EDITOR’S NOTE: The following is a note from the UNMC Office of the Vice Chancellor for Research.
UNMC and the College of Information Science and Technology at the University of Nebraska at Omaha have formed a new partnership for the operation of the Genetic Sequence Analysis Facility (GSAF), a core facility for the computational analysis of DNA sequences.
The goal of this partnership is to build upon core infrastructure and provide expertise necessary to assist and support researchers in the use of bioinformatics related software from participating institutions.
In addition, GSAF will develop new software and technologies for the biosciences, health care and clinical-decision support.
This new partnership will provide scientists and students with advanced computational resources (both hardware and software) to aid in the genomics and proteomics high-throughput data analysis.
This partnership is an extension and expansion of current research initiatives between UNO/Peter Kiewitt Institute and UNMC, and is an example of collaboration between biologists and computer scientists who work side by side to promote the development of new research initiatives in bioinformatics.
Active participation of GSAF personnel in developing/teaching new courses in bioinformatics at UNO will help to train a core of technically competent graduate students and faculty, who are able to support and assist other investigators wishing to use computational tools in data analysis.
These skills will be especially important to investigators in the area of genomics, proteomics, transcriptomics and health informatics.
Walk-in office hours are 9 a.m. to noon, Monday through Friday in the Durham Research Center, Room 1048.
Additionally, support can be obtained by calling 559-9527, by e-mail at support@gsaf.ist.unomaha.edu or on the Web at http://www.molbio.unmc.edu/support.
If the request is sent electronically, the submitter will receive an automated response acknowledging the nature of the requested support.
This system also will alert appropriate GSAF-personnel regarding the request, who will then respond by email or phone. Scientists also are welcome to call or come to the office in person. The new people you will interact with will include the following:
- Facility Director: Dhundy Bastola, Ph.D. assistant professor, bioinformatics, College of Information Science and Technology (IS&T), University of Nebraska at Omaha.
- System Administrator: Mohammad Shafiullah, UNO IS&T — Research
- Application Support/Development Specialist: Jay Hannah, UNO IS&TM
Software support
In addition to the existing software packages available at the GSAF, new software will be added in the near future. The current software includes:
- Accelysys GCG — Commercial product that includes SeqLab (X Windows) and SeqWeb (web browser based). We host, administer and manage this application package and instruct users at UNMC in its use.
- Vector NTI — Commercial product by invitrogen for sequence analysis and data management. We assist users at UNMC in getting licenses for this software and provide instruction.
The new applications that will be added in the coming months will be:
- wEMBOSS — a Web interface to the popular EMBOSS software package for biological sequence analysis.
- BioPerl — Perl toolkit used for a broad spectrum of bioinformatics application.
- GBrowse – Visualization of genomic data.
- SeqLab.net — Perl toolkit for sequence analysis.
- NCBI BLAST — Basic Local Alignment Search Tool
To ensure that GSAF is effectively delivering needed assistance and support to the researchers, an advisory committee consisting of faculty members from various departments will be formed. It is expected that the members will act as liaison and forward feedback they receive from the users in their respective departments to GSAF.