Frequently Asked Questions


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There are two types of license model for GeneSpring:
1) Desktop License
2) Enterprise/Workgroup License
 
Desktop License:
GeneSpring Desktop licenses can be divided into two categories :
a) Fixed / Standalone license
b) Floating / Concurrent license
 
Enterprise/Workgroup License:
Enterprise licenses can be divided into two categories :
i) Work Group Server (WG Server)
ii) Work Group Client (WG_Client)
GeneSpring Work Group Server/ Enterprise licenses are only available as fixed licenses.
 
GeneSpring Work Group Client can be further classified as:
a) Fixed / Standalone license
b) Floating / Concurrent license
 
Currently module specific licenses are available for GeneSpring (WG Client or Desktop Client) software. There are four modules in GeneSpring which can be obtained separately. They are GeneSpring GX (Gene Expression), GeneSpring MPP (Mass Profiler Professional), GeneSpring NGS (Next Generation Sequencing) and GeneSpring PA (Pathway Architect).

A GeneSpring fixed license is system specific. This type of license can only be activated on individual machines, and cannot be transferred to other machines without being surrendered on the previous machine first.

A floating license / concurrent license allows multiple users to share the use of an application. A single floating license can be used by a number of concurrent users. The Floating License Server holds the license and serves licenses to the users based on availability. The number of concurrent keys has to be specified at the time of purchase. This number determines the maximum number of GeneSpring applications that can be run simultaneously.
 
For example, if you have purchased a floating license with two concurrent keys, GeneSpring can be installed on multiple systems (more than two) but GeneSpring can only be used on two machines at a time.

A fixed license is specific for a single machine and can be accessed by a single user at any given time, whereas a floating/concurrent license can be used by multiple users at a time with the help of concurrent licenses (see Q3.).

If multiple users want to use GeneSpring with a single license, then your organisation can purchase a GeneSpring desktop floating/concurrent license. In this case, a single license with a number of concurrent keys specified by you will be issued. The number of concurrent keys determines how many users are able to use GeneSpring at the same time. This license needs to be activated through the Floating License Server application, which serves licenses to the client installations and controls the number of users that can use GeneSpring simultaneously, based on the number of concurrent keys that were purchased with the license.
 
To activate the GeneSpring client software, the user needs to provide the IP address of the machine where the Floating License Server has been installed. This will assign them one concurrent key from the number of concurrent keys available at the Floating License Server. If another user would like to start GeneSpring after all the concurrent keys have already been assigned, an existing user would have to shut down GeneSpring for the new user to be able to start GeneSpring.

Please visit the GeneSpring support portal at http://genespring-support.com.
 
Select the ‘Request Free Trial’ option and you will be asked to register to download the free trial if you have not registered already.
If you are already registered, please log into the portal to download the software and request the trial license following these instructions:

  1. Review the System Requirements.
  2. Download GeneSpring Software.
  3. Request 7 day trial License.

You will be asked to answer certain questions before we can provide a trial license. Submit the answers and you will be sent an email containing your trial license.

You can work with both GeneSpring GX 7.3 and GeneSpring 12.x simultaneously on the same computer if you have separate licenses for each version.

It is not possible to activate GeneSpring 12.x using a GeneSpring 7.3 license key. To activate GeneSpring 12.x you require a new valid 'Order ID'.

You cannot use one Order ID to activate two instances of GeneSpring.
 
To activate another instance of GeneSpring on a virtual machine which is on the same machine, using the same Order ID, you need to 'Surrender' the license/Order ID from the first instance. Then, use the same license to activate GeneSpring on the virtual machine (To surrender the Order ID: Go to Help -> License Manager -> Surrender).
 
When you want to switch back, you need to surrender the Order ID again.

GeneSpring Workgroup streamlines Multi-Omics data management at large and multi-campus organizations, providing server-side data analysis and secure archiving. It provides a secure repository for complete data analysis, which can be shared among users, whenever required.
 
When there is a large number of users and important data needs to be used in the analysis to-and-fro, it is recommended to use GeneSpring Workgroup, which allows server management capabilities to the users, through which data integrity can be maintained.

Both WorkGroup and Floating License Server are server-based applications but they work in different ways.
 
WorkGroup is used to keep all your data secure and can be shared among authorized WorkGroup users only.
 
The Floating License Server is used to share licenses for the GeneSpring client. The analysis done by multiple users cannot be shared, though it allows multiple users to share a single license with many concurrent keys at any given time. The Floating License Server can be used in conjunction with GeneSpring WorkGroup or GeneSpring Desktop versions, but WorkGroup is also a standalone application.

GeneSpring WG_Client Fixed license is used on a single machine at a time. It is machine specific and gets locked with the machine on which it is activated and cannot be transferred to another machine.
GeneSpring WG_Client Floating License on the other hand is not machine specific and can be used on multiple machines simultaneously by connecting to the Floating License Server to be served an available license. The number of available licenses depends on the number of concurrent keys purchased with the floating license.

No, the license for GeneSpring WorkGroup is different from the license for the Floating License Server.

No, it is not mandatory to use the Floating License Server with GeneSpring WorkGroup. The Floating License Server is used when there are many users of a GeneSpring client and most of them want to use the software at the same time.

The GeneSpring Floating License Server must be installed, activated, and started before the GeneSpring desktop can be used on any client machine.
The Floating License Server holds the license and serves available licenses to the users.
Please download a copy of the Floating License Server from: http://lcosgens.cos.agilent.com/gsLicense/gsFloatingServer.html
 
Installing the Floating License Server on Windows 2000, XP, or 2003 Server:

  1. Download the Floating License Server installable zip file for windows.
  2. Unzip and extract to any location of your choice.
  3. Open the document named FloatingServer.htm and follow the installation instructions for the Windows platform.

Installing the Floating License Server on Linux:

  1. Download the Floating License Server installable zip file for Linux.
  2. Create a user called array on the target machine.
  3. The Floating LIcense Server will run by the array user.
  4. Unzip and extract to any location where array has permissions.
  5. Note that it is not advisable to install and run the Floating License Server as root.
  6. Open the document named FloatingServer.htm and follow the installation instructions for the Linux platform.

Installing the Floating License Server on Mac OS:

  1. Download the Floating License Server installable zip file for Mac
  2. Unzip and extract to any location of your choice
  3. Open the document named FloatingServer.pdf and follow the installation instructions for Mac platform.

If you would like to change the machine on which the Floating License Server is run, delete the installation folder from the existing machine and install the Floating License Server on the new system as described in Q1. Once you have installed the Floating License Server on the new machine, please contact GeneSpring Support for license activation.

The Floating License Server holds the license and serves a license (concurrent key) to each user based on availability. However, GeneSpring can be installed on many more systems than there are concurrent keys associated with the floating license. GeneSpring can only be used simultaneously by as many users as there are concurrent keys.
 
The error 'No License Available' is shown, if an additional user beyond the number of available concurrent keys is trying to start GeneSpring. For that user to be able to launch GeneSpring, one of the existing users has to shut down GeneSpring, which will release a concurrent key that can then be assigned to the new user by the Floating License Server.

Yes, this feature is available in the GeneSpring Floating License Server for version 12.6. To use this feature, you need to have the following:

  • Floating License Server for version 12.6 installed.
  • GeneSpring 12.6 client.

 

You can block or allocate a specific set of licenses to specific users using the Group functionality available from the Group Manager in the Floating License Server.
 
By default, any user connecting to the Floating License Server has access to all the licensed modules. You may create a specific group to allocate only a specific set of licenses by creating a group, specifying the licenses and adding members (users) to the group.

Yes, this can be done by the Floating License Server administrator from Floating License Server -> Users -> Remove.

A client should do the following to access the new Floating License Server:

  1. Navigate to <GeneSpring Installation directory/bin/license> folder.
  2. Backup and delete all the files.
  3. Launch GeneSpring.
  4. Select Shared license in the License Activation Dialog.
  5. Enter <port>@<FloatingServer>,
    where <port> is the port on which the Floating License Server is running and <FloatingServer> is the host name or IP address of the machine where the Floating License Server has been installed (for example: 8080@192.168.1.25).

 

The current status of license usage can be monitored from the Users section of the Floating License Server.

Yes, to be able to add a new license, you have to stop the server. Please follow these steps to add a new license to the Floating License Server:

  1. Go to License > License Manager >Stop service.
  2. Go to License > Activate and enter the Order ID and proxy (if present).
  3. Click Activate.
  4. Go to License > License Manager > Start service.

The Floating License Server is now ready to serve licenses to clients according to the terms of the new license.

When the Floating License Server is stopped, a client immediately receives a corresponding message and the GeneSpring installation closes after 10 minutes. However,  if the Floating License Server is started again within 10 minutes, the client will attempt to connect  with the Floating License Server without closing the installation.

This error appears if you are using the same Order ID to activate GeneSpring on two different systems.
GeneSpring has the 'Surrender' feature which is useful to transfer the Order ID from one system to another. To surrender an Order ID follow the steps below:

  1. Click Help in the main menu.
  2. Select License Manager.
  3. Click Surrender.
  4. Click OK.

The 'License has been surrendered successfully' message comes up. Now the same Order ID can be used on another system.

Please try the following instructions:

  1. Go to GeneSpring installation directory\app\msvc_redist\
  2. Run the following executable vcredist_86.ext (for 32 bit) vcredist_64.ext (for 64 bit)
  3. Delete all files in this folder: \bin\license\
  4. Launch GeneSpring.

If you are still unable to launch GeneSpring, please send the following files to GeneSpring Support (informatics_support [at] agilent [dot] com):

  • Recent log files from the 'logs' folder of the installation directory.
  • The compressed (zipped) \bin\license folder.

These files will help us in identifying why the error has occurred.

You would encounter the Error 3007 due to an issue with the proxy or firewall settings of your system or if you are not connected to the internet.
 
In case the system is behind a proxy server, provide server details in the activation dialog box during activation. Check with your system administrator regarding your organisation's proxy settings.
 
Auto-activation is only possible when you are connected to Internet.
 
If the proxy or firewall settings are fine and your computer is connected to the internet but you are still unable to activate GeneSpring, then please follow the instructions below for Manual Activation:

  1. Please open the link below in a computer which is connected to the internet: http://lcosgens.cos.agilent.com/gsLicense/MultipleActivateNew.html
  2. Enter the Order ID/IDs and attach the manualActivation.txt file (this can be found under \bin\license folder of your GeneSpring installation directory) in the Activation File field.
  3. Click Submit. You will receive one or more .lic files by email.
  4. Copy these .lic files into the \bin\license folder.
  5. Launch GeneSpring.

GeneSpring should be activated now. Please contact GeneSpring Support if the issue persists or if you would like assistance with manual activation.

Error 4015 appears, if the Floating License Server has stopped or the connection between the server and the client is disrupted (LAN or internet). Please note that, each time you reboot the server machine the Floating License Server has to be re-started.
To get the current status of the server (if it is a Windows machine), please follow the steps below:

  1. Open a command prompt and cd to the directory where the Floating License Server is installed.
  2. Run the command ./lmstat -c bin/license/strand.lic -f marray/ genespring
    Please check (in the Task Manager) if the two processes 'lmgrd.exe' and 'strand.exe' are running on the server machine to confirm that the Floating License Server has been started.
  3. Once this is confirmed try to connect to the Floating License Server from the GeneSpring GX client.

The Floating License Server should be accessible through the network on the port used by FlexLM, which is between 27000 and 27010, by default.
If the server is installed on Linux or Mac, please refer to the Floating License Server administration details in the FloatingServer.pdf document in the Floating License Server installation directory.

Please find the file formats supported in GeneSpring application for different Gene expression analysis Experiment Types below:
Affymetrix Expression, Affymetrix Exon Expression, Affymetrix Splicing Experiment Type/Affymetrix copy Number, Affymetrix Association analysis- .CEL / .CHP file format
Illumina Single Color, Illumina Copy Number/Illumina Association Analysis Experiment Type - .txt file format
Agilent Single Color, Agilent Two Color and Agilent miRNA Experiment Type: .txt file format
Pathway Experiment - .txt, .tsv, .csv and .xls
RT-PCR Experiment Type - RQ 1.2, RQ 2.1, RQ 2.2 and RQ 2.3 formats of the ABI's 7900HT RT-PCR system
Generic Single Color and Generic Two Color Experiment Type: .txt, .tsv, .csv and .xls
Note: Here in generic experiment, the user has an option to select the Identifier and the Signal column based on preference, unlike the above mentioned Standard Experiment Types.

Affymetrix text and pivot files can be loaded in GeneSpring 12.x as standard data and is associated to the standard technologies.

A. GeneSpring supports Affymetrix CEL and CHP files as standard format.
The other file formats such as .txt, .xls, .tsv and .csv are not recognised a standard file formats from affymetrix, but can be imported into GeneSpring for analysis.
You could work with .xls file by ‘Creating a Custom Technology’. To create a custom technology, follow the steps below:
1. Go to Annotations in the Menu bar -> Create Technology -> Custom from File
2. After creating the custom technology, you could create the experiment under ‘Generic Single color’ Experiment Type.
For more details please refer Chapter 13 & 14 on ‘Analyzing Generic Single color/Two Color Expression Data’ from the GeneSpring Manual.

This error occurs when special characters appear anywhere within the file path of the input CEL files. The workaround to resolve this error is to place the CEL files in a directory that does not have any special characters in the file path.

It really depends on what kind of samples you are working with. Please find the benchmarking table for GeneSpring version in the table below:

Experiment Type No.of samples Memory used for experiment creation Run time memory Technology type
Agilent Single Color(Sample type-22K) 500 200M 300M 12097
Affymetrix Exon Splicing(RMA-Full) 50 583M 1009M HuEx-1_0-st-V2
Affymetrix Exon Splicing(PLIER-Full) 50 570M 1009M HuEx-1_0-st-V2
Affymetrix Exon Expression(RMA-Full) 50 187M 3589M HuEx-1_0-st-V2
Affymetrix Exon Expression(PLIER-Full) 50 187M 3589M HuEx-1_0-st-V2
Affymetrix Expression(RMA) 51 36M 64M HG_U95Aw2
Affymetrix Expression(PLIER) 52 34M 56M HG_U95Aw2

Note: Benchmarking for copy number and Association analysis are not included here.

You could get this error for the following reasons:
Reason1:
This error could occur while creating the experiment, if the ‘Experiment type’ chosen does not match the data files. Please select the right Experiment type and proceed with the analysis.
Reason 2:
This error could also occur in case you are trying to import the data in an un-supported file format.
For Example: GeneSpring only supports the data files generated by Feature Extractor (FE) version 8.5 and later version. In case the data files generated by earlier versions of FE are imported, this error may occur. In this case you would need to bring the data files as custom data.
To work with custom data, create a custom technology before you load the samples into GeneSpring.
To create custom technology go to -> GeneSpring menu bar -> Annotations ->Create Technology -> Custom from File. For more details on custom technology creation, please refer the chapter 13 and 14 from GeneSpring manual.

GeneSpring supports the Agilent single color miRNA data files from Feature Extraction software, version 8.5 or later version.
In case the user has files in any other format, a Custom technology and a Generic experiment could be created in GeneSpring to perform miRNA analysis.

Yes, There are few standard Agilent miRNA technologies available on GeneSpring update server. Please download the approprite technology from GeneSpring update server before you try to load the data for analysis.
Please contact us for any specific technology you are working with which is not available on update server.

In GeneSpring, the AMADID number field and the Grid_Date fields are considered as unique identifiers for miRNA arrays.
The Grid_Date field gives information on the version of the design file that was used to extract the data during sample creation. This means that even if the AMADID number is same for the same sample (for example: 19118), if they were created using a different design file, then they will not be taken together for experiment creation.
If the data set includes files from different Grid_Dates, you can create a custom technology to analyze them together.
For more details on Custom or generic Single Color/Two Color data analysis, refer to the Chapter 13 and 14 in GeneSpring manual.

To load Affymetrix miRNA data files in txt, csv and xls format, create a Custom Technology ( Annotations-> Create Technology ->Custom from File). Then, import the files under 'Generic Single Color' experiment type.
To perform the 'Target Scan analysis', select the option 'TargetScan' in the Results Interpretations from Workflow Browser.

In GeneSpring, Affymetrix and Illumina data files are supported as standard formats.
Data files in other formats can be converted to the Standard Illumina format and imported into GeneSpring to perform the CNV analysis.
The mandatory columns to be present in the data file to create the technology are dbSNPID, Chromosome Name, Chromosome Position, CNV regions in the same order.
From the data file, GeneSpring directly uses the following values for each sample.
log R - Provides the log (base 2) ratio of the normalized R value for the SNP divided by the expected normalized R value.
BAF (B allele Frequency) Copy Number values and their confidences Genotype of the subject SNP for the sample along with the score.

In GeneSpring, currently it is not possible to merge multiple experiments to create a single experiment.
Create another experiment using all these 150 samples from three different experiment by selecting the Choose Samples option in the data loading step.
Note: Once the data files are imported into GeneSpring GX to create an experiment, the data files are converted into samples and would be stored in the database. If the Choose files option is selected again, then the sample is created the second time which utilizes twice the space in the database.
Sample probe profile file in GeneSpring export format will be supported by GeneSpring.

The possible reason for "Error: -1" in copy number analysis could be the presence of "space" in the sample name.
Yes, it would affect the analysis. For example, running copy number analysis would not generate any output. Hence, please remove "space" from sample name for the successful experiment creation.

GeneSpring currently supports only RQ 1.2, RQ 2.1 , RQ 2.2 and RQ 2.3 formats of the ABIs 7900HT RT-PCR data as a Standard format.
However, to work with SuperArray qRT-PCR data, you need to create a custom single color technology using the path below:
GeneSpring GX Menu Bar → Annotations → Create Technology → Custom From File
You could then import the data by creating an experiment by selecting the Experiment Type as Generic Single Color. Please specify 'Detector' column from the file as the identifier column.

GeneSpring supports the creation of GPR technology ( Annotations → Create Technology → From .gpr file) only for the two color GPR data.
The two color .GPR file used to create the technology should contain the following columns - ID, F635 Median - B635, F532 Median - B532, and Flags.
In the absence of the above specified columns, the error would be seen.

Yes, .GPR files could be imported into GeneSpring.
Please find the details below:
Two color array:
A) Two color .GPR files from Agilent standard array could be imported by selecting the “Agilent two color” as the experiment type in the ‘New Experiment’ window for the standard workflow.
B) Two color .GPR files from custom array could be imported by following the steps below:

  1. Create GPR technology: The technology could be created using one of the files from, Annotations menu Create Technology From .gpr file Follow the wizard.
  2. After creating the technology, you would have to import all the files by creating an Experiment from the Project menu New Experiment Select Experiment Type as “ Generic Two Color”

Single color array:
To import single color .GPR files, please create a custom technology (Annotations  Create Technology custom from file) followed by experiment creation from the Project menu New Experiment Select Experiment Type as “ Generic Single Color”

Currently, the option to add samples to an existing experiment is unavailable. To add a new sample into an experiment, create a new experiment by including that sample with the rest of the samples.

Samples can only be deleted by deleting the experiments associated with them.
Experiments can be deleted using the path below: GeneSpring menu bar -> Search -> Experiments -> In the search wizard select the experiments to be deleted -> Select the ‘Delete’ icon Note: Once the sample is deleted from all the associated experiments, those experiments cannot be accessed.

After experiment creation, the sample information can be found in ‘Sample Inspector’.
Use right click on the sample name in ‘Experiment Navigator’ and select ‘Inspect Sample’ option to launch the inspector.
The Attributes, Parameters and Associated files information is shown in this window.

The Import NCBI GEO Experiment option is available only when an experiment is active under a Project. Open a Project followed by an Experiment in GeneSpring for the data import.

To transfer the data from one machine to another machine, export the data as Project zips from GeneSpring GX 10.x/11.x and import it into latest version of GeneSpring. This could be done from GeneSpring menu bar --> Project --> Export project zip/Import project.
Copying the data folder from one machine to another machine does not allow the data transfer.

GeneSpring supports the data files generated from BeadStudio in GeneSpring format to create standard Illumina single color experiment.
One could export the results from BeadStudio into a variety of formats compatible with other commercially available analysis tools.
To work with Illumina files in GeneSpring, export the files in GeneSpring format. This could be done from Analysis --> Report --> Custom Report --> GeneSpring format.

The error ""No such file or directory " would occur if the row header in the data file has "/".
Hence, please replace "/" with "_" or with any non-special character to import the data into GeneSpring.
This should help you to import the data into GeneSpring.

"The system cannot find the path specified " would occur if the row header in the data file has "\" .
Please replace "\" with "-" to load the data in GeneSpring and create an experiment.
With these changes Genespring would recognize the files and import it to create an experiment.

Following characters are considered as special characters in the tool: ! * # ; ? \ / : " < > |

The error could come up if the technology was earlier created on the fly due to loss of internet connections. This could result in difference in number of rows in the technology created on fly and the one present on the server.

Agilent single Color: Percentile Shift
Agilent Two Color: No Normalization in Genespring
Affymetrix Expression: RMA (Summarization method)
Affymetrix Exon Expression: RMA-16 (summarization method)
Illumina Single Color: Percentile Shift
Agilent miRNA: Percentile Shift

RMA is chosen as the default summarization in the guided work flow because it is more popularly used as the default option, by the micro array community.

RMA considers only Perfect Matches and hence uses positive signal intensities for probe level normalization.
By not considering mismatches it reduces the noise.

The 75th percentile is a more robust intensity value to normalize