Oklahoma IDeA Network for Biomedical Research Excellence (OK INBRE)

The primary objective of Oklahoma's INBRE is to maintain our progress toward developing a nationally competitive biomedical research enterprise. This long-term goal will be accomplished by focusing on three priorities: 1) Supporting the research career development of promising investigators through direct support of their research, 2) Enhancing the pipeline of undergraduate students entering our graduate programs by initiatives at both primarily undergraduate institutions and community colleges, and 3) Sustaining core facilities that support both the research of the INBRE investigators and the statewide biomedical research effort. Our philosophy will be to accomplish these tasks by building on the infrastructure and collegial network developed through the OK BRIN, which has evolved into the OK INBRE.

Looking to register for a conference or workshop? Registration forms are here.

For more information, see the official OK INBRE site . The OK INBRE News site also has information on events supported by the OK INBRE.

 

  OK INBRE microarray cores

The satellite facility at OSU consists of two interoperating units, the OSU Microarray Core Facility and BioinfOSU. The OMCF has modern microarray printing, scanning and data analysis capabilities and provides consultation and training in the form of workshops in microarray analysis. BioinfOSU supplies the OMCF with software for the analysis of microarray data, particularly the popular Gene Pix Autoprocessor (GPAP), a web-based application providing preprocessing of raw microarray data. GPAP performs signal filtering, background correction and signal normalization and provides diagnostic plots and reports to evaluate data quality and the effects of preprocessing. GPAP can also identify the top differentially expressed genes for the user. In addition to supplying the supporting computer infrastructure for the OMCF efforts, BioinfOSU provides other bioinformatics resources to scientists. It hosts the PipeOnline tool for processing and annotation of ESTs and VirOligo, a database of oligonucleotides used in virus detection. A variety of software packages are provided for local users.

The University of Oklahoma Bioinformatics Core Facility hosts a fully functionial, web-accessible microarray database, developed with funding from the NSF-EPSCoR and NIH-BRIN. The OU Microarray Database (OUMDB) provides users of the Oklahoma Bioinformatics Network a web interface to upload, manage, and analyze microarray experiments. The OU Microarray Core Facility provides equipment for microarray printing, hybridization and scanning. The staff of the OU Bioinformatics Core includes skilled programmers who regularly tailor the database to accommodate user needs. Specifically, the OUMDB provides password-protected access to features including a complete LIMS, array-design, data-upload interface, statistical package, experiment organization, and data-mining package. The OU E. coli Gene Expression Database hosted by OUMDB offers the most extensive publicly accessible E. coli microarray datasets in the world.

The Laboratory for Genomics and Bioinformatics is a genomics facility offering DNA sequencing (custom and genome-scale projects), genotyping, microarray design, hybridization and data analysis, and other services. Custom microarrays have been designed for several bacterial genomes, including Actinobacillus actinomycetemcomitans, Haemophilus ducreyi, Neisseria gonorrhoeae, Staphylococcus aureus, and Streptococcus pyogenes. The OUHSC core facility offers microarray hybridization and data analysis services, and data archival using the open source BASE database format. A free Perl workshop is periodically offered on the OUHSC campus to introduce interested individuals to the language and its use in bioinformatics. Among the programming languages available, Perl is arguably the favorite of bioinformatics programmers. Its low learning curve and flexible syntax make it an ideal beginning language for biologists, and its unsurpassed text-parsing ability make it an excellent choice for data such as protein and nucleic acid sequences. This informal, non-accredited workshop consists of four two-hour sessions spanning two weeks. You will not walk away from these sessions a Perl expert, but you should have a working knowledge of the basic syntax of the language and programming structure that will help you carry on further self-study. No previous programming experience is required. The only prerequisites are an understanding of operating system usage in windows or linux, such as creating files and folders and using a text editor. Very general knowledge of biological processes such as transcription and translation also will be assumed. Class sizes will be small and students will follow the instructor on laptop computers provided by the workshop.

Scientists at the OMRF Microarray Research Facility collaborate with researchers at OMRF and around the world to study differential gene expression in order to understand pathophysiologic states at the molecular levels. They manufacture human, mouse, and Candida albicans oligonucleotide microarrays, plus a variety of custom cDNA microarrays containing genes from libraries produced by individual investigators. Links to gene lists on oligonucleotide arrays are available to download to your computer. A variety of protocols, available online, have been developed and optimized at OMRF to assist investigators here and elsewhere in the use of microarrays. The Microarray Facility Bioinformatics Section designs novel analytical tools for use in microarray studies, and assists users in analyzing and understanding microarray data obtained from experiments performed at the Facility. Links to recent publications and public databases available for downloading to your computer are also listed.

The Department of Biological Science at the University of Tulsa recently purchased the Affymetrix GeneChip® platform for the measurement of mRNA expression. The system includes the GeneArray® Scanner, the Fluidics Station 400, the Hybridization Oven 640, and a powerful computer workstation. GeneChip® expression arrays are available for the study of human, rat, mouse, drosophila, C. elegans, E. coli, and many other model systems. The services available from the TU Microarray Core include Northern blot for mRNA quality control, clean-up of total RNA, target labeling, hybridization, scanning, and biostatistical analysis of the data.

 

  OK INBRE institutions

• Langston University
• Northeastern State University
• Southwestern Oklahoma State University
• Southeastern Oklahoma State University
• Cameron University
• University of Central Oklahoma
• Oklahoma City Community College
• Redlands Community College
• Comanche Nation College

 

  Links to some bioinformatics tutorials

• 2can Bioinformatics Educational Resource
• BioTeach
• A Science Primer Menu
• NCBI Education
• Bioinformatics.org: Bioinformatics FAQ
• Guide to Selected Bioinformatics Internet Resources
• Lecture notes on biological sequence analysis (pdf)
• Bioinformatics Tutorials & Articles
• Tutorials - Bioinformatics.net

For a list of books on bioinformatics please go here, "Bioinformatics Book Recommendations".