Download RELEASE NOTES GeneMapper® Software 5

RELEASE NOTES
GeneMapper® Software 5
Fragment analysis sizing and genotyping software
Copyright 2012, Life Technologies Corporation and/or its affiliate(s).
All rights reserved.
June 2012
CONTENTS:
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Software Overview
Supported Data Files
Changes in GeneMapper® v5.0 as Compared to GeneMapper® v.4.1
Compatible Operating Systems and PC Requirements
Installing GeneMapper® v.5.0
General Tips and Recommendations
Known Issues and Limitations
SOFTWARE OVERVIEW
GeneMapper® Software 5 is an updated and improved version of a popular fragment analysis software
designed for ease of use, flexibility and quality allele calls when performing various types of genotyping
experiments. GeneMapper® Software 5 is designed to run on Microsoft Windows® 7 Professional (32-bit)
SP1 operating system. GeneMapper® Software 5 is offering flexible and user-friendly solutions for sizing,
peak analysis, and allele calls based on the input from the fragment analysis performed on Capillary
Electrophoresis (CE) instruments from Life Technologies. It includes major fragment analysis genotyping
workflows such as AFLP®, LOH, Microsatellite and SNapShot analysis.
SUPPORTED DATA FILES
GeneMapper® Software 5 is designed to import and analyze fragment analysis sample files (.fsa) from all
currently supported genetic analyzers including 3500 series.
GeneMapper® Software 5 fully supports data generated from the following Applied Biosystems
instruments:
- Applied Biosystems 3500 Genetic Analyzer
- Applied Biosystems 3500xl Genetic Analyzer
- Applied Biosystems 3130 Genetic Analyzer
- Applied Biosystems 3130xl Genetic Analyzer
- Applied Biosystems 3730 DNA Analyzer
- Applied Biosystems 3730xl DNA Analyzer
- 310 Genetic Analyzer
GeneMapper® Software 5 offers limited support for data generated on 3100 and 3700 instruments.
CHANGES IN GENEMAPPER® v.5.0 AS COMPARED TO GENEMAPPER® v.4.1
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GeneMapper® Software 5 supports Microsoft Windows® 7 Professional (32-bit) SP1 operating
system.
GeneMapper® Software 5 relies on Oracle 11g R2 database to store all project-related data. In
addition to serving as a common data repository, the database provides user authentication,
robust and scalable data management, and flexible archiving capabilities through the utilities
provided with GeneMapper® software.
GeneMapper® Software 5 incorporates Oracle Password 180-days expiration patch. The user no
longer needs to apply a separate patch, to ensure that Oracle database password is set for a
period longer than 180 days.
GeneMapper® Software 5 incorporates Hotfix 2 patch. The user no longer needs to ensure that
computer has MAC (Media Access Control) address starting with the “00” hexcode. There is no
longer a need to apply a special patch if the MAC address starts with hexcode other than “00”.
GeneMapper® Installation and Administration Guide was substantially revised and updated for
GeneMapper® Software 5.
GeneMapper® Software 5 no longer supports Auto-analysis functionality.
GeneMapper® Software 5 no longer has a separate Server configuration. Use the Full version
instead.
COMPATIBLE OPERATING SYSTEMS AND PC REQUIREMENTS
1. Recommended configuration
The software can be installed, launched and run on a computer with the following specification:
 The software shall be supported on Dell OptiPlex XE Windows® 7 SP1 professional 32-bit
operating system.
 CPU: Core 2 Duo E8400/3.0GHz
 Memory: 4GB
 Disk: Free space: 500MB on the boot drive, 7 GB on the drive on which the GeneMapper®
Software 5 is installed
2. Minimum configuration
The software can be installed, launched and run as a standalone on a computer with the following
specification: Windows® 7 Professional SP1, 32-bit
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CPU: 2GHz or faster Intel processor
Memory: 2GB
Disk: Free space: 500MB on the boot drive, 7 GB on the drive on which the full version of
GeneMapper® Software 5 is installed (if only GeneMapper Client Software 5 is installed, 1
GB of free space on that drive is sufficient).
3. Display Requirements
 User can view all UI elements of the application on the screen without having to scroll
vertically if the software is run on a monitor with minimum 1280x1024 pixel resolution for full
screen display.
 User should use Windows® 7 default theme
NOTE: This software has been extensively tested on Windows® 7 SP1 (32-bit) version. While there are
some indications that software will run normally on the 64-bit version of Windows® 7 SP1 operating
system, the 64-bit configuration is not officially supported. It is strongly recommended that this software is
run on Windows® 7 SP1 (32-bit).
INSTALLING GENEMAPPER® v.5.0
1. The TCP/IP protocol must be installed and configured on the computer prior to installation of
GeneMapper® Software 5.
2. The user must have administrator privileges to install this application.
a) Insert the installation CD or access installation directory from Windows Explorer. Follow the
install wizard steps during the installation. If the launcher does not start automatically,
manually click setup.exe from Windows Explorer.
b) Once installation is completed, go to the Start menu. From the Start menu, go to All
Programs > Applied Biosystems > GeneMapper 5 folder and click on the GeneMapper 5
shortcut to start GeneMapper® Software 5.
3. The Oracle® database version in GeneMapper® Software 5 is an embedded license database. This
license allows for 5 "named users" to access the database at any time. To accommodate for more
than 5 "named users", customers should either purchase additional GeneMapper® software licenses
or purchase additional Oracle "named user" privileges.
4. For uninstalling GeneMapper® Software 5, the user must have administrator privileges.
5. If co-installing GeneMapper® Software 5 with 3x30 Data Collection (UDC) or 3500 Data Collection
(MDC), make sure that Data Collecton version is compatible with Windows® 7 (32-bit) SP1.
Specifically, GeneMapper® Software 5 can be co-installed only with the following versions of Data
Collection software:
 3130xl UDC v4.0
 3730/3730xl UDC v4.0
 3500 MDC v.2.0
GENERAL TIPS & RECOMMENDATIONS
1. For a typical multi-user client-server environment, the GeneMapper® Software 5 has been tested with
5 concurrent users only.
2. For optimal performance, copy sample files stored on a network drive to the local drive before using
them in the software.
3. It is strongly recommended that the installation of GeneMapper® Software occur on drive with a
sufficient free disk space.
4. When entering text into text boxes or tables in GeneMapper software, avoid using non-standard
ASCII characters including the following characters: / \ : * ? " ' < > | & #
5. When naming a sample file in Data Collection or another application, avoid using non-standard ASCII
characters and accents including the following characters: / \ : * ? " ' < > | & #
KNOWN ISSUES AND LIMITATIONS
1. Make sure a printer is turned on and is available (i.e. it is set to Online) before using the print
command.
2. Using the Ctrl+C keyboard command to copy Cluster Plot Tables and SNP Tables may result in
inconsistent copy results. Use the Copy menu command instead.
3. For the SNPlexTM analysis method SNPlex_Model_373O some of the default settings are not
optimal and will allow low quality SNPs to pass. The setting for SNP Quality Pass range
(GeneMapper Manager, open SNPlex_Model__3730, select the Quality Flags tab) should be set to
0.95. SNP Quality Low Quality Pass range should be set to 0.80.
4. When importing settings created in previous GeneMapper® software versions, please check that all
values are set as expected.
5. When auto-panelizing SNaPshot® Kit samples, the affected project(s) will not be marked as ready for
analysis. Use Analyze All from the Analysis menu to reanalyze samples.
6. If the memory is insufficient, user may encounter the “Could not create the Java virtual machine" error
message when they try to launch GeneMapper® via command line. The same might happen at the
end of the installation. See above Recommended specifications for computer running GeneMapper®.
7. On rare occasions, the GeneMapper® server-side module can be disconnected when the Oracle
server is down. When this occurs, if user tries to perform any task on the client application it will
cause a series of "failed to save to database" messages.
8. Upon installation and first launch of GeneMapper® software, the EULA will appear twice.
9. In some cases, firewall settings on the computer where GeneMapper® database is installed might
prevent GeneMapper® software client applications from connecting to the database. Check with your
IT department regarding creating access to that computer for GeneMapper® clients.
10. In the scenario of migrating data, in Software Extras > GeneMapper® Utility Wizard, the window that
indicates a completion of the data export, incorrectly displays version 4.1 instead of version 5.
11. Security/Access Control, Auditing & Electronic Signature:
 To apply changes made in the Security Manager, it is recommended that all clients log off
from the database first.
 lf a Study is renamed and assigned to a different security group, projects associated with that
Study remain assigned to their previous security group.
 The Electronic Signature challenge may not be presented if a Study is modified but not saved
before opening another Study. Be sure to save the modified Study first.
 Concurrent users may be able to modify the Audit Map settings in the Audit Manager at the
same time.
 If a GeneMapper® software client terminates unexpectedly (e. g. due to network or power
failure) the client’s lock will not be released from the GeneMapper® Server Database. In this
situation, the server and all clients should be immediately rebooted, otherwise client/server
functionality could potentially be compromised.
12. Plot View
 It is recommended that the plot window be closed before making changes to the universal
marker in Panel Manager.
 In the Plot View, it is recommended to use integer values when specifying Zoom to Marker
Ranges.
 ln the Samples plot, if user zooms into a specific location in the electropherogram, zooms out
to full view, then selects Show/Hide Dye icon, it will cause the electropherogram to zoom
back in.
 In the Cluster Plot, if file name already exists, user will not be prompted to Save As JPEG,
the existing file will be automatically overwritten.
 In the Cluster Plot, SNP selection will always return to the 1st row when user tries to enable
the overlay function in Cluster Plots Manager.
13. Panel Manager
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When markers are copied or moved from one panel to another, the associated reference
alleles are also carried along with the markers. It is recommended that these reference
alleles be deleted.
 While editing data in the kit tables, users may have to press the tab key more than once to
move to the next field.
14. Study Manager
 An Internal error message may be displayed when viewing cluster plots by selecting
individual samples in the Replicate Test Details view. It is recommended that users select 4
the SNP instead to view the cluster plot.
 Make sure all open windows are closed when installing or uninstalling the QC plugins in the
Study Manager.
 If re-extraction from 3x30 Data Collection (also known as Unified Data Collection or UDC) to
a study is needed, it is recommended that previous samples be removed from the Study first.
 If a project is opened from within the Study Manager, study menus will be locked until the
project is closed.
 In some circumstances an internal error will be generated when viewing cluster plots from
replicates. It is recommended that viewing be done on an individual level.
 If a sample is rejected (WQ fails), then HW in secondary QC will fail as well.
 Number of samples in a study is updated only when the study is opened.
15. Database Dashboard Utility:
 The software will not identify any 3x30 Data Collection (UDC) connections to the database.
 Client connection information can be accessed from the Dashboard tab – client connections
section. Only GeneMapper® connections to the database will be identified.
 In order to successfully import the database, the target computer must have the same folder
structure as the computer from which the database was exported.
 The folder structure refers to the location of .DBF files, for which the default is
<DRIVE>:\OracleGM\oradata\IFA and also
<DRIVE>:\AppliedBiosystems\Database\IFA (if extra allocation was carried out
during the install).
 The software will check the folder structure on the target computer before importing and will
report any errors in the log. The import button will only be enabled if there are no errors.
 Database Dashboard v2.0 will display an SQL error if the user tries to allocate more space
than is physically available on the drive. Once this error is dismissed users can then try to
allocate space again.
 lf the user tries to connect to a computer that does not exist on the network, the application
will display a SQL error and not launch. Before restarting the application, the user will have to
use Windows Task Manager to stop the application.
 Database Dashboard v2.0 will not allow the user to export the database if there are any Data
Collection software connections to the GeneMapper® software database. The utility will
display a message asking all client connections to log off. However, the software will not
identify any of the Data Collection connections to the database in the client connections
section.
 For Project Data, the software will not allow the user to allocate less than 2.5GB (2560 MB) of
space. If a lesser value is specified, the software will still allocate 2560 MB which is the
default value shown in the message dialog.
 Database Dashboard v2.0 does not display a progress bar when allocating additionalspace in
the custom allocation tab.
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While maintenance activities, such as space allocation, import/export, etc. are being
performed on the database using Database Dashboard v2.0, GeneMapper® software client
applications should be disconnected from the database. GeneMapper® software clients do
not have the ability to detect if maintenance activities are being performed.
The GeneMapper® application will show a warning message once the disk space allocation
for Oracle® database is 70% full. When this happens the GeneMapper® software will report
that the disk space allocation for Oracle database is 70% full even if some of the projects are
deleted. This is an Oracle Database issue. Deleting project would not release disk space at
all. User need execute the batch script ifa_shrink_tablespace.bat to release disk
space. The ifa_shrink_tablespace.bat is located at
<DRlVE>:\AppliedBiosystems\GeneMapper\Database\Admin folder.
Import operation from Dashboard when GeneMapper® Software 5 is co-installed with 3130xl
UDC v4.0 or 3730/3730xl UDC v4.0 might fail, with the import log file displaying message
"enter login ID and Password" and not able to proceed further. It is recommended that for
GeneMapper® co-installed with UDC v.4.0, Export/Import of data was performed via manual
exporting and importing groups of objects (Projects, Libraries, etc). For more detail, see
GeneMapper® Installation and Administration Guide.
LEGAL DISCLAIMER AND TERMS AND CONDITIONS OF CUSTOMER
INSTALLATIONS OR USE
LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) MAKE NO REPRESENTATIONS
REGARDING GENEMAPPER® SOFTWARE 5 USE OR PERFORMANCE AND ACCEPTS NO
LIABILITY AS A RESULT OF THE INSTALLATION OR USE OF GENEMAPPER® SOFTWARE 5.
GENEMAPPER® SOFTWARE 5 IS PROVIDED "AS IS" AND "WITH ALL FAULTS". LIFE
TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES
RELATING TO GENEMAPPER® SOFTWARE 5, EXPRESS OR IMPLIED, INCLUDING THE
WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NONINFRINGEMENT.
IN NO EVENT SHALL LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) OR ITS
SUPPLIERS BE RESPONSIBLE OR LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR
UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR
COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR
SPECIAL, INDIRECT, INCIDENTAL, MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES
ARISING OUT OF THE POSSESSION OR USE OF, OR THE INABILITY TO USE, GENEMAPPER®
SOFTWARE 5 RELEASE OR DOCUMENTATION, EVEN IF LIFE TECHNOLOGIES CORPORATION
AND/OR ITS AFFILIATE(S) IS ADVISED IN ADVANCE OF THE POSSIBILITY OF SUCH DAMAGES,
INCLUDING WITHOUT LIMITATION DAMAGES ARISING FROM OR RELATED TO LOSS OF USE,
LOSS OF DATA, DOWNTIME, OR FOR LOSS OF REVENUE, PROFITS, GOODWILL OR BUSINESS
OR OTHER FINANCIAL LOSS. IN ANY CASE, THE ENTIRE LIABILITY OF LIFE TECHNOLOGIES
CORPORATION AND/OR ITS AFFILIATE(S)’ AND ITS SUPPLIERS UNDER THIS LICENSE, OR
ARISING OUT OF THE USE OF GENEMAPPER® SOFTWARE 5 RELEASE, SHALL NOT EXCEED IN
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JURISDICTION.
For Research Use Only. Not intended for animal or human therapeutic or diagnostic use.
Information in this document is subject to change without notice.
Life Technologies Corporation and/or its affiliate(s) assumes no responsibility for any errors that may
appear in this document.
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
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