The OK-INBRE Bioinformatics Core
Biomedical research has evolved into an increasingly
technology-driven endeavor and like the rest of society, has become
critically dependent on computational tools and methods for data
analysis, archiving and retrieval. This is particularly true as NIH
moves into the era of Big Data. The OK-INBRE Bioinformatics Core
supports this continuing evolution within the state of Oklahoma, by
providing bioinformatics support for both the Oklahoma research and
educational enterprises. Collectively, these efforts will enhance the
competitiveness of Oklahoma investigators for local, state and national
funding, and increase the pool of skilled young biomedical research
scientists in Oklahoma.
Research Support. Our mission is to enhance Oklahoma
research expertise and infrastructure by providing state-of-the-art
bioinformatics support to investigators performing biomedical research
on the campuses that participate in the Oklahoma IDeA Network. We
currently provide bioinformatics research support for over 150
investigators in the state, enriching many scientific disciplines
including cancer biology, cell and developmental biology, diabetes and
microbial pathogenesis. This breadth demonstrates the wide-ranging power
of bioinformatics to advance biomedical research. Our services include
DNA sequence data cleanup and analysis of DNA sequence-based experiments
including microbial genome sequencing and annotation, RNA-seq and
ChIP-seq analysis, 16S rRNA-based microbiomics. Where possible, we will
train laboratory personnel in the analysis of these data using
commercial software that exploits a graphical user interface, to avoid
the necessity of working on the command line to analyze this data. We
also provide access to the Ingenuity Pathway Analysis (IPA) software
suite, which is essential for exploring whole transcriptome data
obtained from eukaryotic cells. If you need access to the IPA software
for your project, please contact Dr. Dyer at the email address above to
arrange for a user account. In all your studies, we strongly suggest
that you contact us before you begin experiments that will require
bioinformatics support, so that we can advise on your experimental
design. A well-organized experiment is crucial for obtaining a
statistically robust outcome for many of these experiments. In addition
to these services, we have experience in protein structure modeling,
including the analysis of protein interactions with small molecules for
drug and inhibitory design. Support for other custom bioinformatics
applications is available as needed. Please contact us for more details.
As needed, we also will partner with the newly established OK-INBRE
Proteomics Core to support your discovery and targeted proteomics
experiments.
Educational Support. We provide support for bioinformatics education at Oklahoma IDeA Network Primarily Undergraduate Institutions (PUI) and Community Colleges (CC), by offering didactic coursework and hands-on computing laboratories, such as laboratory exercises in DNA Barcoding and 16S rRNA-based Microbial Ecology. These classes have enriched the educational experiences of undergraduate students, graduate students and high school science teachers in the state. We also provide custom lecture material on other topics such as structural bioinformatics and phylogenetic analysis. Beginning in 2020, we will offer a new course on the OUHSC campus, MI6401 Introduction to Bioinformatics. Holding this course in the summer session will eliminate potential overlap with existing coursework, making the scheduling more flexible and available to a wider selection of graduate students on the OUHSC campus, postdoctoral fellows and OUHSC faculty. This course will not be designed to teach attendees to write code and work extensively on the command line; rather, this is planned as a survey course intended to ensure that students, trainees, and faculty will gain familiarity with the basic tools and databases that are available to researchers for these types of studies.We will make use, where possible, of GUI-based commercial software such as CLC Genomics Workbench.The availability of GUI-driven bioinformatics software greatly enhances the ability of novice researchers to rapidly engage the full power of bioinformatics tools and their capabilities.We have in the planning stages a more formal instruction in writing code (R, Python, etc.) for solving problems in data management and analysis using a more advanced bioinformatics methods. Scheduling MI6401 in the summer also will ease the participation by OK-INBRE PUI and CC faculty; in fact, we plan to develop an on-line version of this course that will be available to PUI and CC faculty. This class will increase faculty familiarity with bioinformatics, and aid in incorporating these materials into coursework on the PUI and CC campuses. It is possible that this course could be included as part of the support offered to PUI and CC faculty who receive OK-INBRE funding for curriculum development. In sum, these bioinformatics educational efforts will stimulate the movement of promising students into the post-graduate education pipeline, foster the career development of young biomedical scientists at all stages of their training, and enable the use of state-of-the-art bioinformatics tools by Oklahoma investigators.