Cystic Fibrosis Foundation Therapeutics, Inc. (CFFTI) National Bioinformatics Center At UNC-CH

Frequently Asked Questions

1. How to install GeneSpring on your local computer?
2. How to set up GeneSpring license key through CFFT license server?
3. How many people can use GeneSpring simultaneously through CFFT?
4. What to do when I have trouble running GeneSpring through CFFT?
5. How to install Pseudomonas Genome in GeneSpring?
6. How to add new annotations for the Pseudomonas Genome?
7. Where to find GeneSpring tutorial?
8. How to upgrade your copy of GeneSpring to the latest version?
9. What is GeNet for CFFT at UNC-CH?
10. How do I create a GeNet account?
11. How do I begin using GeNet?
12. How do I upload data into my own directory on GeNet?
13. How do I upload data to GeNet for sharing?
14. How do I change my GeNet default login password?
15. Who do I contact for help?
16. How do I join the CFFT-Investigators mailing list?
17. What is the system requirement for my local machine in order to run GeneSpring?

1. How to install GeneSpring on your local computer?

GeneSpring is supported on multiple platforms with versions available for Windows, Mac OS 9.2, Mac OS X. We are currently NOT supporting the newest version of GeneSpring v.9.0. To install GeneSpring (v.7.3.1) on your local machine, please email your request to cfgenomics@unc.edu. The installer for GeneSpring 7.3.1 is no longer available from Agilent.

Note: You have to be an approved investigator (or a member of lab of an approved investigator) participating in the CFFT microarray grant program to request access to GeneSpring.

2. How to set up GeneSpring license key through CFFT license server?

      In order to run GeneSpring through CFFT, you need to set up GeneSpring license key and genome preference on GeneSpring. If you are already using GeneSpring via a static license or a network license available through your institution, DO NOT install these files.

      Please contact CFFT bioinformatics support to obtain the necessary License file.

      Secondly, locate the GeneSpring data folder on your local machine. In case of a PC, this folder is normally located at C:\Program Files --> Agilent --> GeneSpring GX --> Data. With Mac OSX/Linux, this folder is located in following folder hierarchy [Home Directory of user]/Agilent/GeneSpring/data.

      Thirdly, rename the two files “GeneSpring Preferences” and “LicenseKey” that are already present in that folder to something like “GeneSpring Preferences_bak” and “LicenseKey_bak”. Now copy the two files that were emailed to you by CFFT informatics support into the “GeneSpring Data” directory.

      Finally, start GeneSpring and chances are, you may see a small window that says “trying to contact concurrent licenser server”. If this window disappears after a few seconds, then you have successfully connected to CFFT GeneSpring license key server. Go ahead and start using GeneSpring. It this window stays there, you need to reset your GeneSpring preferences. In order to do this, go to the main program window. Click on Edit --> Preferences to bring up the preferences dialog box. Click on the “system” tab and make sure that the license server name says “cfgenet.unc.edu” (without the quotes). If there is a generic entry like “mymachine.mycompany.com” in that field, replace it with cfgenet.unc.edu. Remember to click “Apply” followed by “Ok”. Restart GeneSpring. It should work properly.

      Here is a Word document with the above information in screenshots. Please contact CFFT bioinformatics support if you run into any problems.

3. How many people can use GeneSpring through CFFT simultaneously?

GeneSpring comes with a “demonstration” license that will let you use the program without any restriction for 15 days from the date of installation. You will need to follow the directions in the FAQ section “How to set up GeneSpring license key” before the end of the 15 day trial period to set your copy of GeneSpring to use the GeneSpring license server for the CFFT located at UNC-CH.

We have a “4-user concurrent license” for GeneSpring. This means that any four CFFT approved users can use GeneSpring at any given time. As a result, be sure to close the program when you are done with your analysis session. Leaving the program open will prevent the next user from accessing GeneSpring if all licenses are in use.

4. What to do when I have trouble running GeneSpring through CFFT?

If you have just installed GeneSpring and can not run it through CFFT license server, please contact cfgenomics@unc.edu for assistance to make sure that GeneSpring has been installed correctly and you have set up the license key correctly. If you have been able to run GeneSpring before and currently get a message (with repeated tries) that a GeneSpring license if not available, please contact cfgenomics@unc.edu to make sure that the license server is running properly and we have not reached the limit of seats for our concurrent GeneSpring license.

5. How to install Pseudomonas/BCC Genome in GeneSpring?

In GeneSpring, the term “genome” is used to refer to information about all the genes in a particular chip or microarray setup. Please note that a GeneSpring genome does not correspond exactly to the biological definition of a genome. However, full genomic sequence of the Pseudomonas aeruginosa is available as one of the annotation features for the Pseudomonas genome in GeneSpring.

Contact CFFT informatics support to obtain the correct genome file (P. aeruginosa "genome" --> “Pae_G1a_cf .zip” or B. cenocepacia "genome" --> "BCC_CF.zip").

Use the "File" --> "Genome Manager" to open the GeneSpring Genome Manager. Click on the "Import zip" command to import the genome into GeneSpring.

If things have worked correctly, next time you start GeneSpring, depending on your preference setting, you would either get the option of being able to select the Pseudomonas genome as GeneSpring starts up or you should be able to select it from the “File --> Open Genome or Array” menu. After you select “Pae_G1a_cf/BCC_CF”, this array will open in a new GeneSpring window.

6. How to add new annotations for the Pseudomonas Genome?

Extra gene annotations (ID, Homology, Pathway, Biofunction, Medline and Rating) are available for the Pseudomonas GeneChips. There are two ways in which you can obtain the revised annotation:

1. To download the revised annotation file to your local machine, please follow this link http://cfgenomics.unc.edu/annotations.txt. Right click the link or copy the link to a web browser and choose File --> Save As --> to download and save the "annotations.txt" file onto your local computer. Close GeneSpring, if it is open. To upgrade the Pseudomonas genome annotation in your local copy of GeneSpring, you need to put this file in the correct location in GeneSpring "data" folder. On my computer (PC), the annotations.txt file is located in C:\ProgramFiles\Agilent\GeneSpring\data\Demo Chips\Pae_G1a_cf. Depending on your GeneSpring installation, this file may be in a different location. Rename the original "annotations.txt" file to something else like "annotations.txt.bak". Copy the new "annotations.txt" file into this directory.

To access the annotations from Pseudomonas.com in GeneSpring: within GeneSpring, in the "annotation" drop-down menu choose "make gene list from properties" and then use the drop-down menu "make from property" to scroll towards the end of the list. Annotations from "pseudomonas.com" site are labeled with Hemant's name e.g. "Biofunction_Hemant". Once you select a category (e.g. "Biofunction_Hemant") and click the "ok" button, a new gene list corresponding to that property will be made in the "Gene Lists" folder hierarchy in the GeneSpring left-hand pane.

You can then use these folders in many ways. e.g. for venn diagrams or for "color by" etc. Highlight and right click on the folder names to choose these display options.

2. If you have a GeNet account: after logging-in to GeNet, choose file --> open genome/array --> Pae_G1a_cf. If you had saved a local copy of this "GeNet" genome then GeneSpring will prompt you to update the local copy.

Choose "yes" to update the genome. Additional annotations from Pseudomonas.com should now become accessible as described above.

7. Where to find GeneSpring tutorial?

Agilent has created a series of animated step-by-step tutorials that cover some of the main functions in GeneSpring. If you are a new GeneSpring user, these tutorials may be very useful to get you started.

Coming soon, we will have an animated tutorial specifically designed for the Pseudomonas genome.

8. How to upgrade your copy of GeneSpring to the latest version?

You can upgrade GeneSpring to the latest version by selecting the “Upgrade” option under the “Help” drop-down menu as well. Choosing this option will bring up the “Upgrade license dialog box”. Check the “I agree” box and then choose the “Update program” button.

For a quick tutorial with screenshots on how to upgrade your local GeneSpring on a PC, please click here. For a Mac version tutorial with screenshots, please click here.

Note: Please do NOT install GeneSpring v.9.0. We are currently NOT supporting this version.

9. What is GeNet for CFFT at UNC-CH?

      GeNet is an Oracle based relational database that is used for storing/sharing microarray data on servers at UNC-Chapel Hill.

      More information about GeNet is available here.

      If you are an approved investigator in the CFFT-affymetrix Pseudomonas aeruginosa GeneChip Genome grant project, you can request for a free GeNet account (see Q10).

10. How do I create a GeNet account?

      If you are an approved investigator in the CFFT-Affymetrix Pseudomonas aeruginosa GeneChip Genome grant project, you can request a free GeNet account or GeNet installation at UNC-Chapel Hill.

      Please email to cfgenomics@unc.edu with the following information. All the members of the research group should send in individual requests to obtain accounts.
a. Name
b. Affiliation
c. Office Address
d. Telephone/Fax Numbers
e. Email address
f. Principal investigator's name
g. Preferred user name (on a first come basis, if available). (We can use your unity login names).
h. Alternate use name (in case preferred user name is not available).
i. A secret question and answer combination of your preference. (e.g. Place of Birth?). This combination will be required if the user needs to have his/her password reset by the administrators.
j. Please specify what operating system you are using (e.g. PC, Mac OS 9/X).

      You will be notified by email when your GeNet account has been created.

11. How do I begin using GeNet?

You can access GeNet through GeneSpring or through the internet.

      To access GeNet through GeneSpring, you need to have GeneSpring v.7.3 or newer installed in order to be able to connect to the CFFT-GeNet server at UNC. Please make sure that an entry for CFFT-GeNet server “cfgenet.unc.edu” exists in your GeneSpring preferences. If you haven’t done so, start GeneSpring, go to Edit --> Preferences, you will see the GeneSpring Preferences page. Click on the “GeNet” tab at the top of the page and click the “New” button in the middle of the page. You will now see a resulting page “New GeNet Server” pops open. Please fill in the following information:

GeNet Server Name: CFFT-GeNet
GeNet Server Address: cfgenet.unc.edu

      Leave everything else as default. Press “Ok” to accept changes. Be sure to “Apply” the changes before clicking “Ok” to close the preferences dialog.

      Now you can choose to log in to GeNet server by choosing “File”--> “Login to GeNet” through GeneSpring application. This should bring up the dialog page for the “GeNet Server” login. Use your account name and the password provided (see Q10).

      Once you log in to GeNet, you should be able to see an additional folder show up in the left hand pane which will be labeled “CFFT-GeNet” provided that is the name you had used for identifying the CFFT-GeNet server when you entered the server preferences.

      For a tutorial with screenshots on this issue, please click here for a PC version and here for the Mac version.

      To access GeNet through the internet, go to http://cfgenet.unc.edu, login with your GeNet user name and password. This login and password should not be shared with others in your research group. For a tutorial with screenshots on how to access GeNet through the web, click here.

12. How do I upload data into my own directory on GeNet?

You can upload data to you own directory on GeNet. You have full privileges to your own workspace. Uploading data onto shared folder on GeNet can only be done by administrators. The folder containing the shared data has "read-only" privileges for everyone else.

To upload data onto your own workplace, the data file should be named in the following format: “[what_ever_name_you_want]_PivotData.txt” for the PivotData data files. Once you have imported data to your local GeneSpring and generated folders for Experiments, Gene Lists, Pathway…, simply right click on the folder that you want to upload and select “upload to Genet”. A new window will pop out for GeNet login. Enter your GeNet username and password. If login is successful, an “Upload to GeNet” window will appear. The default destination directory should be your workspace. Click on the “start” button to upload your data. If uploading is successful, you should see “Upload complete (1 item(s) uploaded) in the window. Click the “close” button to end this transaction. All folders on GeNet have “CFFT-GeNet” label on them under each category (Gene List, Experiments, Gene Trees…). You should be able to see your uploaded data in the corresponding folders.

13. How do I upload data to GeNet for sharing?

      To upload data to the shared data directory, please send a data CD including a copy of the word document describing your experiment together with the EXP and corresponding DAT files.

      GeNet administrators will process the files with Microarray Suite Software(MAS) (ensuring that all the shared data is processed identically) and then load the data into GeNet shared workspace.

      Here is a word document that covers all the required information in order to submit your Affymetrix array data. You can right click on the link to download the word file and simply fill in the blanks.

14. How do I change my GeNet default login password?

After you log in to GeNet, choose Pae_G1a_cf genome. Then click the “Utilities” button on the top menu bar. Then click on “personal profile” and in that page, you will have the option to reset your password. Once you changed your password, it should be effective immediately.

For a quick tutorial with screenshot on how to change your login password on GeNet, please click here.

15. Who do I contact for help?

Hemant Kelkar, Ph.D.
Center for BioInformatics
University of North Carolina at Chapel Hill
CB #7104, Rm. 3130, Bioinformatics Bldg.
130 Mason Farm Road
Chapel Hill, NC 27599-7104

Tel : 919-843-5933
Fax : 919-843-3103
Email : cfgenomics@unc.edu

Other Contact Information

16. How do I join the CFFT-GeneSpring/GeNet mailing list?

You are automatically added to the listserv email system when you obtain GeneSpring or your GeNet account is created. The email is: cfgenet@listserv.unc.edu.

17. What is the system requirement for my local machine in order to run GeneSpring?

Windows:
Windows 98/NT/2000/XP
Pentium III or better
256MB RAM (512MB recommended)
1024x768 display
250 MB of free disk space

Macintosh:
MacOS 9.1/9.2 or MacOS X 10.2.1 or higher
MRJ 2.2.5 (OS 9 only)
256MB RAM
1024x768 display
250 MB of free disk space