CN108121925B - Generation method and generation system of electron microscope data label - Google Patents
Generation method and generation system of electron microscope data label Download PDFInfo
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Abstract
The invention provides a generation method and a generation system of an electron microscope data label, wherein the electron microscope data label is associated with electron microscope data and used for storing relevant information of the electron microscope data; the preset content of the electron microscope data label comprises the following steps: the system comprises a topic type, an experiment name, a data acquisition time length, data acquisition equipment, resolution precision, a topic code number, a sample type, a sample frame size width, a sample frame size height, a sample preparation condition 1, a sample preparation condition 2, a magnification factor, a sampling condition, data expectation precision, a topic group, a teacher, a cooperative topic group and a cooperative teacher. Based on the electron microscope data label provided by the invention, multi-dimensional analysis and management can be carried out on electron microscope data stored in a big data system.
Description
Technical Field
The invention relates to the field of computers, in particular to a method and a system for generating an electron microscope data label.
Background
With the progress of hardware technology, the analysis of the structure of biomacromolecules by using a cryoelectron microscope technology is becoming a new research direction of structural biology. In recent years, many research teams have published dozens of high-resolution results on three-dimensional structure analysis of proteins in the international top academic journal, Nature, Science, Cell, and the like based on the cryoelectron microscopy technique, which has a significant effect on the development of life sciences.
In order to reconstruct a high-precision molecular structure, a large number of two-dimensional high-resolution images need to be shot by a cryoelectron microscope, and since the cryoelectron microscope is difficult to avoid problems such as under-focus in the shooting process, some image information is lost.
However, in the process of reconstructing a three-dimensional molecular structure, in order to construct an accurate high-resolution three-dimensional molecular structure, a large number of high-resolution two-dimensional images need to be taken from different angles by a cryoelectron microscope, a large number of two-dimensional images need to be taken by slight angle changes, several tens of TB of electron microscope data are generated each day under the condition that the electron microscope is in full-load operation, for example, the electron microscope platform Titan of the life institute of qinghua university has a shooting rate of 7 GB/min, that is, about 7GB of image data is generated each minute, so that one electron microscope can generate data of 7 GB/min 60 min/h 24 h 10.08TB in one day, and thus storage capacity of up to 4PB is consumed each year.
Big data governance is a big problem which generally exists at present. The data is treated by dividing into two parts, namely, the data is individually managed in different categories, which is a basic starting point and principle of data management. For example, data migration operation is performed on cold data and non-key data, so that the cold data and the non-key data are precipitated into a low-speed, low-cost and large-capacity storage system, and the maximum benefit of storage space and cost is obtained at the cost of reading and writing time. In fact, this cost is entirely acceptable.
The label of the data is data judged by human experience and is data after the data. Tag management is an important technology for realizing data 'divide-and-conquer' and is widely applied to various big data systems. In general, a "tag" is an attribute of data, and a tag is data judged by human experience and is data after data. Labeling management is a very important trend.
However, at present, the storage system of (freezing) electron microscope data has no label or only has a simple data label, and cannot support multi-dimensional large data analysis and management.
Disclosure of Invention
In view of this, the invention provides an electron microscope data tag, a generation method and a generation system thereof, which can solve the problem of electron microscope data tags required by multidimensional analysis and management of a large data system.
The invention provides an electron microscope data label, which is associated with electron microscope data and used for storing related information of the electron microscope data;
the preset content of the electron microscope data label comprises the following steps: the system comprises a topic type, an experiment name, a data acquisition time length, data acquisition equipment, resolution precision, a topic code number, a sample type, a sample frame size width, a sample frame size height, a sample preparation condition 1, a sample preparation condition 2, a magnification factor, a sampling condition, data expectation precision, a topic group, a teacher, a cooperative topic group and a cooperative teacher.
The invention also provides a generation method of the electron microscope data label, which comprises the following steps:
step A: analyzing the name of the electron microscope data file and/or the header information of the electron microscope data file, and writing label information obtained through analysis into an electron microscope data label associated with the electron microscope data file;
and B: displaying an input interface of the electron microscope data label, wherein the input interface is used for a user to input and/or modify the label content;
and C: and after a label generation instruction is triggered, detecting whether the content of the electron microscope data label meets the preset requirement, if so, generating the electron microscope data label, otherwise, prompting a user to modify the content of the label which does not meet the preset requirement, and returning to an input interface.
The invention also provides a system for generating the electron microscope data label, which comprises:
an analysis module: analyzing the name of the electron microscope data file and/or the header information of the electron microscope data file, and writing label information obtained through analysis into an electron microscope data label associated with the electron microscope data file;
and (3) label interface: displaying an input interface of the electron microscope data label, wherein the input interface is used for a user to input and/or modify the label content;
a generation module: and after a label generation instruction is triggered, detecting whether the content of the electron microscope data label meets the preset requirement, if so, generating the electron microscope data label, otherwise, prompting a user to modify the content of the label which does not meet the preset requirement, and returning to an input interface.
The electron microscope data label, the generation method and the generation system thereof provide an information source for big data management of electron microscope data, can effectively reduce the working intensity of mass data management of a frozen electron microscope, improve the fineness of data management, and support multi-dimensional data analysis and management.
Drawings
FIG. 1 is a flow chart of a method for generating an electron microscope data tag according to the present invention;
fig. 2 is a structural diagram of a system for generating an electron microscope data tag according to the present invention.
Detailed Description
In order to make the objects, technical solutions and advantages of the present invention more apparent, the present invention will be described in detail with reference to the accompanying drawings and specific embodiments.
It should be noted that the terms first, second and the like in the description and in the claims, and in the drawings, are used for distinguishing between similar elements and not necessarily for describing a particular sequential or chronological order. It is to be understood that the data so used is interchangeable under appropriate circumstances such that the embodiments of the invention described herein are capable of operation in sequences other than those illustrated or described herein.
In actual work, the main challenges faced by the storage of electron microscope data are: the multiplied electron microscope original data and process data bring great challenges to the capacity of a storage system and a user quota allocation management strategy, and indirectly influence the scientific research efficiency and the overall progress. The method specifically comprises the following steps:
1. the data volume is flexible: the field of a refrigeration electron microscope is a particularly active scientific research field at present, and various software and hardware technical innovations are infinite; the combination of the same set of original data and different analysis processes can generate various processes and result data, and the data scale becomes huge and complex day by day; between the topic groups, the topic groups and the outside-school organization generate a large amount of data copies during cooperative research, and although the diversified requirements such as data sharing convenience and original data integrity can be met at the same time, capacity pressure is brought to the storage system. Therefore, the data collected by the electron microscope has great elasticity. There is a lack of more efficient and economical management strategies in the areas of storage system rationalization and data copy management.
2. Data management related information is isolated and dispersed, and content-based perception is lacked: most of electron microscope data are managed by scientific research personnel, a unified management strategy is not available, and daily management of a large amount of off-line data occupies too much energy of a subject group. Meanwhile, the data are adjusted and migrated by the administrator based on the purpose of system optimization, and how to more quickly and accurately release the information to scientific research personnel is also a problem to be solved.
3. Management hysteresis: the administrator user permission is separated from the data permission, a platform manager is difficult to mine the use rule of the user and deeply matches with the requirements of scientific research services to adjust the platform management strategy and long-term operation planning in time, the solution has hysteresis to a certain extent, and the initiative is lacked in the process of assisting the high-efficiency output of scientific research achievements.
4. The manual data migration task is too burdensome: lacking effective automated or semi-automated tool software or scripts, the migration task for data by administrators is too burdensome and prone to operational accidents.
In order to meet the above challenges, it is necessary to develop an online data management system, which effectively controls and manages data copies and reduces storage pressure; and (4) formulating a data standard by combining scientific research services, forming a standard system for electron microscope data management, gradually enlarging the influence and forming a demonstration effect in the field of structural biology scientific research.
The invention provides a standard data label for storing the relevant information of the electron microscope data, and the electron microscope data label can support the multi-dimensional analysis and management of the electron microscope data.
The invention comprises an electron microscope data label, wherein the electron microscope data label is associated with electron microscope data and used for storing related information of the electron microscope data;
the preset content of the electron microscope data label comprises the following steps: the system comprises a topic type, an experiment name, a data acquisition time length, data acquisition equipment, resolution precision, a topic code number, a sample type, a sample frame size width, a sample frame size height, a sample preparation condition 1, a sample preparation condition 2, a magnification factor, a sampling condition, data expectation precision, a topic group, a teacher, a cooperative topic group and a cooperative teacher.
Optionally, the electronic microscope data tag further includes an extension item, and the extension item is used for storing other information except the preset content.
Each item of data tag content can be preset bytes, such as "topic type", for each item of content, as shown in table 1, the preset bytes are 2 bytes, where 0 represents the importance, and 1 represents the generality, and in the electronic microscope data tag generation interface, the user inputs or makes a pull-down candidate menu to allow the user to select and fill.
TABLE 1
In the present invention, the sample code may be a protein code, or other codes.
In the present invention, the sample preparation condition 1 is a carbon film, the sample preparation condition 2 is a negative dyeing, or the sample preparation condition 1 is a negative dyeing, and the sample preparation condition 2 is a carbon film, or other sample preparation condition combinations are possible.
Optionally, the electron microscope data tag is stored in a preset special storage device, and the electron microscope data tag is stored in isolation from the electron microscope data. The electron microscope data label and the electron microscope data file are correlated and stored independently, so that a user can edit or modify the electron microscope data label directly without directly changing electron microscope data (original files).
The storage system for the electron microscope data comprises: a parallel file system, an object storage system, a tape library system, a database system, and/or a key-value system. The electron microscope data tags may be stored in a database system, and the electron microscope data stored in other storage devices than the database system.
Based on the label content of the electron microscope data, an automatic migration management strategy can be implemented on the electron microscope data stored in the storage system. Or the electron microscope data stored in the storage system can be monitored and managed in real time based on the electron microscope data label.
Optionally, based on the electron microscope data tag, the invention sets corresponding user modules, supervisor modules and administrator modules for users, supervisors and administrators of the electron microscope data storage system, wherein the user modules, supervisor modules and administrator modules have different functions and authorities.
For example, the user module: the method is mainly used for managing the electron microscope data for the user, and helps the user to intuitively manage the data in the whole life cycle from electron microscope data collection, preprocessing, image analysis, three-dimensional reconstruction to result display.
The method specifically comprises the following steps:
(1) and data import: a user manages file directories in respective authority ranges in a bottom storage device file system of the computing platform through a Web interface, and batch retrieval and entry of the electron microscope data files and folders are supported. And when the data input is supported, the data is verified and the check code is recorded, and when the input data is completely consistent or partially consistent with the existing data of the system, a user is prompted and guided to pay attention to the data repeated event.
(2) And data management: the electronic microscope data retrieval method supports a user to retrieve and list and display the electronic microscope data based on characteristic information such as 'labels', 'timestamps', 'addition/deletion', 'entry', 'sharing', 'subject groups' and the like, and supports a report to be exported to a format file such as CSV and the like. For example: the data recorded by the system in 3 months in the past year can be retrieved and displayed on the statistical interface, the rule of the data can be observed, and a reference basis is provided for the data recording quantity in 3 months in the next year. The list of corresponding folders or files and the file path can also be obtained by fuzzy search or advanced search of the complete or partial affix content of the "tag". The system supports user's "delete" operations through the Web UI and provides administrative logic like "recycle bin".
(3) The data sharing method includes the steps of receiving user permissions of a bottom storage system of a computing platform, supporting users to open data access permissions to designated users through Web UI, managing data sets in a centralized mode, in a batch mode and in an efficient mode through the Web UI by administrators and users, enabling data collaboration and sharing behaviors among the users to be conducted spontaneously, and not relying on the administrators to adjust L inux system permissions manually.
(4) Self-defining a label; and the user is supported to customize the 'tag' (such as using a guide, a partner and the like as tags) in a limited range to serve as a candidate tag for the next iteration (re-screening) of the system tag.
(5) Notification and alarm: and sending daily management and operation and maintenance related notifications and quota exhaustion alarms to the user.
For example, the supervisor module: the method is mainly used for managing the electron microscope data facing a master.
The method specifically comprises the following steps:
(1) and a data statistics report form: fuzzy search and advanced search functions for system and user tags are supported. Through the statistics of relevant information such as reports, the information is used as basic operation and maintenance information and decision support information, and materials are provided for reporting materials such as annual reports.
(2) And data aided decision making: and the small knowledge base is used for precipitating the auxiliary decision-making experience information, so that an accurate decision-making basis is provided for the next correction and iteration of the system.
(3) And authorization: the work authority of the administrator is adjusted with the authorization.
(4) Exception emergency treatment: and the overall operation efficiency and uninterrupted service capability of the system are enhanced through exception and emergency measures.
For example, the administrator module: the method is mainly used for managing the electron microscope data for an administrator.
The method specifically comprises the following steps:
(1) and managing the life cycle of the user: providing basic user management functions: adding users, revising user information, resetting user passwords, deleting users, deactivating and activating accounts and the like.
(2) And system monitoring: and supporting an administrator to observe basic information such as total capacity, available capacity and the like of each storage system.
(3) Log and alarm: and log recording and system alarming (short messages, mails and the like) are supported.
(4) And data recovery: the system supports the administrator to perform recovery operations on data recently (e.g., 7 days) deleted by the user, and supports recovery of data in the "recycle bin".
Based on the electron microscope data label, an information source is provided for big data management of electron microscope data, the working intensity of mass data management of a refrigeration electron microscope can be effectively reduced, the fineness of data management is improved, and multi-dimensional data analysis and management are supported.
As shown in fig. 1, the present invention further includes a method for generating an electron microscope data tag, including:
a (S101) analyzing the file name and/or the header information of the electron microscope data file, and writing the label information obtained by analysis into an electron microscope data label associated with the electron microscope data file;
step B (S102): displaying an input interface of the electron microscope data label, wherein the input interface is used for a user to input and/or modify the label content;
step C (S103): and after a label generation instruction is triggered, detecting whether the content of the electron microscope data label meets the preset requirement, if so, generating the electron microscope data label, otherwise, prompting a user to modify the content of the label which does not meet the preset requirement, and returning to an input interface.
Optionally, the preset content of the electronic microscope data tag includes: the system comprises a topic type, an experiment name, a data acquisition time length, data acquisition equipment, resolution precision, a topic code number, a sample type, a sample frame size width, a sample frame size height, a sample preparation condition 1, a sample preparation condition 2, a magnification factor, a sampling condition, data expectation precision, a topic group, a teacher, a cooperative topic group and a cooperative teacher.
Referring to table 1, assuming that step a is executed, and the "data acquisition duration" information is obtained through analysis, the information is written into the preset byte of the "data acquisition duration" in the electron microscope data tag.
The information that needs to be written by the user in step B is the label content left after the analysis in step a, and of course, the user may also modify the label content obtained through the analysis in step a.
Optionally, the electronic microscope data tag further comprises an extension item, and the extension item is used for storing other information besides the preset content.
Optionally, step C in fig. 1 further includes:
and after the electron microscope data label is generated, the electron microscope data label is stored in a preset special storage device, and other storage devices except the special storage system for storing the electron microscope data are also stored. .
As shown in fig. 2, the present invention further includes a system for generating an electron microscope data tag, including:
an analysis module: analyzing the name of the electron microscope data file and/or the header information of the electron microscope data file, and writing label information obtained through analysis into an electron microscope data label associated with the electron microscope data file;
and (3) label interface: displaying an input interface of the electron microscope data label, wherein the input interface is used for a user to input and/or modify the label content;
a generation module: and after a label generation instruction is triggered, detecting whether the content of the electron microscope data label meets the preset requirement, if so, generating the electron microscope data label, otherwise, prompting a user to modify the content of the label which does not meet the preset requirement, and returning to an input interface.
Optionally, the preset content of the electronic microscope data tag includes: the system comprises a project type, an experiment name, a data acquisition time length, data acquisition equipment, resolution precision, a project code number, a sample type, a sample frame size width, a sample frame size height, a sample preparation condition 1, a sample preparation condition 2, a magnification factor, a sampling condition, data expectation precision, a subject group, a teacher, a cooperative subject group, a cooperative teacher and/or an extension item; the extension is used to save other information than the preset content.
Optionally, the generating module of fig. 2 further includes:
and after the electron microscope data label is generated, the electron microscope data label is stored in a preset special storage device, and other storage devices except the special storage system for storing the electron microscope data are also stored. .
Based on the electron microscope data label and the generation method and system thereof, an information source is provided for big data management of electron microscope data, the working intensity of mass data management of a freezing electron microscope can be effectively reduced, the data management fineness is improved, and multi-dimensional data analysis and management are supported.
It should be noted that the embodiments of the electron microscope data tag of the present invention have the same principle as the embodiments of the electron microscope data tag generation method and generation system, and the relevant points can be referred to each other.
The above description is only exemplary of the present invention and should not be taken as limiting the scope of the present invention, and any modifications, equivalents, improvements and the like made within the spirit and principle of the present invention should be included in the scope of the present invention.
Claims (4)
1. A generation method of an electron microscope data label is characterized by comprising the following steps: the method comprises the following steps:
step A: analyzing the name of the electron microscope data file and/or the header information of the electron microscope data file, and writing the label information obtained by analysis into an electron microscope data label associated with the electron microscope data file;
and B: displaying an input interface of the electron microscope data label, wherein the input interface is used for a user to input and/or modify label content;
and C: after a label generation instruction is triggered, detecting whether the content of the electron microscope data label meets a preset requirement, if so, generating the electron microscope data label, otherwise, prompting a user to modify the content of the label which does not meet the preset requirement, and returning to the input interface;
after the electron microscope data label is generated, storing the electron microscope data label in a preset special storage device, wherein the electron microscope data label stores other storage devices except the special storage device, and the electron microscope data label is associated with an electron microscope data file;
the preset content of the electron microscope data label comprises the following steps: the system comprises a topic type, an experiment name, a data acquisition time length, data acquisition equipment, resolution precision, a topic code number, a sample type, a sample frame size width, a sample frame size height, a sample preparation condition 1, a sample preparation condition 2, a magnification factor, a sampling condition, data expectation precision, a topic group, a teacher, a cooperative topic group and a cooperative teacher.
2. The method of claim 1, wherein the tag further comprises an extension for holding other information than the preset content.
3. The utility model provides a generation system of electron microscope data label which characterized in that: the system comprises:
an analysis module: analyzing the name of the electron microscope data file and/or the header information of the electron microscope data file, and writing the label information obtained by analysis into an electron microscope data label associated with the electron microscope data file;
and (3) label interface: displaying an input interface of the electron microscope data label, wherein the input interface is used for a user to input and/or modify label content;
a generation module: after a label generation instruction is triggered, detecting whether the content of the electron microscope data label meets a preset requirement, if so, generating the electron microscope data label, otherwise, prompting a user to modify the content of the label which does not meet the preset requirement, and returning to the input interface;
after the electron microscope data label is generated, storing the electron microscope data label in a preset special storage device, wherein the electron microscope data label stores other storage devices except the special storage device, and the electron microscope data label is associated with an electron microscope data file;
the preset content of the electron microscope data label comprises the following steps: the system comprises a topic type, an experiment name, a data acquisition time length, data acquisition equipment, resolution precision, a topic code number, a sample type, a sample frame size width, a sample frame size height, a sample preparation condition 1, a sample preparation condition 2, a magnification factor, a sampling condition, data expectation precision, a topic group, a teacher, a cooperative topic group and a cooperative teacher.
4. The system of claim 3, wherein the preset contents of the electron microscope data tag further comprise: an extension item;
the extension item is used for storing other information except the preset content.
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