Table of contents
1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . 3
2. Installation . . . . . . . . . . . . . . . . . . . . . . . . 4
3. Deinstallation . . . . . . . . . . . . . . . . . . . . . . . . 4
4. License . . . . . . . . . . . . . . . . . . . . . . . . 5
5. The main window of NMRArchive . . . . . . . . . . . . . . . . 6
6. Transfer of NMR data to the archiving system . . . . . . . . . . . . . 7
7. Reading Information from the NMR-data in the database . . . . . . . . 9
8. Archiving of provided data on a CD . . . . . . . . . . . . . 11
9. Database structure . . . . . . . . . . . . . . . . . . . . . . . . . 12
10. Searching for specific data sets . . . . . . . . . . . . . . . . . . . . . 13
11. Backtransfer of queried data sets . . . . . . . . . . . . . . . . . . . . 14
12. Use of specific data servers (LabArchiveStore) . . . . . . . . . . . . . . . 15
13. Printing data or creating an Excel table . . . . . . . . . . . . . . . . . . . 16
14. Customer specific data transfer . . . . . . . . . . . . . . . . . . . . 17
15. Additional features of the software . . . . . . . . . . . . . . . . . . . . 19
16. Multi user system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
1. Introduction
The software package NMRArchive enables the user to deal with large amounts of NMR data, organises archiving processes, administrates the produced NMR-archives and gives easy access to certain data.
NMRArchive includes several function to accomplish these tasks:
1. Manual or automatic transfer of NMR data to prepare archiving
2. Reading of information from archived data into a database
3. Search and filter functions in the database for selection of certain defined data and back transfer options of archived data sets
4. Customer specific data transfer via local area network or e-mail
NMRArchive uses the data base of Microsoft Access, enabling easy implentation of your own specific search criteria and options in the database system in addition to the existing functions of the program. Database access in NMRArchive is always done with the standard language SQL making usage of other database systems like Orakel or Informix very comfortable. This makes the integration of NMRArchive in existing laboratory systems very easy.
Standard versions for single work places but also versions for multi work place system in laboratory networks are available. Additionally the program can be adjusted to meet specific requirements in analytic laboratories.
NMRArchive requires Windows NT SP4 or higher or Windows 2000. Connection of spectrometers with UNIX workstations, like SGI Indy or O2, requires installation of Samba or any aquivalent program to enable Windows to recognize the UNIX disc as logical drive.
2. Installation
The program is distributed on a CD containig directories for Windows NT 4.0 german version (NMRArchive_deutsch) and english version (NMRArchive_english), a version for Windows 2000 (NMRArchive_W2000) and the documentations (Manuals).
Local administrator rights are necesarry in order to install NMRArchive on your workstation. Clicking on Setup.exe in the Exlporer in the corresponding directory will start the installation. Alternatively the complete path of the setup file can be entered e.g. D:\NMRArchive_english\Setup.exe.
Attention: Please close all applications before starting the installation. Afterwards warnings of files not being updated due to use can be ignored. Udating of system files and a restart of the computer during installtion is to be done. Restart setup after reboot.
To enable the program to access data on UNIX machines it is necesarry to integrate these machines in the Windows NT enviroment. This is done by installing Samba on these machines. An other options for the realisation of data access is to install NFS on the Windows Computer making it possible to directly wright data from UNIX machines on the PC disc.
3. Deinstallation
Deinstalltion of NMRArchive is done by clicking Start/Settings/Control Panel/Add/RemSoftware, choosing NMRArchive and Add/Remove.
4. License
The program can be tested without functional restrictions for a defined period of time. After this test time license is necesarry for further use (created databases will be preserved)
Licenses can be order from MR Resources. The System-ID displayed prior to the start of NMRArchive must be passed on.
You will receive a password changing the test version into a fully licensed program. Clicking on licensing in the above shown window will produce the window below. Just enter the password an the licensing is complete.
5. The main window of NMRArchive
The main window consists of three main screens displaying information from the database. There is a menu bar on the top and buttons in the lower left corner to activate certain actions. Three fields for entering search criteria are below the menu bar and the status of the backup folder in displayed at the bottom right corner. You also find the current time and the time for the next transfer if automatic data transfer is activated. A status bar at the bottom of the screen reports on selected files or experiments.
In the left screen you find the different archives (CDs). After choosing an archive the included filenames will be displayed and additional information will appear on the right side. Clicking on a filename in the left screen will produce acquisition parameters in the right upper screen and the content of the file 'title' from the processing folder in the right bottom screen.
The data transfer can be configure by clicking on 'settings' and 'change'. Automatic data transfer can be activated and stopped in the 'automation' menu. Selected Archives in the left screen can be deleted or exported to another LIMS system (e.g. SampleTrack from Bruker) in the 'extras' menu.
Reading NMR data to the database is done be clicking on the 'archive' button. The 'transfer' button enables manual transfer an the 'close' button will exit the program.
6. Transfer of NMR data to the archiving system
For archiving purposes the NMR data has to be transferred from the spectrometer to the archiving system (i.e. a pc with CD-burner and suitable software). It will be collected in a seperate folder. The burning process itself is concluded by the burning software of the CD-burner.
NMRArchive allows for ten different sources of NMR data. These include NMR spectrometers or certain folders on the disc of the spectrometer's computer (e.g. /u/data and /v/data). The data will be transferred to a folder and collected there. If the data excedes a certain memory size (e.g. 650 MB for a CD) a second folder will take over and the first folder is available for burning. The status of the backup folder is displayed in the right bottom corner of the main screen of the program. Folders ready for burning are marked in red.
Data transfer parameters are altered in a seperate screen which can be accessed through "change" in the "settings" menu.
To define source and aim folders first choose the drive of the source data in the upper left corner. Then select the NMR data folder on the drive in the large window below. To add the selected folder to the corresponding variable (?) click the "add" button on the right.
Deleting not anymore required data from a source folder is done automatically if the corresponding field is checked. The storage period in the bottom part of the window determines the age of the data that should be deleted. E.g. if the storage period is set to 300 days, all data older than 300 days will be deleted from the source folder when the next transfer is started.
Using the qualifying period enables protection from transfer of NMR data currently being measured. When transferring only data older than the qualifying period is being taken into account. The 'date of birth' of the NMR data is stored by the time stamp in the file 'acqus' located in the folder of each experiment. The real acquistion parameters are stored here.
Automatic transfer is started with 'start' from the 'automation' menu in the main window and stopped with 'stop'. The parameter 'last transfer' sets the limiting age of data to be transferred. After an automatic transfer this parameter will be reset to the current time minus the qualifying period and the next transfer will be set to the current time plus the the transfer interval. In general all data is being transferred that is younger than the parameter 'last transfer' and older than the current time plus the qualifying period. This ensures NMR data not to be transferred twice.
Manual transfer is started with the 'transfer' button in the main window and will not alter the parameters 'last transfer' and 'next transfer'. But it will be checked if the chosen data set is allready located in the aim folder. In this case no data will be transferred. Experiments are generally transferred seperately. To stop the manually initiated transfer click again on the 'transfer' button.
Deleting processed data files in the aim folder can save disc space in the archives (CDs). This can be done by checking the corresponding boxes in th aim folder. This is relevant to all files with the names 1r, 1i, 2rr, 2ri, 2ir, 2ii and dsp.
If two aim folders are not sufficient to store all transferred data, up to 18 additional folders can be used. An extra mode allows to statically assign source and aim folders. This way e.g source 1 can be linked to aim 1 and 2, and source to 2 can be linked to aim 3 and 4. This mode allows to seperate data from different spektrometers.
Clicking on 'ok' will confirm the parameters and exit the window. Choosing 'cancel' will close the window without changing the parameters.
7. Reading Information from the NMR-data in the database
Clicking on the 'archiv' button in the main window will open up the following window. This initiates the incorporation of information from the NMR data included in a full backup folder, on a CD or in another drive.
The name of the archiv (e.g. CD label) has to be entered in the first field. If no name is entered NMRArchive will automatically assign a name including the date.
Remarks can be entered in the second field. This will be include in the database and can altered later on.
Step three allows to choose wether the NMR data is in a full backup folder or allready archived on a disc. In the latter case the corresponding drive and folder of the NMR data has to be entered in the fourth field.
The 'start' button will initiate reading of the information on the chosen archives with NMR data into the database. If a full backup folder has been selected, an additional copy of the current database will be prepared. This copy is ready to be burned on CD for storage purposes.
Aspect 3000 data stored on CDs can be added to databases using the conv-routine of Bruker Analytik. To use this feature the XWINNMR-CD from Bruker is needed, but not necessarily a license for XWIN-NMR. If such an option is required please contact MR Resources.
NMRArchive automatically recognises different formats of UNIX software from Bruker. Only Aspect 3000 data has to be marked manually, because these data sets only consist of one file with any kind of name.
8. Archiving of provided data on a CD
After the information from NMR data in the backup folder has been written to the database and a current kopie of the complete database exists in the backup folder, the CD burner's software can burn the data on CD.
It is recommended to stick with the follwing general folder structure to be able to use simple 'drag and drop' operations. This ensures easy copying of backup folder data to the burner software and at the same time provides a uniform structure on the CDs.
Backupfolder 1: \backup\backup1\NMR-data
Backupfolder 2: \backup\backup2\NMR-data
The subdirectory NMR-data can simply be dragged to the burning software and the data will be located in the folder NMR-data on the CD.
After the burning is complete it is possible and should be checked if all data was burned on CD correctly. This can be done by reentering the window for reading data into database through the 'archiv' button in the main window.
The drive of the CD has to be entered in field 4. Click on 'verify' afterwards. NMRArchive will compare the data on CD with the backup folder data regarding size and completeness of the data sets.
Checking the box above the 'verify' button will allow NMRArchive to automatically delete the NMR data in the backup folder after verifying correct burning, making the empty available for new automatic transfer.
9. Database structure
The database consist of six tables. Five of these are hierachically structured in the following scheme:
It is assumed that the NMR archiv consists of n seperate archivs (CDs). Each archiv includes n data sets (filenames), each data set includes n experiments and each experiment includes n evaluations ('processing'). An additional remark table is attached to the 'processing' tabel to prepare for possible, later implemented options.
The sixth table consists of configuration data of the program, like source folder, backup folder and flags.
The structure provides best data packaging and shortest access times for search processes in certain data sets. If for example the data set are scanned for specific acquisition parameters, the whole table 'acquis' is queried. After a succesful enquiry the filenumber in the table 'files' and the CD number in the table 'CD_number' are determined.
In the same way all filenames in an archiv, all experiments from a certain filename and all evaluations in a certain experiment can be queried and displayed in the main window.
10. Searching for specific data sets
The enquiry for specific data sets is carried out in the main window of NMRArchiv. The screens can be looked through manually or the search functions can be used.
There are three different search fields available in the database. The first field includes criteria for acquisition parameter queries. For an easy search the field incorporaters so called "comboboxes". These consist of a drop down menu with all used values. The values can just be picked and do not need to be entered manually. They are refreshed when the program is started or new data is stored in the database.
Filenames, plot titles and remarks concerning the plot title can be queried by any set of signs. The signs are recognized within the corresponding catagories. Two different sets of signs can be used in the plot title. They must be connected with a "&"-sign.
All parameter fields can be used at the same time and are automatically linked with an "and" connection. The query can be started with the "search" button.
11. Backtransfer of queried data sets
Having found a certain data set in a data base, NMRArchive displays the name of the CD, on which the data has been archived, in the status line at the bottom of the screen.
The corresponding CD has to be put the CD drive. In the menu 'settings/change' the CD drive has to be set to source prior to retransferring the data. At the same a goal drive has to be defined. This drive can be located on the workstation with NMRArchive. The data set can also be retransferred to any network drive or folder connected and free(?).
The data set has to be picked in the right upper screen and is displayed in the status line (EXPNO). Retransfer is started from the menu 'extras/retranfer'. The data set is transferred from CD to the chosen drive or folder and can be used in any NMR program after transfer has been complete.
If XWIN-NMR is used, the goal folder has to have the proper Bruker syntax structure (i.e. data/<username>/nmr/<filename>).
12. Use of specific data servers (LabArchiveStore)
NMRArchive expects NMR data to be stored on CDs (or DVDs). After succesful inquiry the name of the CD with the specific set of data is displayed in the status bar. It has to be placed in the CD drive and the drive letter has to selected in „Einstellungen“ „Quelle des Rücktransfers“.The data set can be used be choosing „Extras/Rücktransfer“ and either „Experiment“ or „Ordner“.
Additionally NMRArchive is able to automatically create CD images on a data server providing data online. NMRArchive can administrate this data in the same way. The name of the folder following the drive letter has to be „LabArchiveStore“ and the last folders name has to be „NMR_data“ to enable NMRArchive to recognize the appropriate mode.
To provide data online stick with the following procedure:
1. Create folders on the data server
to store data:
x:\LabArchiveStore\Backup1\NMR_data
x:\LabArchiveStore\Backup2\NMR_data
2. Insert these folders in the window
„Einstellungen“.
3. Transfer data (manually or automatically)
in these folders until the chosen size of the folder is reached ant the archiving
can be started.
4. Read the data of the filled folder
in the data base by clicking on the „Archivierung“ button. Enter
the name of the CD in the pop up window, check the box for archiving of the
filled folder and press „Starten“. This will not only save the significant
information from the data to the data base, but also create a copy of the updated
data base in the filled folder.
5. The next step is burning the data
to CD. Any CD burner program can be used. The NMR_date subfolder with the NMR-data
can be moved by „drag and drop“ into the burner program. Start burning
the CD afterwards.
6. To verify the new CD enter drive
letter in the window on top of the „Archivieren“ button and click
on the „Überprüfen CD“ button. Usually after verifying
the CD the data can be deleted from the folder by checking the corresponding
box. In the new mode an alternativ box can be checked that will move the folder
to LabArchiveStore. This will rename the folder from x:\LabArchiveStore\Backup1\NMR_data
to x:\LabArchiveStore\CD_neu\NMR_data and create a new folder x:\LabArchiveStore\Backup1\NMR_data.
7. When retransferring the data from
LabArchiveStore no source may be selected. If the data is to be retransferred
from a CD chose the drive letter as usually.
13. Printing data or creating an Excel table
Data sets displayed in ListView (e.g. results of a data base quiry) can be printed or exported to an Excel table. All parameters can be selected freely. All actions are started by clicking on the header of the cirst column in the ListView window. The following window will pop up and another click will start the selected action.
Print list
Export list to Excel file
Define list selection
Display list selection
Reorder list
14. Customer specific data transfer
Additionally to manual or automatic data transfer to goal folders a selective data tranfer can be performed. This transferred is intended to enable fastest possible access to measuring results for customers of laboratories.
The administration of customers is done in an extra data base. This data base includes the information on specific customers and also the information on how the customer wants to access the measuring results. This databank is available in 'extras/customer administration'.
Measuring results can be automatically transferred via the local network or email. This is done by checking the corresponding box in the right bottom corner of the above window. 'Send' and 'Deliver' boxes produce additional information for laboratory management.
If both 'transfer' and 'email' are checked, the data is being transferred via the local network and the customer receives an additional email reminder including information that the measuring results have been transferred. A valid goal folder has to be entered to enable transfer via LAN. A valid email address has to be entered to ensured proper mail delivery.
To enable NMRArchive to attach measuring data to an email following entries have to be made in the 'settings' of the data base 'NMRcustomer.mdb':
| Fieldname | Entry |
| Winzip_Path | Pathname of Winzip |
| Winzipse_Path | Pathname of Winzip Selfextractor |
| Mailer | Name of mail server in LAN |
| Sender | E-mail-address of sender (laboratory) |
The measuring data is assigned to specific customer via a 'cusomer-ID'. This ID is generated from a specific procedure using the NMR data and entries from the field 'customer ID'. This procedure is chosen with the second number from the right side of the field 'version' in the table 'settings' from the bata base 'NMRtranfer.mdb'. There are following options:
2. number
0 -- no customer specific data transfer
1 -- the first 2 or 3 letters of the filename will be compared to the 'customer-ID'.
2 -- the 'title'-file will be queried for the string '-xyz-'. The next letter is the 'customer-ID'.
3 -- the 4 letters following the second space will be used as 'customer-ID'.
15. Additional features of the software
NMRArchive includes additional function which can be activateted in the menu 'extras'. These are:
The laboratory accounting allows for a customer specific invoice for services. Using this option requires adjusting of the program for the specific requirements of the laboratory.
This is also necessary for the plot administration. Here an archive on paper can be generated. This allows for the search in shelves, drawers and files and to rearrange these. An additional program allows the query of the archive from the spectrometer computer.
Updating of combo boxes in very large data bases can take very long especially if the data base is on an central drive and accessed via the network. To avoid these waiting times the update is not executed automatically at all times. The program update combo boxes initiates updating manually.
Activate protocol will create a protocol file recording all actions from the user and the program.
The five numbers in the field 'version' of the table 'settings' in the data base 'NMRtransfer.mdb' have the following meaning:
16. Multi user system
In mutli user systems NMRArchive is being installed on every workstation. Licensing distinguishs basis and supplementary versions. Data transfer to backup folders, gathering of information to the data base and verification of CDS can only be conducted from one program (basis lincens). Supplementary licensed workstations can use all tools to query the data base and can retransfer data.
While each program has got its own local data base with the settings for the installation path, the data base with the information on the NMR data (i.e. archive name, filename, acquisition parameters and title file entry) must be stored on a central server in the network accessible for all users.
In single user systems only one data base exists in the current program path. In multi user systems the data base has to be placed on a server or a freely accessible folder, ensuring access for all users.
The data base from the installation
path ot he basis license will be copied to the designated folder (e.g. an NT-server)
to install a multi user system. In basis license and supplementary lincensed
programs this path has to be entered in 'establish central DB' in the menu 'extras'.