Roche cobas s 201 system User manual

Brand: Roche

Model: cobas s 201 system

Type: User manual

Roche cobas s 201 system is an easy to use instrument that offers fully automated nucleic acid extraction and real-time PCR amplification and detection. It includes features such as automated sample processing, user-friendly software, and comprehensive reporting capabilities. The system is commonly used for the detection of pathogens, genetic mutations, and other genetic markers in a variety of clinical and research settings.

03/2008, version 1.0 1.1

PDM Software

Overview

Roche PDM software includes three applications that allow the system

administrator to configure the Roche PDM system and to monitor

system activity.

This section describes these administrative applications.

Refer to Section 2 for a description of the Archive Management

application, which is used to retrieve, review, and print archive records.

In addition to these functions certain Roche PDM Pooling

Manager and Data Manager functions are restricted to users

assigned a LABADMIN or higher role (refer to page 1.34).

The administrative application screens have the same layout and

contain the same global command buttons as other PDM

applications. Refer to Screen Layout in the cobas s 201 system

Hardware and Software Reference Manual for WNV for details.

Application Name Purpose

PDM Configuration • Store the laboratory name and address.

• Configure donor accept and release options.

• Setup an FTP client to transmit LIS export files.

• Determine Library Plate usage.

• Select pooling methods.

• Enable UDECs.

• Select the donor tube carrier size.

• Configure user authentication parameters.

• Configure the LIS export file.

User Administration • Create a user account.

• Enable or disable a user account.

• Retire a user account.

Report Manager • Retrieve, review, and print audit records.

1.2 03/2008, version 1.0

PDM Configuration

The PDM Configuration application allows the laboratory administrator

to set certain configuration settings.

Additional settings, including archive and backup options, are set

during installation. Contact your Roche representative if one of

these settings must be changed.

Click the Config button in the global command button area in other

PDM applications to start the PDM Configuration application

(Figure 1.1).

Figure 1.1

PDM Configuration Application

Navigator Panel Work Area Global Command

Buttons

PDM Software

03/2008, version 1.0 1.3

The PDM Configuration screen is divided into two panels:

Once a field record is selected the field value can be updated by clicking

the Browse button , highlighting an entry in the Selection List dialog

box (Figure 1.2), and then clicking OK.

If the Browse button is not available, the field can be updated by

typing a new value in the Value text box.

The PDM Configuration window contains the following local command

buttons:

Panel Description

Navigator Panel Contains a hierarchical tree format similar to

that used by Windows Explorer. A dotted

yellow circle before an item indicates the

item is a category or topic. Click the plus

symbol before a category or topic to see

related field items.

Work Area Displays the name and description of the

selected category or topic. Displays field

records and allows field values to be viewed

and modified.

Note: Only the Entry tab is accessible.

Figure 1.2

Example Selection List Dialog Box

Button Function

Apply Saves changes to temporary storage.

Save All Displays the Electronic Signature Form.

Applied changes are saved when the form is

signed.

Discard Clears all entries made since the last save

operation.

1.4 03/2008, version 1.0

Storing Address Information

The Address topic allows the laboratory name and address to be entered.

The laboratory name and address are displayed on Roche PDM Pooling

Manager and Data Manager reports.

1 Click the Config button to start the PDM Configuration

application.

2 In the left panel, expand the General category and then expand the

Address topic (Figure 1.3).

3 Select the field to be updated:

4 Type a new value in the Value text box, and then click Apply.

5 Click Save all. The Electronic Signature Form is displayed.

6 Enter the assigned login ID and password and click Sign.

Figure 1.3

Address Topic

Apply

Save all

Name Value

Field Description

Address The laboratory address.

Name The laboratory name.

PDM Software

03/2008, version 1.0 1.5

Configuring Donor Options

The Donors topic allows the auto accept feature to be enabled or disabled,

and limits to be entered for the donor tube barcode reuse time and the

donor sample viability time.

1 Click the Config button to start the PDM Configuration

application.

2 In the left panel, expand the General category and then expand the

Donors topic (Figure 1.4).

3 Select the field to be updated:

Figure 1.4

Donors Topic

Apply Save all

Browse Button

Field Description

Auto Accept Ye s if donor results should be automatically accepted

without operator review. No if results must be

manually accepted using the Accept button in the

PDM Data Manager Donor Review tab.

Donor

Release in

days

The reuse time. The period of time that must elapse

after final results for a donor tube have been received

before that donor tube barcode ID can be reused.

The default is 365 days.

1.6 03/2008, version 1.0

Click the

Browse

button ,

select a value from the Selection List dialog

box, and then click OK.

If the Browse button is not available, type the new value directly

into the Value text box.

5 Click Apply.

6 Click Save all. The Electronic Signature Form is displayed.

7 Enter the assigned login ID and password and click Sign.

Donor

Timeout in

days

The viability time. The elapsed time between initial

pipetting and assignment of final results. If a result is

not accepted within the viability time limit, the sample

is automatically assigned a status of Complete,

Unresolved, unless the sample tested reactive in an

individual pool (Primary Pool of 1 or Resolution Pool).

In that case, the sample is automatically assigned a

status of Complete, Reactive. The default is 10 days.

Donor

Timeout

remaining

days

The timeout notification period. The number of days

before a donor sample times out that a notification

message is displayed.

Field Description

PDM Software

03/2008, version 1.0 1.7

Setting Up an FTP Client for LIS Export

The LIS Export topic allows the auto transmit feature to be enabled or

disabled, and an FTP client to be configured to transmit LIS export files to

an FTP server.

1 Click the Config button to start the PDM Configuration

application.

2 In the left panel, expand the General category and then expand the LIS

Export topic (Figure 1.5).

3 Select the field to be updated:

Figure 1.5

LIS Export Topics

LIS Export Topic

Apply Save all

Browse Button

Field Description

Auto

Tra nsmit

Yes if accepted donor results should be automatically

transmitted to the LIS. No if accepted results must

be manually transmitted using the Send to LIS

button in the PDM Data Manager Donor Review tab.

FTP Connect

TimeOut (in

seconds)

Value in seconds for the timeout of the connect

operation. If a response is not received after this

number of seconds, the FTP client aborts the

connection attempt. The default is 10 seconds.

1.8 03/2008, version 1.0

Click the

Browse

button ,

select a value from the Selection List dialog

box, and then click OK.

If the Browse button is not available, type the new value directly

into the Value text box.

5 Click Apply.

6 Click Save all. The Electronic Signature Form is displayed.

7 Enter the assigned login ID and password and click Sign.

FTP

Password

Password to be used when connecting to the FTP

server.

FTP Polling

Interval (in

seconds)

Frequency to check for files that may be pending

transmission to the FTP server.

FTP Server The FTP server address e.g., myftp.myserver.com

FTP User User name to be used when connecting to the FTP

server.

Use Format for the LIS export file. Options are Version 1.1

Mode (DOMS format) and Configurable. Refer to

Configuring the LIS Export File on page 1.22 for

additional information.

Field Description

PDM Software

03/2008, version 1.0 1.9

Determining Library Plate Usage

The Library Plate topics allow the laboratory administrator to determine

whether a Library Plate is prepared during Primary Pooling and whether

Secondary Pooling is performed from the Library Plate.

1 Click the Config button to start the PDM Configuration

application.

2 In the left panel, expand the General category and then expand the

Library Plate WNV topic (Figure 1.6).

3 Select the pooling method.

Primary Pools of 1 is selected in Figure 1.6.

Click the

Browse

button ,

select On or Off from the Selection List dialog

box, and then click OK.

Figure 1.6

Library Plate Topics

Apply Save all

Browse Button

Library Plate

Topics

Setting Primary Pooling Secondary Pooling

On A Library Plate is prepared

to save an aliquot of each

donor sample in case

Secondary Pooling is

required.

Secondary Pooling must be

performed from the Library

Plate if the well is usable.

1.10 03/2008, version 1.0

5 Click Apply.

6 Click Save all. The Electronic Signature Form is displayed.

7 Enter the assigned login ID and password and click Sign.

Off No Library Plate is

prepared.

Secondary Pooling is

performed from the donor

tube.

Setting Primary Pooling Secondary Pooling

PDM Software

03/2008, version 1.0 1.11

Selecting Pooling Methods

The laboratory administrator can determine which Primary Pooling

methods are available for small pools.

1 Click the Config button to start the PDM Configuration

application.

2 In the left panel, expand the General category and then expand the

Pooling topic.

Select a pooling method in the left panel, e.g.,

Primary Pools of 1 (WNV

), and

then click the

Browse

button to display the

Selection List

dialog box

(

Figure 1.7).

4 Choose Ye s to add the selected pooling method to the list of available

pooling options or select No to exclude the pooling method.

5 Click OK to close the Selection List dialog box.

6 Click Apply.

7 Repeat steps 3 through 6 for the listed pooling methods.

8 Click Save all. The Electronic Signature Form is displayed.

9 Enter the assigned login ID and password and click Sign.

Figure 1.7

Pooling Topic

Small Pools

Browse Button

1.12 03/2008, version 1.0

Methods that are enabled (value Ye s ) appear as Primary Pooling buttons

in the Pooling Wizard (Figure 1.8).

Secondary Pooling options are determined by the system and cannot

be modified by the laboratory administrator.

Figure 1.8

Pooling Tab

Primary Pooling Buttons Secondary Pooling Buttons

PDM Software

03/2008, version 1.0 1.13

Enabling UDECs

The cobas s 201 system supports processing of user-defined external

controls (UDECs). The User Defined External Controls topic allows the

laboratory administrator to specify whether the laboratory can process

UDECs and to specify the position of the UDECs in the SK24 rack.

If UDECs are enabled, the operator is prompted at the beginning of

each pooling run whether to include UDECs in that run.

1 Click the Config button to start the PDM Configuration

application.

2 In the left panel, expand the General category and then expand the User

Defined External Controls topic (Figure 1.9).

3 Select WNV.

4 Select UDEC 1.

Up to five UDECs can be configured for each assay.

Figure 1.9

User Defined External Controls Topic

UDEC Topic

1.14 03/2008, version 1.0

Select a UDEC field:

Click the

Browse

button ,

select a value for the field, and then click

Apply.

7 Repeat steps 5 and 6 for UDEC 2 through UDEC 5.

8 In the left panel, select the Use UDECs field.

9 Click the

Browse

button

and select Ye s to enable use of UDECs. Select

No to disable UDECs.

An individual UDEC can be enabled (Yes) or disabled (No) by the

selection in the In Use field. The Use UDECs field selection affects

all UDECs, overriding individual settings.

10 Click Apply.

11 Click Save all. The Electronic Signature Form is displayed.

12 Enter the assigned login ID and password and click Sign.

Field Description

Batch Position The position (1 to 22) that the UDEC S-tube will

occupy in the SK24 rack.

Batch Rack Not currently used. UDECs are always pipetted

in rack 1 during a pipetting run.

In Use Enable (Ye s) or disable (No) use of this UDEC. All

UDECs can be enabled or disabled with the Use

UDEC field (see below).

Name A unique name for the UDEC. The name will be

used on screens and reports.

PDM Software

03/2008, version 1.0 1.15

Entering UDEC Barcodes, Lot Numbers, and Expiration Dates

When UDECs are loaded on the pipettor deck, the barcode reader scans

the barcodes of each tube and compares the scanned value with the UDEC

barcodes defined by the laboratory administrator. UDEC barcodes, lot

numbers, and expiration dates are entered using the PDM Data Manager

application UDEC tab (Figure 1.10).

In order to access the UDEC tab, the Data Management

workstation must be restarted after UDECs are enabled in the PDM

Configuration application (page 1.13).

Information in the User Defined External Control panel, at the top of the

UDEC tab, is specified in the PDM Configuration application.

Figure 1.10

PDM Data Manager UDEC Tab

UDEC Tab

Selected

Test

User Defined External Control Panel

Field Description

(1st field) Test name (selected in the left panel).

Batch Position SK24 rack position for the S-tube that will contain

the UDEC.

Expanded

Batch Position

Not currently used.

Expanded

Batch Rack

Not currently used. UDECs are always pipetted in

rack 1 during a pipetting run.

1.16 03/2008, version 1.0

Adding UDECs

Access the PDM Data Manager application.

Click the DMS button in the global command button area if

another PDM application is currently running.

2 Select the UDEC tab.

3 Select WNV.

4 Select the test in the left panel and click New.

The UDEC Barcode Definition dialog box is displayed (Figure 1.11).

5 Type the control test name.

6 Type or scan the barcode ID.

The Remaining Length field updates as each character is typed,

indicating the maximum number of additional characters that the

barcode can contain.

The barcode on the control tube must match a barcode defined

for the assay if a UDEC is loaded during a pipetting run.

7 Type the control lot number.

This lot number will appear on screens, in reports, and be

included in the export file to allow statistical tracking.

8 Type the expiration date using the indicated format.

If a UDEC is expired, it will not be processed.

9 Click Apply.

The new test is added to the list in the left panel.

Figure 1.11

UDEC Barcode Definition Dialog Box

PDM Software

03/2008, version 1.0 1.17

Editing a UDEC Definition

Access the PDM Data Manager application.

2 Select the UDEC tab.

3 Select WNV.

4 Select the test in the left panel and click Edit.

The UDEC Barcode Definition dialog box is displayed (Figure 1.11).

5 Update the desired fields then click Apply.

The test name cannot be modified.

Deleting a UDEC

Access the PDM Data Manager application.

2 Select the UDEC tab.

3 Select WNV.

4 Select the test in the left panel and click Delete.

5 Click Ye s to confirm the deletion.

1.18 03/2008, version 1.0

Selecting the Donor Tube Carrier Size

The Donor Carrier Size setting determines the type of donor tube carrier

that can be loaded onto the Hamilton Microlab STAR IVD / STARlet IVD

Pipettor.

1 Click the Config button to start the PDM Configuration

application.

2 In the left panel, expand the General category and then select the Donor

Carrier Size field (Figure 1.3).

Click the

Browse

button ,

select an option from the Selection List dialog

box, and then click OK.

Figure 1.12

Donor Carrier Size Field

Apply Save all

Browse Button

Donor Carrier

Size Field

Setting Description

24 Only 24-position donor tube carriers, containing

10 mL (16 mm x 100 mm) donor tubes, can be loaded.

32 Only 32-position donor tube carriers, containing

5 mL (12 mm x 75 mm) or 7 mL (13 mm x 100 mm)

donor tubes, can be loaded.

PDM Software

03/2008, version 1.0 1.19

4 Click Apply.

5 Click Save all. The Electronic Signature Form is displayed.

6 Enter the assigned login ID and password and click Sign.

Autodetect Either 24-position or 32-position donor tube carriers

can be loaded. The system automatically detects the

type when the first carrier is loaded, and that type

must then be used for the remainder of the run.

Setting Description

1.20 03/2008, version 1.0

Configuring User Authentication Parameters

User Authentication parameters set limits on the size and complexity of

user account login IDs and passwords, and determine password expiration

and inactivity time limits.

1 Click the Config button to start the PDM Configuration

application.

2 In the left panel, expand the User Authentication topic (Figure 1.13).

3 Select the fie

ld to be updated:

Figure 1.13

User Authentication Topic

Apply Save all

User

Authentication

Topic

Field Description

Maximum failed logins Maximum number of failed login

attempts before an account is

temporarily disabled for ten minutes.

Maximum length of

LoginID

Maximum number of characters that

a login ID can contain.

Maximum length of

Password

Maximum number of characters that

a password can contain.

Minimum length of

LoginID

Minimum number of characters that a

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Roche cobas s 201 system User manual

Roche cobas s 201 system User manual

Roche cobas s 201 system User manual

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