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Undergraduate Summer Program Application and information Pilot program for providing patents to regional university faculty click here INBRE Rebudget Form for participating universities (not OUHSC) click here Acknowledging INBRE: For each publication that results from grant support provided by the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), grantees must include an acknowledgment of support and a disclaimer stating the following: “This publication was made possible by Grant Number P2PRR016478 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH).” or “The project described was supported by Grant Number P2PRR016478 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH) and “Its contents are solely the responsibility of the authors and do not necessarily represent the official views of NCRR or NIH.” INBRE LABS University of Oklahoma Health Sciences Center Oklahoma Medical Research Foundation University of Oklahoma, Norman OTHER LINKS Oklahoma Bioinformatics Group (OBUG) Biotechnology Associate Degree Program at Oklahoma City Community College Bioinformatics Graduate Program at University of Oklahoma, Norman
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The IDeA Network of Biomedical Research Excellence (INBRE) is a grant awarded to NIH through the National Institutes of Health Institutional Development Award (IDeA) Program. The award will bring over $17 million in research funding to fourteen Oklahoma institutions. The Network is diverse, comprising two lead institutions whose primary missions are biomedical research, education and patient care, and twelve collaborating institutions. Oklahoma's INBRE builds State capacity to carry out biomedical research by supporting promising new faculty, recruiting students into biomedical research careers, and sustaining vital core facilities. The scientific themes of Oklahoma's INBRE are multi-disciplinary, targeting the fields of Microbiology & Immunology, Cancer, and Neurosciences. This thematic focus is closely linked with the strategic research plans of the two lead biomedical research-intensive institutions. Support for students is provided by summer internships, participation in the faculty research projects and enrollment in new educational programs in bioinformatics and genomics. The primary core facilities are focused on functional genomics. An integrated network of bioinformatics facilities dedicated to supporting research in functional genomics is supported, as well as the development of a new core facility whose centerpiece is a functional magnetic resonance imager (MRI) devoted exclusively to animal research to support statewide research in cancer and neuroscience.
NEW
NIH POLICY:
NIH
PUBLIC ACCESS POLICY EFFECTIVE APRIL 7, 2008
NIH
now requires submission of all final manuscripts to PubMed
Central for research funded in whole
or
in part by the NIH. The PubMed Central reference number must be included in
NIH applications,
proposals,
and progress reports effective May 25, 2008. See the NIH website on the Public
Access
Policy
for details (http://publicaccess.nih.gov)
and the ORA website for a summary of the requirements
(see links at left)
Bioinformatics Core (OUHSC Laboratory for Genomics and Bioinformatics) 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, adn 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 will be assumed. Class sizes will be small and students will follow the instructor on laptop computers provided by the workshop.
MRI and Microarray Facility (Oklahoma Medical Research Foundation) Scientist at the OMRF Microarray Research Facilty 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.
University of Oklahoma, Norman - Bioinformatics/Microarray Satellite Facility The University of Oklahoma Bioinformatics Core Facility hosts a fully functional, 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-minig package. The OU E. coli Gene Expression Database hosted by OUMDB offers the most extensive publicly accessible E. coli microarray datasets in the world.
Oklahoma State University - Bioinformatics/Microarray Satellite Facility The satellite facility at OSU consist of two interoperating units, the OSU Microarray Core Facility and BioinfOSU. The OMCF has modern microarray printing, scanning and data analysis capabiliities 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.
University of Tulsa - Bioinformatics/Microarray Satellite Facility 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 biostatistacal analysis of the data.
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