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Software for Functional Genomics and Bioinformatics

Software for Functional Genomics and Bioinformatics

Software for Functional Genomics and Bioinformatics
The Analysis Tools and Training initiative is designed to enhance research in functional genomics and pathway analysis. The university has purchased subscriptions to commercial software programs designed to help researchers integrate, analyze and visualize genome-scale data sets from several different sources of information. The initiative, which is funded by the Institute for Integration of Medicine and Science (IIMS) and administered through the institutional research core facilities, provides site licenses for the following software packages:

Ingenuity Pathway Analysis (IPA)
JMP Genomics (by SAS)
Partek Genomics Suite

One advantage of these packages is that the typical biomedical researcher can learn how to perform some important applications using biostatistics and bioinformatics without needing skills in programming. The initiative provides university scientists with discounted access to premier software packages, and it places an emphasis on the training needed to get started.

View the flyers for the program:

Two-day, on-site training workshops will be provided by each vendor. Training workshops are free and open to researchers outside of UTHSCSA. However, registration is required because space is limited and priority will be given to licensed users.

Training Workshops
Software Date Location Agenda
Partek Genomics Suite TBD TBD TBD
Ingenuity Pathway Analysis June 3-4, 2010 Briscoe Library 2.011 (computer classroom) IPA_training.pdf
JMP Genomics Oct 21, 2010

9:00 am – noon

Briscoe Library 2.011 (computer classroom) TBD

Gaining Access
The software packages are provided under a UTHSCSA site license or a concurrent user model. These mechanisms introduce the software to the research community at a fraction of the cost to the individual user. A fee will be charged to gain access to the programs that are available on a prorated annual license. Each package is renewable for a second year, and those software programs with sufficient usage will be continued in subsequent years. Training is free.

How to register for software or training
Log in (or create a new account) at the institutional core facility portal. The Principle Investigator (PI), who authorizes charges to the account must also be registered in the portal. People in the laboratory must associate themselves with the PI (authorized account holder) before a service request can be validated. Use the “Resource Services” menu tab to “request new services”. Pull down the “Choose Facility” list in the main table to select “Microarray Services.” Choose the software package or the training session and submit the request.

Researchers outside of the UTHSCSA system who want to participate in the training workshops should contact Mike Wilson, Director of the Institutional Research Core Facilities.


License Options for Software
Software Concurrent Users Pool of Users Implementation
IPA (5-named)
5 named
Web — Software as a service
IPA (site license)
Web– Software as a service
JMP Genomics
Installed on local computer
Partek Genomics Suite
Installed on local computer, server key enforces license

A concurrent license limits the number of users who can be logged in and actively using the software at a given time. For example, an investigator who is registered for IPA under the university-wide license will be granted access to the IPA web-service if no more than two other people are using the system at that particular time. If an account is inactive for a designated number of minutes, the system will end the session so that another licensed user can gain access to the system.

The scenario is similar under the 5-named user license. In this case, the system allows one concurrent user, but access is limited to only five designated people. This option is intended for frequent users of IPA who need more reliable access to the system. Under this license, each user will know the other four people under the shared license, so that coordinating times to use the software is simplified.

For more information related to the software, licensing or training, contact Mike Wilson 567-2059.

Other Software Resources: Computational Biology Initiative
More related computational resources can be accessed through the Computational Biology Initiative (CBI), an interdisciplinary initiative at the University of Texas Health Science Center at San Antonio (UTHSCSA) and the University of Texas at San Antonio (UTSA). The objectives of the CBI are to foster the use of state-of-the-art core computational and analytic facilities, to enhance local expertise in San Antonio bioscience community, and to develop training opportunities. For more information contact:

Computational Biology Initiative