CN108121925A - Electron microscopic data label and its generation method and generation system - Google Patents
Electron microscopic data label and its generation method and generation system Download PDFInfo
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- CN108121925A CN108121925A CN201711178893.9A CN201711178893A CN108121925A CN 108121925 A CN108121925 A CN 108121925A CN 201711178893 A CN201711178893 A CN 201711178893A CN 108121925 A CN108121925 A CN 108121925A
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- G—PHYSICS
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- G06K—GRAPHICAL DATA READING; PRESENTATION OF DATA; RECORD CARRIERS; HANDLING RECORD CARRIERS
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Abstract
The present invention provides a kind of electron microscopic data label, which associates with electron microscopic data, for preserving the relevant information of electron microscopic data；The preset content of electron microscopic data label includes：Problem species, Experiment name, data acquisition duration, data acquisition equipment, resolution accuracy, problem code name, sample code name, sample type, sample frame size are wide, sample frame size height, sampling 1, sampling 2, amplification factor, sampling condition, data expectation quality, affiliated seminar, affiliated teacher, collaborative project group and cooperation teacher.Based on electron microscopic data label provided by the invention, the analysis and management of various dimensions can be implemented to the electron microscopic data stored in big data system.
Description
Technical field
The present invention relates to computer realm, more particularly to a kind of electron microscopic data label and its generation method and generation system.
Background technology
With the progress of hardware technology, using the structure of Ice mapping technology parsing large biological molecule becoming one it is fine
New structure biology research direction.In recent years, many research teams are based on Ice mapping technology in international top academic journal
Nature, Science, Cell etc. delivered a tens of pieces it is high-resolution on protein three-dimensional structure parse achievement, to life
The reach of science generates significant impact, and Ice mapping is playing very important effect among these.
In order to reconstruct high-precision molecular structure, Ice mapping needs to shoot the high-definition picture of a large amount of two dimensions, by
In Ice mapping is difficult to avoid such as owing coke in shooting process the problems such as, so as to cause to lose some image informations, in order to
The loss of effective information is avoided, Ice mapping would generally shoot a large amount of high-resolution under different deficient burnt horizontal and different angles
The two dimensional image of rate is synthesized, and to make up the information of single image loss, finally utilizes captured substantial amounts of high-resolution
Two dimensional image, high-resolution molecular structure is reconstructed by relevant three-dimensionalreconstruction software such as Relion etc..
However, during three-dimensional molecular structure is reconstructed, in order to build accurate high-resolution three-dimensional molecular structure,
Ice mapping needs to shoot substantial amounts of high-resolution two dimensional image from different angles, and subtle angle change is required to shoot
Substantial amounts of two dimensional image in the case where Electronic Speculum is operated at full capacity, can generate the electron microscopic data of several tens TB daily, big with Tsing-Hua University
Exemplified by learning Life Sciences Electronic Speculum platform Titan, the capture rate of every Titan 7GB/ minutes is that is, per minute to generate 7GB's or so
Image data, such Electronic Speculum in one day with regard to can generate 7GB/ minutes it is * 60 minutes/hours * 24 small when=10.08TB number
According to so as to cause every year the memory capacity for being up to 4PB will be consumed.
Big data is administered, and is a big problem of current generally existing.It divides and rule to data, i.e., it is other to carry out point door to data
The personal management of class formula is the basic point of departure and principle of data management.For example, to cold data, non-emphasis data into line number
It according to migration operation, is allowed to be deposited in low speed, low cost, mass-storage system, it is empty to exchange storage for using access time as cost
Between and cost maximum return.In fact, this cost is completely can be received.
The label of data is the data that human experience judges, is the data after data.Tag control be realize data " point and
Control it " a kind of important technology, be widely used in various big data systems.Generally speaking, " label " is the category of data
Property label be human experience judge data, be the data after data.Tagging management is a very important trend.
But at present, the storage system of (freezing) electron microscopic data does not have label or only simple data label, still cannot
Support big data analysis and the management of various dimensions.
The content of the invention
In view of this, the present invention provides a kind of electron microscopic data label and its generation method and generation system, can solve big
Electron microscopic data label problem needed for the analysis and management of data system various dimensions.
The present invention provides a kind of electron microscopic data label, which associates with electron microscopic data, for preserving Electronic Speculum
The relevant information of data；
The preset content of electron microscopic data label includes：Problem species, Experiment name, data acquisition duration, data acquisition are set
Standby, resolution accuracy, problem code name, sample code name, sample type, sample frame size are wide, sample frame size height, sampling 1,
Sampling 2, amplification factor, sampling condition, data expectation quality, affiliated seminar, affiliated teacher, collaborative project group and cooperation
Teacher.
The present invention also provides a kind of generation method of electron microscopic data label, including：
Step A：Electron microscopic data filename and/or electron microscopic data file header are parsed, the label for parsing acquisition is believed
In the electron microscopic data label of breath, write-in and electron microscopic data file association；
Step B：Show the input interface of electron microscopic data label, input interface inputs and/or change label substance for user；
Step C：After label generation instruction triggers, whether detection electron microscopic data label substance meets preset requirement, if
Electron microscopic data label is then generated, if not, prompting user's modification does not meet the label substance of preset requirement, returns to input interface.
The present invention also provides a kind of generation system of electron microscopic data label, including：
Parsing module：Electron microscopic data filename and/or electron microscopic data file header are parsed, the label of acquisition will be parsed
In the electron microscopic data label of information, write-in and electron microscopic data file association；
Label interface：Show the input interface of electron microscopic data label, input interface is inputted for user and/or changed in label
Hold；
Generation module：After label generation instruction triggers, whether detection electron microscopic data label substance meets preset requirement, if
It is to generate electron microscopic data label, if not, prompting user's modification does not meet the label substance of preset requirement, returns to input circle
Face.
Electron microscopic data label of the present invention and its generation method and generation system provide for the big data improvement of electron microscopic data
Information source can effectively reduce the working strength of Ice mapping Mass Data Management, improve the fineness that data are administered, and support
The data analysis and management of various dimensions.
Description of the drawings
Fig. 1 is the flow chart of the generation method of electron microscopic data label of the present invention；
Fig. 2 is the structure chart of the generation system of electron microscopic data label of the present invention.
Specific embodiment
It is right in the following with reference to the drawings and specific embodiments in order to make the object, technical solutions and advantages of the present invention clearer
The present invention is described in detail.
It should be noted that term " first " in description and claims of this specification and above-mentioned attached drawing, "
Two " etc. be for distinguishing similar object, without being used to describe specific order and precedence.It should be understood that so make
Data can exchange in the appropriate case, so that the embodiment of the present invention described herein can be with except illustrating herein
Or the order beyond those of description is implemented.
In real work, the significant challenge that electron microscopic data storage faces is：Into multiple increase Electronic Speculum initial data and
Process data brings great challenge, and influences scientific research indirectly to storage system capacity, user's allocation of quota management strategy
Efficiency and overall progress.It specifically includes with subsurface：
1. data volume elasticity is big：Ice mapping field is a current especially active scientific research field, various software and hardware skills
Art innovation emerges in an endless stream；Same set of initial data, which combines different analysis process, can generate various procedures and result data, data
Scale can be increasingly huge and complicated；Between seminar and seminar, seminar can generate a large amount of when being studied with institution cooperation outside school
Data copy, though the diversified demands such as data sharing convenience and initial data integrality can be met simultaneously, but also for storage
System brings capacity pressure.Therefore, the data of Electronic Speculum acquisition possess very big elasticity.Rationalize use and data in storage system
Lack more efficient, more economical management strategy in terms of replica management.
2. data management relevant information isolates scattered, perception of the shortage based on content：Most of electron microscopic data is by scientific research people
Member voluntarily manages, and there is no unified management strategy, the daily management of a large amount of off-line datas occupies the excessive energy of seminar.Together
When, administrator is adjusted data, is migrated based on system optimization purpose, this type of information how more fast and accurately towards
Scientific research personnel issues and one has the problem of to be solved.
3. management hysteresis：Administrator's permission is separated with data permission, and platform management person is difficult to excavate user's use rule
It restrains and gos deep into that scientific research business demand is coordinated to adjust platform management strategy and long-term operation planning in time, tackle the certain journey of solution
There are hysteresis quality on degree, lack initiative during the efficient output of scientific achievement is aided in.
4. manual data migration task is too heavy：Lack effective automation or semi-automatic tool software or script, pipe
Reason person is too heavy to the migration task workload of data, and is easy to cause operating accident.
In order to tackle above-mentioned challenge, it is necessary to develop a set of online data management system, efficiently control and manage number
According to copy, mitigate storage pressure；Data standard is formulated with reference to scientific research business, forms the standards system and progressively of electron microscopic data management
Widen one's influence power, and demonstration effect is formed in structure biology scientific research field.
And the basis of online data management system is the collection of electron microscopic data relevant information, the present invention is in order to solve
Problem above, it is proposed that the data label of specification, for preserving the relevant information of electron microscopic data, the electron microscopic data label of the application
It can support the analysis and management of electron microscopic data various dimensions.
The present invention includes a kind of electron microscopic data label, which associates with electron microscopic data, for preserving Electronic Speculum
The relevant information of data；
The preset content of electron microscopic data label includes：Problem species, Experiment name, data acquisition duration, data acquisition are set
Standby, resolution accuracy, problem code name, sample code name, sample type, sample frame size are wide, sample frame size height, sampling 1,
Sampling 2, amplification factor, sampling condition, data expectation quality, affiliated seminar, affiliated teacher, collaborative project group and cooperation
Teacher.
Optionally, the electron microscopic data label of the application further includes extension, and extension is for preservation in addition to preset content
Other information.
Each data label content can be as shown in table 1, to each content preset byte, such as " problem species ", predetermined word
It saves as 2 bytes, wherein 0 represents great, 1 represents general, generates interface in electron microscopic data label, inputted or made down by user
Draw candidate's menu that user's choosing is allowed to fill out.
Table 1
In the present invention, sample code name can be albumen code name or other code names.
In the present invention, sampling 1 is carbon film, and sampling 2 is negative staining or sampling 1 is negative staining, sampling 2
It is combined for carbon film or other samplings.
Optionally, electron microscopic data label is stored in default special purpose memory devices, electron microscopic data label and electron microscopic data every
From storage.Electron microscopic data label and electron microscopic data file are interrelated, and separate storage, and user can be directly to electron microscopic data mark
It signs into edlin or modification, without doing direct change to electron microscopic data (original document).
Assuming that the storage system of electron microscopic data includes：Parallel file system, object storage system, tape library system, database
System, and/or key-value system.Then, electron microscopic data label is storable in Database Systems, and electron microscopic data is stored in except database
In other storage devices outside system.
Label substance based on electron microscopic data can implement the electron microscopic data that storage system stores the management of Autonomic Migration Framework
Strategy.Or based on electron microscopic data label, the electron microscopic data that can be stored to storage system is monitored in real time and managed.
Optionally, the present invention is based on more than electron microscopic data label, for the user, supervisor and pipe of electron microscopic data storage system
Reason person, sets corresponding line module, administration module and administrator module, each has the function of different and permission.
For example, line module：User oriented management electron microscopic data is mainly responsible for be used, collect, pre-process from electron microscopic data,
In the Life cycle that graphical analysis, three-dimensionalreconstruction to result are shown, user is helped intuitively to manage data.
It specifically includes：
(1), data import：User is managed in computing platform bottom storage device file system by web interface and each weighed
File directory in the range of limit supports bulk retrieval and typing electron microscopic data file and file.It supports to carry out during logging data
Verify and record check code, when typing data with system data with existing is completely the same or part is consistent when, prompt and guide use
Family pays attention to Data duplication event.
(2), data management：Support " label " of the user based on electron microscopic data, " timestamp ", " addition/deletion ", " record
Enter ", " shared ", the characteristic informations such as " affiliated seminar " are retrieved and list display, supporting will the forms text such as report export CSV
Part.Such as：It in statistical circles region retrieval and can show the data of system in March typing over the years, observe its rule, be data in March in the coming year
Typing amount provides reference frame.It can also be obtained by searching for generally or the complete or part affixe content of Advanced Search " label "
Corresponding document presss from both sides or list and the file path of file.System supports user carries out " deletion " by Web UI and operates, and carries
For the management logic of similar " recycle bin ".
(3), data sharing：Computing platform bottom storage system user right is docked, supports user by WebUI to specifying
User opens data access authority.Administrator and user can by Web UI intensively, in bulk, efficiently manage data
Collection；Data collaborative and shared behavior between user spontaneous can carry out, and are no longer dependent on administrator and manually adjust linux system
Permission.
(4), customized label；User's self-defined in the range of restriction " label " is supported (such as to utilize tutor, partner's work
For label), candidate's label as system label next iteration (screening again).
(5), notify and alert：Daily management is sent to user, the announcement that the relevant notice of O＆M and quota are used up etc
It is alert.
For example, administration module：It is mainly responsible for towards supervisor's management electron microscopic data and is used.
It specifically includes：
(1), data statistics report：Support to system and user tag search for generally and Advanced Search function.Pass through report
The statistical correlations information such as table, based on O＆M information and information for supporting some decision, provide material for the statistics presentation packages such as annual report.
(2), data aid decision：Aid decision posterior infromation is precipitated by small-sized knowledge base, for repairing for system next time
Just accurate decision-making foundation is provided with iteration.
(3), authorize：The work permission of administrator is adjusted using mandate.
(4), make an exception emergency disposal：By making an exception, emergent behave takes come the operational efficiency of strengthening system entirety and uninterruptedly
Business ability.
For example, administrator module：It is mainly responsible for towards Admin Administration's electron microscopic data and is used.
It specifically includes：
(1), subscriber lifecycle management：Basic subscriber management function is provided：It Adds User, user information is revised, is used
Family password resets, deletes user, account is disabled and enabled.
(2), system monitoring：Administrator is supported to observe the basic informations such as each storage system total capacity, active volume.
(3), daily record and alarm：Support log recording and system alarm (short message, mail etc.).
(4), data are recovered：System supports the data that administrator (such as 7 days) recent to user deletes to carry out recovery operation, branch
Hold the data in recovery " recycle bin ".
Based on electron microscopic data label of the present invention, information source is provided for the big data improvement of electron microscopic data, can effectively be dropped
The working strength of low Ice mapping Mass Data Management improves the fineness that data are administered, and supports the data analysis of various dimensions
And management.
As shown in Figure 1, present invention additionally comprises a kind of generation method of electron microscopic data label, including：
Step A (S101) parses electron microscopic data filename and/or electron microscopic data file header, will parse the mark of acquisition
Information is signed, is write in the electron microscopic data label with electron microscopic data file association；
Step B (S102)：Show the input interface of electron microscopic data label, input interface inputs and/or change mark for user
Sign content；
Step C (S103)：After label generation instruction triggers, whether detection electron microscopic data label substance meets preset requirement,
If it is electron microscopic data label is generated, if not, prompting user's modification does not meet the label substance of preset requirement, returns to input
Interface.
Optionally, the preset content of electron microscopic data label includes：Problem species, Experiment name, data acquisition duration, data
Collecting device, resolution accuracy, problem code name, sample code name, sample type, sample frame size are wide, sample frame size is high, sample preparation
Condition 1, sampling 2, amplification factor, sampling condition, data expectation quality, affiliated seminar, affiliated teacher, collaborative project group
With cooperation teacher.
Reference table 1, it is assumed that perform step A, parsing obtains " data acquisition duration " information, then the information is write Electronic Speculum number
According to the preset byte of " data acquisition duration " in label.
It is that step A has been parsed that the information that user writes is needed in step B, and remaining label substance, certainly, user can also
The label substance obtained to step A parsings is modified.
Optionally, electron microscopic data label further includes extension, other letters of extension for preservation in addition to preset content
Breath.
Optionally, Fig. 1 steps C is further included：
After generating electron microscopic data label, electron microscopic data label is stored in default special purpose memory devices, electron microscopic data is deposited
Store up other storage devices outside specific store system..
As shown in Fig. 2, present invention additionally comprises a kind of generation system of electron microscopic data label, including：
Parsing module：Electron microscopic data filename and/or electron microscopic data file header are parsed, the label of acquisition will be parsed
In the electron microscopic data label of information, write-in and electron microscopic data file association；
Label interface：Show the input interface of electron microscopic data label, input interface is inputted for user and/or changed in label
Hold；
Generation module：After label generation instruction triggers, whether detection electron microscopic data label substance meets preset requirement, if
It is to generate electron microscopic data label, if not, prompting user's modification does not meet the label substance of preset requirement, returns to input circle
Face.
Optionally, the preset content of electron microscopic data label includes：Problem species, Experiment name, data acquisition duration, data
Collecting device, resolution accuracy, problem code name, sample code name, sample type, sample frame size are wide, sample frame size is high, sample preparation
Condition 1, sampling 2, amplification factor, sampling condition, data expectation quality, affiliated seminar, affiliated teacher, collaborative project
Group, cooperation teacher, and/or extension；Other information of the extension for preservation in addition to preset content.
Optionally, the generation module of Fig. 2 further includes：
After generating electron microscopic data label, electron microscopic data label is stored in default special purpose memory devices, electron microscopic data is deposited
Store up other storage devices outside specific store system..
Based on electron microscopic data label of the present invention and its generation method and system, provided for the big data improvement of electron microscopic data
Information source can effectively reduce the working strength of Ice mapping Mass Data Management, improve the fineness that data are administered, and support
The data analysis and management of various dimensions.
It should be noted that the embodiment of the electron microscopic data label of the present invention, with the generation method of electron microscopic data label and
The embodiment principle of generation system is identical, and related part can mutual reference.
The foregoing is merely illustrative of the preferred embodiments of the present invention, not to limit the present invention scope, it is all
The spirit of technical solution of the present invention and any modification, equivalent substitution, improvement and etc. within principle, done, should be included in this hair
Within bright protection domain.
Claims (10)
1. a kind of electron microscopic data label, which is characterized in that the electron microscopic data label is associated with electron microscopic data, described for preserving
The relevant information of electron microscopic data；
The preset content of the electron microscopic data label includes：Problem species, Experiment name, data acquisition duration, data acquisition are set
Standby, resolution accuracy, problem code name, sample code name, sample type, sample frame size are wide, sample frame size height, sampling 1,
Sampling 2, amplification factor, sampling condition, data expectation quality, affiliated seminar, affiliated teacher, collaborative project group and cooperation
Teacher.
2. electron microscopic data label according to claim 1, which is characterized in that the label further includes extension, the expansion
Other information of the exhibition item for preservation in addition to the preset content.
3. electron microscopic data label according to claim 1, which is characterized in that the electron microscopic data label is stored in default
Special purpose memory devices, the electron microscopic data store other storage devices outside the special purpose memory devices.
4. a kind of generation method of electron microscopic data label, it is characterised in that：The described method includes：
Step A：Electron microscopic data filename and/or electron microscopic data file header are parsed, the label information of acquisition will be parsed, write
Enter in the electron microscopic data label of the electron microscopic data file association；
Step B：Show the input interface of the electron microscopic data label, the input interface inputs and/or change label for user
Content；
Step C：After label generation instruction triggers, detect whether the electron microscopic data label substance meets preset requirement, if
The electron microscopic data label is then generated, if not, prompting user's modification does not meet the label substance of preset requirement, is returned described defeated
Enter interface.
5. according to the method described in claim 4, it is characterized in that, the preset content of the electron microscopic data label includes：Problem
Species, Experiment name, data acquisition duration, data acquisition equipment, resolution accuracy, problem code name, sample code name, sample class
Type, sample frame size are wide, sample frame size height, sampling 1, sampling 2, amplification factor, sampling condition, data expectation essence
Degree, affiliated seminar, affiliated teacher, collaborative project group and cooperation teacher.
6. according to the method described in claim 5, it is characterized in that, the label further includes extension, the extension is used for
Preserve the other information in addition to the preset content.
7. according to the method described in claim 5, it is characterized in that, the step C is further included：
After generating the electron microscopic data label, the electron microscopic data label is stored in default special purpose memory devices, the electricity
Mirror data store other storage devices outside the special purpose memory devices.
8. a kind of generation system of electron microscopic data label, it is characterised in that：The system comprises：
Parsing module：Electron microscopic data filename and/or electron microscopic data file header are parsed, the label for parsing acquisition is believed
In the electron microscopic data label of breath, write-in and the electron microscopic data file association；
Label interface：Show the input interface of the electron microscopic data label, the input interface inputs and/or change mark for user
Sign content；
Generation module：After label generation instruction triggers, detect whether the electron microscopic data label substance meets preset requirement, if
It is to generate the electron microscopic data label, if not, prompting user's modification does not meet the label substance of preset requirement, described in return
Input interface.
9. system according to claim 8, which is characterized in that the preset content of the electron microscopic data label includes：Problem
Species, Experiment name, data acquisition duration, data acquisition equipment, resolution accuracy, problem code name, sample code name, sample class
Type, sample frame size are wide, sample frame size height, sampling 1, sampling 2, amplification factor, sampling condition, data expectation essence
Degree, affiliated seminar, affiliated teacher, collaborative project group, cooperation teacher, and/or extension；
Other information of the extension for preservation in addition to the preset content.
10. according to the method described in claim 8, it is characterized in that, the generation module further includes：
After generating the electron microscopic data label, the electron microscopic data label is stored in default special purpose memory devices, the electricity
Mirror data store other storage devices outside the special purpose memory devices.
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Cited By (1)
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| CN109460184A (en) * | 2018-09-06 | 2019-03-12 | 清华大学 | Electron microscopic data dump method, storage medium and device |
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