Accessing GeneSpring on the Linux Cluster

The following instructions are for users who would like to use GeneSpring on the Linux cluster. If you need technical assistance with GeneSpring on the cluster, please contact the BMI Help Desk.

Starting GeneSpring

To run GeneSpring, a graphical application, you must use X11. Other "terminal" programs do not forward the X session correctly. Here's how to access this installation:

Log on to bmiclusterp.chmcres.cchmc.org, the DMZ cluster login node (if you're using a Mac, substitute -Y for the -X):

ssh -X bmiclusterp.chmcres.cchmc.org

Now to start up an interactive GeneSpring job, just type the following in a terminal:

GeneSpring

Downloading a working genome (required for first-time users)

If starting GeneSpring for the first time, you will need to download a working genome.

From the menu at the top of the screen, choose Edit, then Preferences, and select the Workgroup tab. Click New, and enter the following:

Workgroup Server Name: Signet

Workgroup Server Address: 205.142.199.139:1104
Default Username: The username you use to access Signet
Select "Different sides" and "No" for the options at bottom and click "OK"

Workgroup Server Name: Architect
Workgroup Server Address: 205.142.199.178:80
Default Username: The username you use to access Architect
Select "Different sides" and "No" for the options at bottom and click "OK"

From the menu at the top of the screen, choose File, then Login to Workgroup Server to log in to Signet.

From the menu at the top of the screen, choose File, then Genome Manager.

Expand the folder Signet, select the genome you want,and click Copy from Workgroup Server.

Need Help?

For technical assistance with other research software, email software@bmi.cchmc.org. For basic desktop support or assistance with clinical information systems, call the Cincinnati Children's Service Desk, 513-636-4100, or visit the Information Services CenterLink site. UC employees should call the UCit Help Desk, 513-556-HELP.

A note about UCit software

UC researchers are served with desktop software by UCIT. In many cases this software is licensed specifically to UC employees only (i.e., people who receive paychecks from UC) or must be run on UC-owned or controlled equipment, making it inaccessible to Cincinnati Children's personnel. Please make sure you read the license agreement carefully before you use UC software.

Faculty and students of UC are eligible to purchase software from UC. However, when purchasing from UC, the license agreement states that the software can be installed only on your personally owned or UC-owned computer and not on machines owned by other institutions. Since Children’s Hospital is a separate entity from UC, installing software purchased from UC on CCHMC owned computers is a violation of that license agreement. There is a difference in the price of software purchased from Biomedical Informatics at Children’s Hospital versus from the UC Bookstore. This difference is because UC qualifies for the educational discount whereas Children’s Hospital does not. Although Cincinnati Children’s Hospital is affiliated with UC, we are not a degree granting institution. We are a hospital, therefore we only qualify for the healthcare/non-profit discount.