Roche cobas s 201 system is a fully automated sample preparation and PCR setup system for molecular diagnostics. It integrates sample preparation and PCR setup into a single workflow, enabling walkaway time for lab personnel and increased lab productivity. The system features random access, allowing users to load samples and reagents in any order, and processes up to 96 samples in approximately 2.5 hours. It also has the capability to perform nucleic acid extraction from a variety of sample types, including swabs, serum, plasma, and whole blood.
Roche cobas s 201 system is a fully automated sample preparation and PCR setup system for molecular diagnostics. It integrates sample preparation and PCR setup into a single workflow, enabling walkaway time for lab personnel and increased lab productivity. The system features random access, allowing users to load samples and reagents in any order, and processes up to 96 samples in approximately 2.5 hours. It also has the capability to perform nucleic acid extraction from a variety of sample types, including swabs, serum, plasma, and whole blood.
03/2008, version 1.0 2.1
Database
Maintenance
2
Archive Management
The system automatically archives data at intervals and times that are
specified during installation of the system.
The criteria for archiving data (for example, archiving all data that are
older than 30 days) are also set during installation.
Data can be manually archived at any time.
Preparing a DVD-R for Archiving
1
Obtain a new DVD-R and label it with today’s date.
A DVD-R must be used. Do not use a DVD-RW. Use a good
quality DVD-R to limit read/write errors and to allow the disc to
be read on multiple readers.
Label the disc using a felt tipped marking pen that is solvent free
and intended for use in labeling DVDs. Markers that contain
solvents can attack the DVD’s protective coating.
2 Insert the labeled disc into the DVD-ROM drive.
The disc should be inserted in the drive shortly before archiving is
scheduled and removed after archiving is completed. Do not allow
the disc to remain in the drive when it is not in use. Do not store
DVDs in a laboratory environment.
3 Select Format from the displayed menu. The Format E: dialog box is
displayed (Figure 2.1).
4 Leave the Volume Label blank and select Start. A message box is displayed
indicating that existing data on the DVD-R will be lost.
The volume label is automatically assigned during the formatting
process.
Figure 2.1
Format E: Dialog Box
2.2 03/2008, version 1.0
5 Respond Ye s to the prompt to proceed. A progress bar indicates the
progress of the formatting (Figure 2.2).
6 Upon completion of formatting, a message box is displayed indicating that
formatting of the DVD-R is complete but that the media must be made
compatible before data can be read (Figure 2.3).
Do not perform the Make Compatible procedure until all data have
been written to the DVD-R. Once the Make Compatible procedure
is performed, additional data cannot be written to the DVD-R.
7 Respond OK to the prompt. The DVD-R is now formatted and ready to
use.
Figure 2.2
Display of DVD Formatting Progress
Figure 2.3
Notification of Formatting Completion
Database Maintenance
03/2008, version 1.0 2.3
Initiating Manual Archiving
Right-click the Archive Management icon in the Data Management
workstation taskbar and select Perform Archiving now from the displayed
popup menu (Figure 2.4).
The Archive Management icon updates to show archiving is in progress.
The system does not need to be shutdown for archiving to take
place.
Data records that have resided in the Roche PDM database for
more than the specified number of days are automatically archived
and purged from the system.
Making a DVD-R Compatible
When archiving and purging are completed, the disc must be made
compatible so the data can be read on most disc drives.
Do not perform the Make Compatible procedure until all data have
been written to the DVD-R. Once the Make Compatible procedure
is performed, additional data cannot be written to the DVD-R.
1 Insert the disc into the DVD-ROM drive.
2 Select Make Compatible from the displayed menu, then click Start.
Storing Archival Media
Remove the disc from the drive and place it in the storage box provided.
Do not allow the disc to remain in the drive when it is not in use.
Follow the disc manufacturer’s instructions for storage of the disc.
Do not store the DVD in a laboratory environment.
It is recommended that the DVD be copied, to reduce the risk of
the loss of archived data. The DVD can be copied on another
computer.
Archiving Backup History
Select the Audit Trail > Backup History List report in the Report Manager
application to examine backup history (see page 1.39).
Figure 2.4
Archive Management Popup Menu
Archive Management Icon
Perform Archiving now
2.4 03/2008, version 1.0
Loading Archived Data to a Temporary Database
Archived data can be retrieved and reviewed. An archived record is
retrieved by loading the archive disc and performing a query for a
specific donor, pool, batch, control, plate well, or pooling run.
The archived data is reviewed in a temporary database. It is not
restored to the active database
1 Click the Archive button in the global command button area in
other PDM applications to start the Archive Viewer.
The Archive Viewer starts. The Management > Query tab is selected by
default (Figure 2.5).
2 If archived data that includes a particular batch ID, S-tube ID, donor tube
ID, control ID, or run ID is to be retrieved, enter the ID in the Identifier
field. If data archived during a particular date range is to be retrieved,
enter the beginning and ending dates in the Date range fields.
Select Last Month or Last Year to retrieve archived data that were
created during the indicated time period. If needed, select Reset to
clear the fields for re-entry.
If no barcode number or date range is entered, all archives that have
been created on the system are listed.
If a foreign archive is being retrieved (an archive created on a
different system), entries are not needed in the Identifier and Date
range fields.
Figure 2.5
Archive Viewer Management > Query Tab
Database Maintenance
03/2008, version 1.0 2.5
3 Click Next. All archives created on the system that match the entered
search criteria are displayed in the upper portion of the screen
(Figure 2.6).
Previously loaded archives are displayed in green.
Previously retrieved archives are listed in the Import History section
of the window in the order they were retrieved.
4 Place a check mark in the Mark column for an archive to be loaded.
5 Obtain the archive disc for the selected archive.
6 Load the archive disc into the DVD-ROM drive.
Do not allow the disc to remain in the drive for longer than several
hours.
7 If data archived on a different system is being retrieved, click Foreign
Archive to browse for the archive file, select the archive file, and click
Open.
8 Select Next. The archived data is loaded to the temporary database.
Loading of archived data may take several minutes, depending
upon the amount of data being loaded.
Figure 2.6
View Loaded Tab
All Archives
Created by the
Import History
the System
2.6 03/2008, version 1.0
Viewing Loaded Data
1
Click the Archive button to start the Archive Viewer.
2 Access the Management > Query tab and load the archive data to the
temporary database (see Loading Archived Data to a Temporary Database
on page 2.4).
3 Select the View > Query tab and enter the desired search criteria.
4 Select the ID type (for example Controls or Pools), then select Next. The
corresponding tab (for example Controls or Pools) is displayed.
5 Select Next or Previous to display another tab (Batch, Pools, Donor,
Controls, Plate Well, or Run) of the archived data.
Pertinent data for the selected tab is shown at the top of the screen. For
example, when the Pools Archive tab is displayed the S-tube reading and
pipetting status and result data for the pool are shown at the top of the
screen.
Database Maintenance
03/2008, version 1.0 2.7
Batch Archive Tab
Information displayed in the Batch Archive tab is summarized below:
Figure 2.7
Batch Archive Tab
Batch Information
Audit Trail Information
Pool Information
Control Information
Field Description
Batch Information
Batch ID The batch ID that contains the selected item.
Batch Status The processing status for the batch.
Run ID The ID of the pooling run in which the batch
was created.
Thermocycler ID
The ID of the COBAS
®
TaqMan
®
Analyzer
thermal cycler where the batch was analyzed.
CAP Instrument ID
The ID of the COBAS
®
AmpliPrep Instrument
where the batch was prepared.
CTM Instrument ID
The ID of the COBAS
®
TaqMan
®
Analyzer
where the batch was analyzed.
STAR S/N The ID of the Hamilton Microlab STAR IVD/
STARlet IVD pipettor where the batch was
pipetted.
Batch Date The date and time the batch was pipetted.
2.8 03/2008, version 1.0
Field Description
Audit Trail Information
Audit Date The date and time the event occurred.
User Full Name The name of the logged-on user when the event
occurred.
Message Code The code that accompanied the event message.
Description The message that was displayed for the event.
Workstation Identification and location of the workstation
on which the event occurred.
Pool Information
SK24 Pos The position of the pool on the SK24 rack.
S-tube ID The barcode clip ID on the S-tube containing
the pool.
IC Result Internal control result for the pool.
Test Result Target result for the pool.
Calculated Result Result based on the IC result and test result.
Final Result Result based on the calculated result and batch
validity.
Control Information
SK24 Pos The position of the control on the SK24 rack.
Control ID The barcode ID of the S-tube containing the
control.
IC Result Internal control result for the control.
Test Result Target result for the control.
Calculated Result Result based on the IC result and test result.
Final Result Result based on the calculated result and batch
validity.
Database Maintenance
03/2008, version 1.0 2.9
Pools Archive Tab
Information displayed in the Pools Archive tab is summarized below:
Figure 2.8
Pools Archive Tab
S-tube Information
Audit Trail Information
Batch Information
Pooling Run Information
Field Description
S-tube Information
S-tube ID The barcode clip ID on the S-tube containing
the pool.
Assay The test that was run on the pool.
Volu me The volume of liquid that was pipetted into the
S-tube.
Reading Status The barcode reading status for the S-tube.
Pipetting Status The pipetting status for the pool.
Final Result Result based on the calculated result and batch
validity.
Calculated Result Result based on the IC result and test result.
IC Result Internal control result for the pool.
Test Result Target result for the pool.
2.10 03/2008, version 1.0
Field Description
Audit Trail Information
Audit Date The date and time the event occurred.
User Full Name The name of the logged-on user when the
event occurred.
Message Code The code that accompanied the event message.
Description The message that was displayed for the event.
Workstation Identification and location of the workstation
on which the event occurred.
Batch Information
Batch ID The batch ID that contains the selected item.
Batch Status The processing status for the batch.
CAP Instrument ID
The ID of the COBAS
®
AmpliPrep Instrument
where the batch was prepared.
CTM Instrument ID
The ID of the COBAS
®
TaqMan
®
Analyzer
where the batch was analyzed.
Thermocycler ID
The ID of the COBAS
®
TaqMan
®
Analyzer
thermal cycler where the batch was analyzed.
Donor Tube ID The barcode IDs of the individual donor tubes
that were included in the pool.
Pooling Run Information
Run ID The ID of the pooling run in which the batch
was created.
Pooling Type The type of pooling run in which the batch was
created.
STAR S/N The ID of the Hamilton Microlab STAR IVD/
STARlet IVD pipettor where the batch was
pipetted.
Pooling Operator The name of the logged-on user when the
pooling run was performed.
Create Date The date and time the batch was pipetted.
Database Maintenance
03/2008, version 1.0 2.11
Donor Archive Tab
Information displayed in the Donor Archive tab is summarized below:
Figure 2.9
Donor Archive Tab
Donor Tube Information
Audit Trail Information
Pooling Run Information
Pool Information
Plate Well Information
Field Description
Donor Tube Information
Donor Tube ID The barcode ID on the tube containing the
donor sample.
Assay The test that was run on the donor sample.
Final Result Reportable result for the donor sample.
Acceptance Operator The name of the logged-on user when the
donor results were accepted.
Plate Well Information
Plate ID The barcode ID on the plate containing an
aliquot of the donor sample.
Plate Type Library Plate.
Plate Well Pos The plate well (i.e., E6) that contains an
aliquot of the donor sample.
Pipetting Status The pipetting status for the plate well.
2.12 03/2008, version 1.0
Field Description
Audit Trail Information
Audit Date The date and time the event occurred.
User Full Name The name of the logged-on user when the
event occurred.
Message Code The code that accompanied the event message.
Description The message that was displayed for the event.
Workstation Identification and location of the workstation
on which the event occurred.
Pooling Run Information
Run ID The ID of the pooling run in which the batch
was created.
Pooling Type The type of pooling run in which the batch was
created.
Instrument The ID of the Hamilton Microlab STAR IVD/
STARlet IVD pipettor where the batch was
pipetted.
Create Date The date and time the batch was pipetted.
Pooling Operator The name of the logged-on user when the
pooling run was performed.
Pool Information
S-tube ID The barcode clip ID on the S-tube containing
the donor sample.
Final Result Pool result based on the IC result, target result,
and batch validity.
Batch ID The batch ID that includes the donor sample.
Database Maintenance
03/2008, version 1.0 2.13
Controls Archive Tab
Information displayed in the Controls Archive tab is summarized below:
Figure 2.10
Controls Archive Tab
Control Information
Audit Trail Information
S-tube Information
Field Description
Control Information
Control ID The barcode ID on the control tube
Assay Control type NC (negative control) or PC
(positive control) plus the analyte.
Reading Status The barcode reading status for the control
tube.
Expiration Date The control expiration date read from the
control barcode.
Batch ID The batch ID that included the control.
Lot Number The control lot number read from the control
barcode.
Audit Trail Information
Audit Date The date and time the event occurred.
User Full Name The name of the logged-on user when the
event occurred.
Message Code The code that accompanied the event message.
2.14 03/2008, version 1.0
Description The message that was displayed for the event.
Workstation Identification and location of the workstation
on which the event occurred.
S-tube Information
S-tube ID The barcode clip ID on the S-tube containing
the control sample.
Assay The test that was run on the pool.
Volu me The volume of liquid that was pipetted into the
S-tube.
Reading Status The barcode reading status for the S-tube.
Pipetting Status The pipetting status for the pool.
Final Result Result based on the calculated result and batch
validity.
Calculated Result Result based on the IC result and test result.
IC Result Internal control result for the pool.
Test Result Target result for the pool.
Field Description
Database Maintenance
03/2008, version 1.0 2.15
Plate Well Archive Tab
Information displayed in the Plate Well Archive tab is summarized
below:
Figure 2.11
Plate Well Archive Tab
Plate Well Information
Audit Trail Information
Donor Tube Information
Pooling Run Information
Field Description
Plate Well Information
Plate ID The barcode ID on the Library Plate
containing an aliquot of the donor sample.
Plate Type Library Plate.
Donor Tube ID The barcode ID on the tube from which the
contents of the well were pipetted.
Pipetting Status The pipetting status for the plate well.
Plate Well Pos The well (i.e., E6) that contains an aliquot of
the donor sample.
Audit Trail Information
Audit Date The date and time the event occurred.
User Full Name The name of the logged-on user when the
event occurred.
Message Code The code that accompanied the event message.
Description The message that was displayed for the event.
2.16 03/2008, version 1.0
Workstation Identification and location of the workstation
on which the event occurred.
Donor Tube Information
Donor Tube ID The barcode ID on the tube from which the
contents of the well were pipetted.
Pooling Run Information
Run ID The ID of the pooling run in which the batch
was created.
Pooling Type The type of pooling run in which the batch was
created.
Instrument The ID of the Hamilton Microlab STAR IVD/
STARlet IVD pipettor where the batch was
pipetted.
Create Date The date and time the batch was pipetted
Pooling Operator The name of the logged-on user when the
pooling run was performed.
Field Description
Database Maintenance
03/2008, version 1.0 2.17
Run Archive Tab
Information displayed in the Run Archive tab is summarized below:
Figure 2.12
Run Archive Tab
Pooling Run Information
Audit Trail Information
Library Plate Information
Donor Tube Information
Field Description
Pooling Run Information
Run ID The ID of the pooling run in which the batch
was created.
Pooling Type The type of pooling run in which the batch was
created.
Create Date The date and time the batch was pipetted.
Instrument The ID of the Hamilton Microlab STAR IVD/
STARlet IVD Pipettor where the batch was
pipetted.
Pooling Operator The name of the logged-on user when the
pooling run was performed.
Audit Trail Information
Audit Date The date and time the event occurred.
User Full Name The name of the logged-on user when the
event occurred.
Message Code The code that accompanied the event message.
2.18 03/2008, version 1.0
Description The message that was displayed for the event.
Workstation Identification and location of the workstation
on which the event occurred.
Library Plate Information
Plate ID The barcode ID on the Library Plate that
contains an aliquot of the donor sample.
Plate Type Library Plate.
Donor Tube ID The barcode ID on the tube from which the
contents of the well were pipetted.
Pipetting Status The pipetting status for the plate well.
Plate Well Pos The well (i.e., E6) that contains an aliquot of
the donor sample.
Donor Tube Information
Donor Tube ID The barcode IDs of the individual donor tubes
that were included in the pool.
Field Description
Database Maintenance
03/2008, version 1.0 2.19
Clearing Archive Data from the Temporary Database
1
Display the Management > View Loaded tab (Figure 2.13).
2 Place a check mark in the Mark column for each archive to be cleared
from the temporary database.
3 Click Remove.
Figure 2.13
View Loaded Tab
Mark Column
Remove
2.20 03/2008, version 1.0
Database Backup
The system automatically performs a database backup at intervals and
times that are specified during installation of the system.
If desired, a manual backup can be performed at any time.
If a manual backup is performed, any automatic backup scheduled
for that same day will be rescheduled for the following day.
Preparing for Backup
1
Verify that the tape drive is turned on.
Never turn off the tape drive power while a tape is in the drive.
2 Select the backup tape that is to be used and insert it into the tape drive.
Backups are scheduled so a tape is reused every seven days.
Initiating a Manual Backup
Right-click the Archive Management icon in the Data Management
workstation taskbar and select Perform Backup now from the displayed
popup menu (Figure 2.14).
The Archive Management icon updates to show the tape backup is in
progress.
The system does not need to be shutdown for the backup to take
place.
A full database backup is performed.
Storing Backup Media
The tape is automatically ejected when the backup completes to
prevent inadvertently overwriting the tape when the next backup
occurs.
Tapes used for backup should be stored according to your facility’s
standard operating procedures.
Figure 2.14
Archive Management Popup Menu
Archive Management Icon
Perform Backup now
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Roche cobas s 201 system is a fully automated sample preparation and PCR setup system for molecular diagnostics. It integrates sample preparation and PCR setup into a single workflow, enabling walkaway time for lab personnel and increased lab productivity. The system features random access, allowing users to load samples and reagents in any order, and processes up to 96 samples in approximately 2.5 hours. It also has the capability to perform nucleic acid extraction from a variety of sample types, including swabs, serum, plasma, and whole blood.
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