User Bulletin: Autoanalysis Using GeneMapper® Software v4 ...tools.thermofisher.com/content/sfs/manuals/cms_042356.pdf · 4 User Bulletin Autoanalysis Setup and Workflow Autoanalysis

User BulletinGeneMapper® Software Version 4.0

January 2006

SUBJECT: Autoanalysis

In This UserBulletin

This user bulletin covers:

Autoanalysis Using GeneMapper® Software v4.0 . . . . . . . . . . . . . . 2Autoanalysis Setup and Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . 4Setting Up the GeneMapper® Software . . . . . . . . . . . . . . . . . . . . . . 6Setting Up a Shared Folder (Remote Autoanalysis Only). . . . . . . . . 9Setting Up the Data Collection Software . . . . . . . . . . . . . . . . . . . . 12

Creating Instrument Protocols. . . . . . . . . . . . . . . . . . . . . . . . . 13Creating Results Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Creating and Saving Plate Records . . . . . . . . . . . . . . . . . . . . . . . . . 26Starting the Autoanalysis Manager . . . . . . . . . . . . . . . . . . . . . . . . . 29Scheduling and Starting a Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30What Happens During Autoanalysis . . . . . . . . . . . . . . . . . . . . . . . . 30Autoanalysis Manager Functions . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Overview This user bulletin supplements the GeneMapper® Software v4.0 Installation and Administration Guide (PN 4363080) and provides information about setting up the GeneMapper Software and the Data Collection Software for autoanalysis of data.

GeneMapper® Software Version 4.0

2 User Bulletin

Autoanalysis Using GeneMapper® Software v4.0

Overview The GeneMapper® Software Version 4.0 can perform automatic analysis (autoanalysis) of data generated on the following instruments:

• Applied Biosystems 3130/3130xl Genetic Analyzers• Applied Biosystems 3730/3730xl DNA Analyzers• ABI PRISM® 3100/3100-Avant Genetic Analyzers

With these instruments, you can configure the Data Collection Software and the GeneMapper Software to perform data collection and then data analysis without requiring user interaction. The Data Collection Software and the GeneMapper Software can be installed on the same computer (local autoanalysis) or on separate computers (remote autoanalysis), as shown in Figure 1.

Figure 1 Examples of autoanalysis configurations

Sharedfolder

CompatibleApplied Biosystems

electrophoresis instrument

DataCollectionSoftware

Localcomputer

Remote analysiscomputer

GeneMapper®

Software


electrophoresis instrument

DataCollectionSoftware

Localcomputer

GeneMapper®

Software

Local Autoanalysis(The GeneMapper® Software is installed in

the Instrument configuration)

Remote Autoanalysis(The GeneMapper® Software is installed in

the Remote Autoanalysis configuration)

Autoanalysis Using GeneMapper® Software v4.0

Autoanalysis 3

SoftwareComponents

Autoanalysis requires the following software packages:

• Data Collection Software – Runs the instrument and collects data from samples. Autoanalysis can be performed using the following versions of the Data Collection software:– 3100/3100-Avant Data Collection Software v2.0– 3130/3130xl Data Collection Software v3.0– 3730/3730xl Data Collection Software v2.0 or v3.0

• Autoanalysis Manager – Provides an interface between the Data Collection Software and the GeneMapper Software (Figure 2). It queues jobs and tracks the status of their processing. A job can contain a single run, or multiple runs as part of a result group.The Autoanalysis Manager is installed during installation of the GeneMapper Software. When installing the GeneMapper Software, you must select either the Instrument or Remote Autoanalysis configuration.

Note: Autoanalysis is not available in the Stand-Alone configuration of the GeneMapper Software.

• GeneMapper Software v4.0 – Analyzes data collected by the Data Collection Software.

Figure 2 Relationships between the software components

Data CollectionAutoanalysis

ManagerGeneMapperSoftware v4.0

Message Service

Runcomplete

Open

Closes and reports status

Plate Records

Raw Data

Instrument Protocols

Results Groups

Analysis Methods

Study

SNP Set

Panel/Bin

Size Standard


4 User Bulletin

Autoanalysis Setup and Workflow

AutoanalysisSetup Tasks

To set up the Data Collection Software and the GeneMapper Software to automatically analyze data, perform the following tasks:

To see the typical workflow for performing autoanalysis, go to page 5.

Task See page

1. Set up the GeneMapper Software:a. Install and register the software and create user IDs.

For instructions, see the GeneMapper® Software Installation and Administration Guide (PN 4363080).

b. Create definitions for the analysis method, panel, size standard, SNP sets.For instructions, see the appropriate GeneMapper® Software Getting Started Guide.

6

2. Synchronize the GeneMapper® Software data with the Data Collection Software by restarting the GeneMapper Software while the Data Collection services running.

6

3. Remote autoanalysis only: Set up a shared folder on the remote analysis computer.

9

4. In the Data Collection Software, create an instrument protocol for autoanalysis.

13

5. In the Data Collection Software, create a results group for autoanalysis.

17

Autoanalysis Setup and Workflow

Autoanalysis 5

AutoanalysisWorkflowDiagram

Figure 3 shows the typical workflow for performing autoanalysis. Make sure the GeneMapper Software and the Data Collection Software are already set up for autoanalysis (see page 4).

Figure 3 Autoanalysis workflow

Set up the instrument and prepare samples.

(For instructions, see your instrument user guide)

Create and save the plate record.

Close the GeneMapper® Software.

Start the Autoanalysis Manager.

In the Data Collection Software, search for the plate record, then schedule a run.

(For instructions, see your instrument user guide)

After autoanalysis finshes, review the processed data in the GeneMapper® Software.

NO

YES

In the GeneMapper® Software, create any necessary analysis parameters.

(For instructions, see the appropriate GeneMapper®

Software Getting Started Guide)

Synchronize the data with the Data Collection Software.

Are the necessaryanalysis parameters created?

(See page 29)

(See page 26)

(See page 6)


6 User Bulletin

Setting Up the GeneMapper® SoftwareIf the GeneMapper Software is installed and set up:

• Local autoanalysis – Go to “Setting Up the Data Collection Software” on page 12.

• Remote autoanalysis – Go to “Setting Up a Shared Folder (Remote Autoanalysis Only)” on page 9.

Otherwise:

• Install the software according to the instructions for the Instrument or Remote Autoanalysis configuration (as appropriate)

• Register the GeneMapper Software• Create user accounts• Create analysis parameters (analysis method, size standard, SNP

set, panel/bin)

See the GeneMapper® Software Version 4.0 Installation and Administration Guide for information about installing and registering the GeneMapper Software and creating user IDs.

See the appropriate GeneMapper Software Getting Started Guide for information about creating analysis parameters (analysis method, panel, size standard, study).

SynchronizingGeneMapper

Software Datawith the Data

CollectionSoftware

IMPORTANT! If you create or change any of the analysis parameters in the GeneMapper Software, you need to synchronize the data with the Data Collection software.

To synchronize data:

1. Close the GeneMapper Software.

2. Verify that the Data Collection services are running.

3. Start the GeneMapper Software.

Setting Up the GeneMapper® Software

Autoanalysis 7

GeneMapper®

Software SecuritySettings

To autoanalyze data you need a GeneMapper Software user account to which the Scientist or higher security profile is assigned. Table 1 shows the minimum privilege requirements for a user account that allows autoanalysis:

Creating aNew User

Account forAutoanalysis

(Optional)

Use the following procedure if you want to create a separate user account specifically for performing autoanalysis,

To create a user for performing autoanalysis:

1. Start the Access Control Administration Software.

a. In the GeneMapper window, select Tools Security Manager.

b. In the AdminToolAcc dialog box, type a user name and password for a user account with administrative privileges, then click OK.

2. Select File New User.

3. In the Create User wizard, click Next.

4. In the Configure the New User page, type a name and description for the new user.

IMPORTANT! The user name cannot begin with a number (1, 2, 3, …) or contain symbols (&, $, #, …).

IMPORTANT! You cannot create a user account with the same name as a user account that has been deleted.

5. Specify the user details for the autoanalysis account:

a. For Full Name, type Autoanalysis.

b. Deselect Show EULA.

c. In the Status drop-down list, select Active.

Table 1 Minimum privileges for autoanalysis

Element Minimum privileges

All GeneMapper objects READ

GeneMapper project READ and UPDATE

GeneMapper study READ and UPDATE


8 User Bulletin

6. Select the control properties for the new user:

a. In the Profile drop-down list, select Scientist.

b. Use the default selection for Default Security Group and Control Security Group.

IMPORTANT! Do not set the Default Security Group to AdminSecurityGroup.

IMPORTANT! Do not modify the Control Security Group setting. The Control Security Group drop-down list assigns the security group data object you are editing to an existing security group. If you assign the data object to an unassociated security group, the group you are editing will be unavailable.

7. Set the password for the new user:

a. Click Set Password.

b. In the Change Password dialog box, type a temporary password in the Type and Retype fields.

c. Click OK.

Note: Because the password is configured to Pre-Expire by default, the password that you set in this step is temporary. When the user logs in for the first time, the software prompts the user to enter a password of his or her choice.

8. When you finish assigning rights to the user, click Next.

9. (Optional) Select the appropriate check boxes in the Associate column to associate the user account with the appropriate user groups, then click Next.

Note: The user account must be associated with at least one group that has write privileges to the security group assigned in step 6b.

10. Click Finish to complete the user setup.

11. Select File Save.

Setting Up a Shared Folder (Remote Autoanalysis Only)

Autoanalysis 9


IMPORTANT! If the Data Collection Software and GeneMapper Software are installed on the same computer, go to “Setting Up the Data Collection Software” on page 12.

Creating aShared Folder

Remote autoanalysis of data requires a shared folder on the remote analysis computer.

1. Select Start My Computer, then double-click the drive on which you want the shared folder.

2. Select File New Folder.

3. Name the folder (for example, Remote_Autoanalysis).

4. Right-click the new folder, then select Properties.

5. In the Sharing tab, select Share this folder.

6. (Optional) Type a comment for the folder.

7. Click OK.

6

5

7


10 User Bulletin

Setting SecurityPreferences for

the Shared Folder(Windows XP

Only)

If you are using a Microsoft® Windows® XP® operating system, modify the security preferences of the shared folder as follows:

1. Right-click the shared folder, then select Properties.

2. Select the Sharing tab, then click Permissions.

3. In the Permissions for <shared folder name> dialog box, select the check box for Full Control in the Allow column.

4. Click OK.

5. Select the Security tab, then click Add.

6. In the Select Users, Computers, or Groups dialog box, type Guest in the “Enter the object names to select” field.

7. Click OK.

3

4


Autoanalysis 11

8. In the Group or user names list box in the Security tab:

a. Select Guest.

b. Select the check box for Full Control in the Allow column.

c. Click OK.

The shared folder is now configured for use.

6

7

8a

8b

8c


12 User Bulletin

Setting Up the Data Collection SoftwareFor autoanalysis, the Data Collection Software must have a(n):

• Instrument protocol – Contains all the settings needed to run the instrument, including the protocol name, type of run, run module, and dye set.

• Results group – Defines the file type, file name, file save locations, user name and password, and specifies whether autoanalysis is performed on a run-by-run basis or after the Results Group is complete. The results group organizes samples and certain user settings under a single name. It is used to prepare samples for analysis and to name, sort, and deliver samples that result from a run

If the instrument protocols and results groups have already been created, go to “Creating a Plate Record” on page 26.

Setting Up the Data Collection Software

Autoanalysis 13

Creating Instrument Protocols

For more information about instrument protocols, see your instrument user guide.

You can either create a new instrument protocol or import an existing one.

Creating anInstrument

Protocol forAutoanalysis

1. In the Navigation pane of the Data Collection Software, select GA Instruments <Instrument Name> Protocol Manager.

Create instrumentprotocols here


14 User Bulletin

2. In the Instruments Protocols area, click New to open the Protocol Editor.

3. In the Protocol Editor:

a. Type a name for the protocol.

b. (Optional) Type a description for the protocol.

c. Select REGULAR in the Type drop-down list.

3a

3b

3c

3d

3e


Autoanalysis 15

d. Select the appropriate run module in the Run Module drop-down list.

e. Select the appropriate dye in the Dye Set drop-down list.

f. Click OK.

Instrument Run ModuleCapillary Length

(cm)

3730/3730xl GeneMapper36_POP7 36

GeneMapper50_POP7‡

‡ Available only with Data Collection Software v3.0.

50

HTSNP36_POP7_V3 (SNPlex™) 36

HTSNP50_POP7 (SNPlex)‡ 50

3130/3130xl FragmentAnalysis22_POP4_1 22

FragmentAnalysis36_POP4_1 36





HIDFragmentAnalysis36_POP4_1 36

SNP22_POP4_1 22

3100/ 3100-Avant

FragmentAnalysis22_POP4 22




HIDFragmentAnalysis36_POP4 36

SNP22_POP4 22

SNP36_POP4 36


16 User Bulletin

Importing anInstrument

Protocol

1. In the Navigation pane of the Data Collection Software, select GA Instruments <Instrument Name> Protocol Manager.

2. In the Protocol Manager, click Import in the Instrument Protocols area.

3. Navigate to the protocol you want to import.

Note: The import file type is .xml (extensible markup language).

4. Double-click the protocol to import it.

The imported files are displayed alphabetically in the Instrument Protocol area.


Autoanalysis 17

Creating Results Groups

For more information about results groups, see your instrument user guide.

IMPORTANT! You need to create new results groups after upgrading or reinstalling the GeneMapper Software.

Note: The maximum number of samples that the Data Collection Software can assign to a results group using the GeneMapper-Generic or GeneMapper-<computer name> analysis type is 7000 .fsa files. If you are analyzing more than 7000 sample files, create several results groups.

Creating aResults Group for

Autoanalysis

1. In the Navigation pane of the Data Collection Software, select GA Instruments Results Group.

2. Click New to open the Results Group Editor.

3. In the General tab:

a. Type the Results Group Name, which can be the GeneMapper Software project name. It must be unique (see page 22 for a list of accepted characters).

b. (Optional) Type the Results Group Owner, which can be used in naming and sorting sample files.

c. (Optional) Type a Results Group Comment.

3a3b3c


18 User Bulletin

4. In the Analysis tab:

a. Select GeneMapper-<computer name> for the Analysis Type.

Note: You cannot perform autoanalysis if you select GeneMapper-Generic.

b. Select Do Autoanalysis.

c. (Optional) Select the Results Group Entry Complete if you want autoanalysis to begin after all samples using the same results group have been run.

Note: If you want to manually begin analysis before all the samples from the results group are extracted, click the Analyze Now button.

d. Type the GeneMapper Software Login ID and password.

IMPORTANT! Autoanalysis requires the login ID and password of a user with a Scientist or higher security profile in the GeneMapper Software.

4a

4b4c

4d


Autoanalysis 19

5. Complete the Destination tab if you want to change the destination for the analyzed data or if you are performing remote autoanalysis.

a. Select Use Custom Location.

b. Modify the destination:• Local autoanalysis only – Click Browse, then select a

destination.• Remote autoanalysis only– Enter the destination, using

the format:\\<remote analysis computer name>\<shared folder name>

For example: \\MYPC\Remote_AutoAnalysis

c. For remote autoanalysis only: Establish a connection with the remote analysis computer by selecting Start button Run, entering the destination path as shown step b, then clicking OK.

d. Click Test to test the Location path name connection. If the test:• Passes – The message “Path Name test successful,”

displays.• Fails – The message “Could not make the connection.

Please check that the Path Name is correct,” displays. Click Browse, then select a different location.

5a

5c(For remote autoanalysis only)

5c

5b


20 User Bulletin

6. In the Naming tab, create unique sample file and run folder names. If you want to use a custom naming format, see “Customizing the Sample File and Run Folder Names in the Results Group Editor” on page 22.

The default formats for names are:• Sample files:

<App Prefix>_<Capillary Number>_<Well Position>.<ext>

For example: frag_008_A01.fsa• Run folders:

<Root Destination>\<instrument type>\<instrument name>\<Run Name>

For example: E:\AppliedBiosystems\udc\datacollection\Data\ga3730\ 3730xl-08\ Run_3730xl-08_2003-11-12_11-14_0012

Note: The Root Destination is specified in the Destination tab.

Note: Sample name, run folder name, and path name, combined, can total no more than 250 characters. See page 22 for a list of characters that cannot be used in file and folder names.

Sample file nameformat area

Run folder nameformat area


Autoanalysis 21

7. In the Automated Processing tab (available only if you selected GeneMapper-<computer name> in step 4 on page 18), specify when you want your samples autoanalyzed:

• Only when the result group is complete – If you want samples to be analyzed after all the samples that use the same results group have been processed.

Note: In the Analysis tab, select both Do Autoanalysis and Results Group Entry Complete.

• When every run completes – If you want samples to be analyzed after each run, regardless of the results group.

Note: In the Analysis tab, select only Do Autoanalysis. Do not select Results Group Entry Complete.

8. Click OK to save the Results Group.

Select an autoanalysis option


22 User Bulletin

Customizing theSample File and

Run FolderNames in the

Results GroupEditor

Unique Identifiers in the Sample File or Run Folder Name

Samples from a single run are placed in the same run or results folder, therefore each sample from a single run must have a unique name. Because most of the format components do not differ between samples, take care to select at least one of the format components that makes the sample names unique within a run.

If your custom format does not create unique sample file or run folder names, the Results Group Editor displays a warning message below the Example line (Figure 4).

Figure 4 Invalid name warning message

To remove the warning message and proceed within the Results Group Editor window, select a format component that distinguishes one file from another (for example, the capillary number is unique but the instrument name is not). If you do not correct the format, the software automatically appends numbers (incrementally) before the file extension.

Characters Not Allowed in Sample File or Run Folder Names

The following alphanumeric characters are not allowed in file or folder names:

spaces \ / : * ? " < > |

IMPORTANT! An error message is displayed if you use any of these characters. You must remove the invalid character to continue.


Autoanalysis 23

Customizing the Sample File Name

As you select the components for the file name, they are reflected in the Example line (Figure 5), up to 72 characters.

Figure 5 Sample File Name Format area

1. (Optional) In the Prefix field, type a prefix for the file name.

2. (Optional) In the Name Delimiter drop-down list, select a symbol that will separate the Format elements in the file name. The default symbol is an underscore (_).

Note: You can select only one delimiter symbol.

Example line


24 User Bulletin

3. Select a format component in the Format drop-down list.

Each time you select a format component, another drop-down list of components is added to the Format area.

As you add components to the sample file name format, the drop-down lists shrink until you can no longer read the component name.

To view the component names, place the cursor on the edge of the drop-down list until it turns into a double-arrow, then drag horizontally to expand the list.

Expand the list


Autoanalysis 25

4. (Optional) In the Suffix field, type a suffix for the file name.

The File Extension field displays the appropriate file extension for the Analysis Type specified in the Analysis tab (page 18). For example, fragment analysis produces sample files with an .fsa extension.

Customizing the Run Folder Name

Follow the same steps described in “Unique Identifiers in the Sample File or Run Folder Name” on page 22 to change the name of the sub-folder that is in the run folder.

Figure 6 Run Folder Name Format area


26 User Bulletin

Creating and Saving Plate RecordsEach run of samples must have an instrument protocol and a results group assigned within a plate record, which is created in the Data Collection software. Plate records are data tables in the instrument database that store information about the plates and the samples they contain, such as the instrument protocol, results group, analysis parameters, and study name (SNPlex™ only). For more information about plate records, see your instrument user guide.

IMPORTANT! You need to create new plate records after upgrading or reinstalling the GeneMapper Software.

Note: When you autoanalyze data, you cannot set a specific project type (for example, SNPlex or Microsatellite assay). The software automatically sets the project type to “Generic.”

Creating a PlateRecord

1. Click the Plate Manager icon in the Navigation pane of the Data Collection Software.

2. Click New to open the New Plate Dialog dialog box.

3. In the New Plate Dialog:

a. For 3730/3730xl instruments only: Type an ID (bar code) for the plate.

b. Type a name for the plate.

c. (Optional) Type a description for the plate.

d. Select GeneMapper-<computer name> in the Application drop-down list.

e. Select 96-well or 384-well in the Plate Type drop-down list.

f. For 3730/3730xl instruments only: • Define a scheduling pattern for a 384-well plate.• Select Heat Sealing or Septa in the Plate Sealing

drop-down list.

g. Type names for the owner and operator.

h. Click OK.

Creating and Saving Plate Records

Autoanalysis 27

4. In the Plate Editor:

IMPORTANT! You must create the size standards, panels, analysis methods, and SNP sets in the GeneMapper Software before creating a new plate.

Note: (Optional) For GeneMapper-Generic‡, manually enter the information for steps d through g in the text field.

a. Type the name of the sample.

b. (Optional) Type a comment about the sample.

c. Identify the sample as Sample, Positive Control, Allelic Ladder, or Negative Control.

d. Select a saved size standard from the drop-down list.

e. Select a saved panel from the drop-down list.

f. Select a saved analysis method from the drop-down list.

g. Select a saved SNP set from the drop-down list.

h. For SNPlex systems only – Type the name of the study. The software adds the runs to the study with the name you enter.

i. (Optional) Enter text in the user-defined text columns.

3b

3c

3e3d

3f (Unavailable on the 3130/3130xl, 3100 or 3100-Avant instruments)

3g

3h

3a (Unavailable on the 3130/3130xl, 3100 or 3100-Avant instruments)

‡ You cannot perform autoanalysis if you select GeneMapper-Generic as the application.


28 User Bulletin

j. Select a results group from the drop-down list.The drop-down list also provides the following options:• New – Opens the Results Group Editor dialog box. See

“Creating Results Groups” on page 17 for more information.

• Edit – Opens the Results Group Editor dialog box for the results group listed in the cell

• Duplicate

Note: You must have a results group selected for each sample entered in the Sample Name column.

k. Select an instrument protocol from the drop-down list.The drop-down list also provides the following options:• New – Opens the Protocol Editor dialog box. See

“Creating Instrument Protocols” on page 13 for more information.

• Edit – Opens the Protocol Editor dialog box for the instrument protocol listed in the cell.

• None – Sets the cell to have no selected protocol.

Note: You must have an instrument protocol selected for each sample entered in the Sample Name column.

4a 4b 4c 4d 4e 4f 4g 4h 4i 4j 4k

Starting the Autoanalysis Manager

Autoanalysis 29

Starting the Autoanalysis ManagerAutomatic analysis of data requires that:

• The Autoanalysis Manager and Data Collection Software are running

• The GeneMapper Software is closed• No applications other than the Autoanalysis Manager and Data

Collection Software are running• No other remote clients are connected to the GeneMapper

Software database if the GeneMapper Software is installed on the same computer as the Data Collection Software

• The 3730/3730xl, 3130/3130xl, or 3100/3100-Avant instrument is set up to run, and samples are prepared

• The files for a Data Collection Software plate record are available.

To start the Autoanalysis Manager:

1. Confirm that the GeneMapper Software is closed.

2. Select Start Applied Biosystems Autoanalysis Manager Autoanalysis Manager 3.0.

Figure 7 Autoanalysis Manager

IMPORTANT! The Autoanalysis Manager starts and closes the GeneMapper Software automatically, as necessary. Never manually start the GeneMapper Software or open a project while the Autoanalysis Manager is analyzing active jobs.


30 User Bulletin

Scheduling and Starting a RunFor instructions on scheduling and starting runs, see your instrument user guide.

IMPORTANT! Start the Autoanalysis Manager before scheduling and starting runs.

What Happens During AutoanalysisAutoanalysis occurs in the following sequence (Figure 8 on page 31):

1. When the Data Collection Software finishes a run, the data is stored in the destination specified by the results group

2. The Data Collection Message Service sends the message “Run Completed” to the Autoanalysis Manager. The Autoanalysis Manager receives the message, then adds the job to the job queue.

3. The Autoanalysis Manager polls for jobs every two minutes and opens the GeneMapper Software client to analyze the data stored by the Data Collection Software.

4. The GeneMapper Software client analyzes the data, then saves it to the default host.

Note: The default host is the GeneMapper Software server that is specified by the GeneMapper Software client. For instructions on changing the default host, see “Changing the Default Host” on page 31.

5. At the end of analysis, the Autoanalysis Manager closes the GeneMapper Software client, then updates the status in the job queue.

Note: To maintain sufficient storage space on your hard drive, move or archive the sample files created by the Data Collection Software that are no longer needed.

What Happens During Autoanalysis

Autoanalysis 31

Figure 8 Flow of data during autoanalysis

Changing theDefault Host

The default host is the GeneMapper Software server in which the analyzed data is stored. After installing the GeneMapper Software, the default host is:

• For full installations – The computer on which the GeneMapper Software is installed.

• For client-server installations – The computer specified during installation of the GeneMapper Software client.

Figure 9 Default host in full and client-server installations

Samplefiles

Folder Specified by

the results group


electrophoresisinstrument Analyzed

files

Data Collection Software

AutoanalysisManager

GeneMapper® Softwareanalysis application

(client)

Specified by the GeneMapper® Software client

Specified by the results group

GeneMapper® Softwaresoftware database

(server)

Runcompleted

Closes, thenupdates status

Opens

Computer

Full installation Client-server installation

GeneMapper® Software v4.0

Client(analysis application)

Server(software database)

Client computer


Client(analysis application)

Server computer


Server(software database)

Default host Default host


32 User Bulletin

To change the default host:

1. Open the Login to GeneMapper dialog box by starting the GeneMapper Software or, if you are already logged in, by selecting File Log Out.

2. In the Database Host drop-down list, select the GeneMapper Software database you want to set as the default.

If the host you want to use is not in the drop-down list:

a. Click New Host to open the New Host dialog box.

b. In the Host Name field, type the server name or IP address of the database host.

c. Select the appropriate machine type.

d. Click OK.

3. Click Default Host.

Autoanalysis Manager Functions

Autoanalysis 33


Components The Autoanalysis Manager has the following tabs:

• General• GeneMapper v4.0 • SeqScape x.x (if SeqScape is installed)

Note: The Autoanalysis Manager may show additional tabs, depending on the other software applications that are installed on the computer.

General Tab Use the General tab to view the jobs that have been submitted and their statuses. The following commands are available in the General tab:

• Delete Job – Deletes the selected job from the Autoanalysis Manager

• Delete Completed Jobs – Deletes all the completed jobs from the Autoanalysis Manager.

• Move Job Up – Moves a pending job higher in the queue• Move Job Down – Moves a pending job lower in the queue

Figure 10 Autoanalysis Manager General tab


34 User Bulletin

GeneMapper v4.0Tab

Use the GeneMapper v4.0 tab to view jobs, project, and status information.

Commands

The following commands are available in the GeneMapper v4.0 tab:

• Configure Schedule – Sets the schedule for when autoanalysis can run. Also sets schedule for auto delete.

• Edit Properties – Edits the user name and password (active only if analysis failed due to the wrong user name or password entered in the results group).

• Requeue – If a job fails, resubmits for analysis.• Delete Job – Deletes the selected job from the Autoanalysis

Manager• Delete Completed Jobs – Deletes all the completed jobs from

the Autoanalysis Manager.

Note: For optimal performance, delete the completed jobs from the Autoanalysis Manger every few weeks.

• Move Job Up – Moves a pending job higher in the queue• Move Job Down – Moves a pending job lower in the queue

Autoanalysis Manager GeneMapper v4.0 tab


Autoanalysis 35

GeneMapper Job Queue

The GeneMapper Job Queue area of the GeneMapper v4.0 tab shows the statuses of the jobs that have been submitted for autoanalysis. In addition to the job order, job/project name, and name of the person who scheduled the run, the GeneMapper Job Queue shows the date the job arrived in the queue (Arrival Date), the date the run was completed (Completed Date), and the status of the analysis.

If the status of the analysis is:

• Complete – Analysis completed successfully, without errors.• Failed – Analysis is incomplete (for example, user

name/password is incorrect), or analysis completed with errors.

The Status Message column provides additional information about the status of the analysis.

Figure 11 GeneMapper Job Queue

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For Research Use Only. Not for use in diagnostic procedures.

Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any errors that may appear in this document.

APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF.

Notice to Purchaser: License Disclaimer.

Purchase of this software product alone does not imply any license under any process, instrument or other apparatus, system, composition, reagent or kit rights under patent claims owned or otherwise controlled by Applera Corporation, either expressly, or by estoppel.

TRADEMARKS:

ABI PRISM, Applied Biosystems, AB (Design), and GeneMapper are registered trademarks, and Applera and SNPlex are trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries.

Microsoft, Windows, and XP are registered trademarks of Microsoft Corporation.

All other trademarks are the sole property of their respective owners.

01/2006

Part Number 4367795 Rev. AStock Number 133UB06-01

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