sample size, order status, experiment progress, the management such as data flow.Wherein:
1) project management module design: project, hereinafter to be referred as project, it is the core of laboratory running, the operating process of all experiments and data are all organized centered by project, sample, personnel, lab resources is also divided by project, therefore most data store are divided all related with the numbering of project, system provides a series of allocation functions for each project, comprise the selection sample, personnel and distribution authority, the experiment of project under checking, realize project management, the concrete resource of clear and definite project, so that reasonable distribution resource according to circumstances, large-scale biology laboratory has many mega projects, a mega project or comprise a plurality of sub-projects, some data need to be keep secret between the disparity items, not open to the outside, for this situation, project management module is configured to project team and project secondary structure management mode, namely a project team comprises a plurality of different projects, different authority settings is arranged, allowing to check the state that carries out of ongoing order-checking experiment flow and each experiment under this project in the project, this design is many for large-scale experiment chamber personnel, project is many, need to carry out the actual conditions of Classification Management and produce, under this design, can more effectively manage a large amount of dissimilar order-checkings experiments, improve the efficient that experimental data imports and checks;
2) sample managing modular design: the experimental subjects that is used for managing the order-checking experiment, management to laboratory sample is extremely important in the laboratory information management, an and easy unheeded link, the experimenter more pays close attention to the data that produce in the experiment, but in the order-checking experiment, need to recall every sequencing data and be associated with on the sample, in case sequencing data occurs unusual, also need to find associated sample to re-start order-checking, therefore, strengthen the sample managing link, the sample of project at first will be added in the sample library, and in native system and after item association gets up accordingly, could begin to create experiment and carry out the management of experimental data;
3) experiment management modular design: the experiment management module is used for the experiment flow in control laboratory, manage the data that each experiment produces, and guarantee the reversibility of all data, the experiment management module need to possess task and distribute, information communication, the function of data storage, in the experiment management modular design, we have introduced the concept of experiment chain, each project comprises a plurality of experiment chains, and an experiment chain is comprised of the tactic a plurality of experiments in front and back, after an experiment is finished, formulate and set up next experiment according to specific requirement by the experimenter, so just guarantee that experiment flow can be chaotic, and experimental data can associate, each experiment has allowed unconfirmed in the experiment chain, set up, completion status; In order to follow the tracks of a sample from entering the experiment chain to drawing this process of final sequencing result, and carry out active data related with integrate, need to work out the name format specification of experimental data;
4) user and authority management module: authority management module is responsible for the security of save data in the LIMS system, the security of data is embodied in two aspects: data security, data security, in order to satisfy the demand of these data security aspects, user and authority management module require the user of system to confirm to use native system through registration and through managerial personnel, and each registered user is managed personnel and authorizes corresponding role according to its work authority of office.
The invention has the advantages that: according to Module Division, modules is separate with links in the bioinformatics, is closely connected again to each other; Module Division is the order management, sample managing, and experiment management, four modules of personal management, project management module is in charge of client, project data, reaches gathering and the concluding a research item process of project achievement; The sample managing module is responsible for the management of sample, the warehouse-in of sample data, storage and inquiry; The experiment management module is in charge of the experiment flow of each project, the data exchange between the result of each experiment and experiment; Personnel and authority management module are responsible for the management of laboratory worker, and the distribution of each role-security in the system.Separate between each module, be closely connected again simultaneously, jointly finish allomeric function.Wherein:
1) each link that relates in the bioinformatics is investigated, analyze thorough each link input, output, and the key point that links with next link;
2) the present invention carries out detailed tracking with regard to data stream, guarantees each project or test to track root;
3) the bioinformatics research field is more, relates to different experimental techniques, data processing method, and our analysis-by-synthesis extracts different phase communicating a little in information processing;
4) high-performance calculation part in the biological information, data volume is huge, if manually move or deletion etc. takies the plenty of time, the present invention realizes the robotization migration, the deletion data.
Description of drawings
Fig. 1 is experimental data flow process figure.
Embodiment
Explain below with reference to Figure of description method of the present invention being done.
1) project management module design: project is the core of laboratory running.The operating process of all experiments and data are all organized centered by project, and the lab resources such as sample, personnel are also divided by project, and therefore most data store are divided all related with the numbering of project.System provides a series of allocation functions for each project, as selecting sample, personnel and distribution authority, checks the experiment of affiliated project etc., realizes project management, and the concrete resource of clear and definite project is in order to according to circumstances reallocate resource.Large-scale biology laboratory often all has many projects.A mega project may also comprise a plurality of sub-projects.Disparity items ask some data need to be keep secret, open to the outside.For this situation, this project management module is configured to project team and project secondary structure management mode.Namely a project team comprises a plurality of different projects, and different authority settings is arranged.Can check the state that carries out of ongoing order-checking experiment flow and each experiment under this project in the project.This design is many for large-scale experiment chamber personnel, project is many, need to carry out the actual conditions of Classification Management and produces.Under this design, can a large amount of dissimilar order-checkings of more effective management test, also can improve the efficient that experimental data imports and checks;
2) sample managing modular design: the experimental subjects that is used for managing the order-checking experiment.Management to laboratory sample is extremely important in the laboratory information management, and an easy unheeded link.The experimenter often more pays close attention to the data that produce in the experiment, but in the order-checking experiment, need to recall every sequencing data to be associated with on the sample.In case sequencing data occurs unusual, also needs to find associated sample to re-start order-checking.Therefore we have strengthened the sample managing link.The sample of project at first will be added in the sample library, and in native system and after item association gets up accordingly, just can begin to create experiment and carry out the management of experimental data;
3) experiment management modular design: the experiment management module is used for the experiment flow in control laboratory, manages the data that each experiment produces, and guarantees the reversibility of all data.The experiment management module need to possess task distributes, information communication, the function of data storage.We have introduced the concept of experiment chain in the experiment management modular design, and each project can comprise a plurality of experiment chains.An experiment chain is comprised of the tactic a plurality of experiments in front and back, after an experiment is finished, formulates and set up next experiment according to specific requirement by the experimenter, so just guarantee that experiment flow can be not chaotic, and experimental data can associate.Each experiment can have unconfirmedly in the experiment chain, sets up, completion status.In order to follow the tracks of a sample from entering the experiment chain to drawing this process of final sequencing result, and carry out active data related with integrate, we have worked out the name format specification of experimental data;
4) user and authority management module: authority management module is responsible for the security of save data in the LIMS system.The security of data is embodied in two aspects: data security, data security.In order to satisfy the demand of these data security aspects, require the user of system to confirm that can use each registered user of native system to be managed personnel authorizes corresponding role according to its work authority of office through registration and through managerial personnel with factory and authority management module.
Except the described technical characterictic of instructions, be the known technology of those skilled in the art.
Claims (1)
1. the information system management method for designing of a bioinformatics high-performance calculation platform is characterized in that content comprises: project management module design, sample managing modular design, experiment management modular design, user and authority management module, wherein:
1) project management module design: project, hereinafter to be referred as project, it is the core of laboratory running, the operating process of all experiments and data are all organized centered by project, sample, personnel, lab resources is also divided by project, therefore most data store are divided all related with the numbering of project, system provides a series of allocation functions for each project, comprise the selection sample, personnel and distribution authority, the experiment of project under checking, realize project management, the concrete resource of clear and definite project, so that reasonable distribution resource according to circumstances, large-scale biology laboratory has many mega projects, a mega project or comprise a plurality of sub-projects, some data need to be keep secret between the disparity items, not open to the outside, for this situation, project management module is configured to project team and project secondary structure management mode, namely a project team comprises a plurality of different projects, different authority settings is arranged, allowing to check the state that carries out of ongoing order-checking experiment flow and each experiment under this project in the project, this design is many for large-scale experiment chamber personnel, project is many, need to carry out the actual conditions of Classification Management and produce, under this design, can more effectively manage a large amount of dissimilar order-checkings experiments, improve the efficient that experimental data imports and checks;
2) sample managing modular design: the experimental subjects that is used for managing the order-checking experiment, management to laboratory sample is extremely important in the laboratory information management, an and easy unheeded link, the experimenter more pays close attention to the data that produce in the experiment, but in the order-checking experiment, need to recall every sequencing data and be associated with on the sample, in case sequencing data occurs unusual, also need to find associated sample to re-start order-checking, therefore, strengthen the sample managing link, the sample of project at first will be added in the sample library, and in native system and after item association gets up accordingly, could begin to create experiment and carry out the management of experimental data;
3) experiment management modular design: the experiment management module is used for the experiment flow in control laboratory, manage the data that each experiment produces, and guarantee the reversibility of all data, the experiment management module need to possess task and distribute, information communication, the function of data storage, in the experiment management modular design, we have introduced the concept of experiment chain, each project comprises a plurality of experiment chains, and an experiment chain is comprised of the tactic a plurality of experiments in front and back, after an experiment is finished, formulate and set up next experiment according to specific requirement by the experimenter, so just guarantee that experiment flow can be chaotic, and experimental data can associate, each experiment has allowed unconfirmed in the experiment chain, set up, completion status; In order to follow the tracks of a sample from entering the experiment chain to drawing this process of final sequencing result, and carry out active data related with integrate, need to work out the name format specification of experimental data;
4) user and authority management module: authority management module is responsible for the security of save data in the LIMS system, the security of data is embodied in two aspects: data security, data security, in order to satisfy the demand of these data security aspects, user and authority management module require the user of system to confirm to use native system through registration and through managerial personnel, and each registered user is managed personnel and authorizes corresponding role according to its work authority of office.
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| CN103489069A (en) * | 2013-09-16 | 2014-01-01 | 上海厚浪信息科技有限公司 | RDMP system based on network |
| CN104484375A (en) * | 2014-12-08 | 2015-04-01 | 深圳华大基因科技服务有限公司 | Method and system for automatically building database in item analysis process |
| CN104484581A (en) * | 2014-12-08 | 2015-04-01 | 深圳华大基因科技服务有限公司 | Method and system for automatically analyzing biological information projects |
| CN104484750A (en) * | 2014-12-08 | 2015-04-01 | 深圳华大基因科技服务有限公司 | Method and system for automatically matching product parameters of biological information project |
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| CN105205621A (en) * | 2015-10-26 | 2015-12-30 | 四川理工学院 | High-performance information management system and data processing method for bioinformatics |
| CN105321018A (en) * | 2014-07-18 | 2016-02-10 | 中国农业科学院作物科学研究所 | Automatic DNA sequencing management system |
| CN107577917A (en) * | 2016-07-05 | 2018-01-12 | 魏霖静 | A kind of bioinformatics high performance information management system and data processing method |
| CN116011599A (en) * | 2022-12-29 | 2023-04-25 | 上海邺洋生物技术应用有限公司 | Intelligent reservation method and system for biological laboratory |
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Cited By (13)
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| CN103489069A (en) * | 2013-09-16 | 2014-01-01 | 上海厚浪信息科技有限公司 | RDMP system based on network |
| CN105321018A (en) * | 2014-07-18 | 2016-02-10 | 中国农业科学院作物科学研究所 | Automatic DNA sequencing management system |
| CN104484750A (en) * | 2014-12-08 | 2015-04-01 | 深圳华大基因科技服务有限公司 | Method and system for automatically matching product parameters of biological information project |
| CN104484581A (en) * | 2014-12-08 | 2015-04-01 | 深圳华大基因科技服务有限公司 | Method and system for automatically analyzing biological information projects |
| CN104484375A (en) * | 2014-12-08 | 2015-04-01 | 深圳华大基因科技服务有限公司 | Method and system for automatically building database in item analysis process |
| CN104484375B (en) * | 2014-12-08 | 2017-11-10 | 深圳华大基因科技服务有限公司 | Establish the method and system of database automatically in project analysis flow |
| CN104484750B (en) * | 2014-12-08 | 2018-04-24 | 深圳华大基因科技服务有限公司 | The product parameters automatic matching method and system of biological information project |
| CN104484581B (en) * | 2014-12-08 | 2018-04-24 | 深圳华大基因科技服务有限公司 | The automated analysis method and system of biological information project |
| CN105117619A (en) * | 2015-08-10 | 2015-12-02 | 杨福辉 | Whole genome sequencing data analysis method |
| CN105205621A (en) * | 2015-10-26 | 2015-12-30 | 四川理工学院 | High-performance information management system and data processing method for bioinformatics |
| CN107577917A (en) * | 2016-07-05 | 2018-01-12 | 魏霖静 | A kind of bioinformatics high performance information management system and data processing method |
| CN116011599A (en) * | 2022-12-29 | 2023-04-25 | 上海邺洋生物技术应用有限公司 | Intelligent reservation method and system for biological laboratory |
| CN116011599B (en) * | 2022-12-29 | 2024-04-05 | 上海邺洋生物技术应用有限公司 | Intelligent reservation method and system for biological laboratory |
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Application publication date: 20130320 |