Idaho Bioinformatics Network

The Idaho INBRE Bioinformatics Core provides two types of bioinformatics support for biomedical research in Idaho: human and technological. Each resource, from workbook exercises and help desks to high performance computing and mass spectrometry, is available to every participant in the IDAHO INBRE. Individual institutions’ mission and goals determine the specific bioinformatics resources that an institution uses or provides.

Our strategic vision is to use bioinformatics to bootstrap local research capacity, while building the resources and services available collectively. This provides each institution with the strongest possible motive to develop the best resources for them, and to make them self-sustaining. In all cases, local assets are available to every participant. Each institution has developed specific expertise that they share with each other. Many of these assets are also available to the western INBRE region as a whole.

We help institutions address their educational missions by helping them integrate bioinformatics into the classroom, where students enter the Idaho INBRE student pipeline. This includes every participant, but is most especially important to Outreach partners. Every participant has integrated bioinformatics modules and exercises into various classes, including chemistry, math, computer programming, and ethics as well as the obvious biology classes (Figure 1, item 1). These classes introduce bioinformatics as a toolset. Some institutions have developed courses or degree programs bioinformatics itself, rather than on how to use bioinformatics (Figure 1, item 2). These projects advance the science of bioinformatics, and provide foundational expertise to students headed for graduate studies. In all cases, educational activities are coordinated regionally, to make it easier to share individual instructors, given the difficulties of travel in such a large state as Idaho.

Research Partners use INBRE supported bioinformatics to develop their research programs. To that end, each institution with a research mission supports local hardware, software, and personnel to provide bioinformatics capabilities specific to local research objectives (Figure 1, item 3-5). This ranges from installing, maintaining, and
programming multi-core cluster computers to installing institution specific software.

The three Research Intensive (or aspirational research intensive) institutions provide high-end core services to all INBRE participants, and to western INBRE partners. These services are tailored to local themes and research resources.

Idaho INBRE bioinformatics supports three core facilities with interrelated scientific themes: (i) evolutionary analysis of genomic data (UI), (ii) gene expression analysis (ISU), and (iii) protein structure analysis and proteomics (BSU). UI, through the IBEST Computational Resources Core, provides local databases and a high performance computing that is tightly integrated with the IBEST Genomics Resources Core (Figure 1, item 3). BSU provides a distributed cluster computer and software that is tightly integrated with their mass spectrometer facility (Figure 1, item 4). ISU provides
distributed cluster computers with software that is tightly integrated with their high throughput sequencing facility (Figure 1, item 5). This organization allows us to tightly integrate data generation facilities (sequencers, microarrays, mass spectrometers, etc.) with the data analysis (computational) hardware, software, and expertise. It encourages institutions to develop focused research programs that fill well-defined niches in the state and regional IDEA ecosystem, and which is necessary for post-INBRE support. And it avoids duplication of resources while maximizing sharing. Each of these three regional core facilities is available to faculty and students in every state institution via high-speed telecommunications. High-end computing hardware is available to all INBRE participants through secure Internet connections and access to state-of-the art analytical software, with experts to provide specialized help as necessary. In addition to INBRE support, these facilities received COBRE support, instrumentation awards, substantial material support from each university administration, and support from individual NIH and NSF research awards.

We designed our bioinformatics resource management and oversight structure to enhance local autonomy and authority (see Figure 2). This reflects the fact that we have moved from establishing shared bioinformatics resources to sharing established resources.

Educational oversight rests with regional Bioinformatics Coordinators, to whom Bioinformatics Liaisons from each participant institution reports. We strongly believe that face-to-face contact is critical for bioinformatics (and all) education, so that crossinstitutional classroom visits are critical. Regional organization of education therefore makes sense for very large states like Idaho, where physical proximity can determine when travel is feasible or even possible.

Research oversight rests with Bioinformatics Core (BIC) Directors, and is organized thematically. Individual cores are managed according to local policies, procedures, and customs. For example, at UI the Institute for Bioinformatics and Evolutionary Studies (IBEST) administers a Computational Resources Core that provides evolution and genomics services. This facility is primarily funded by an NIH COBRE and by fee-for-services. At BSU the Proteomics facilities are organized as a shared laboratory facility, rather than a fee-for-service.

The main Bioinformatics Director (Foster) provides overall strategic direction and oversight for bioinformatics resources. And the INBRE PI (Bohach) retains overall responsibility. All directors and coordinators have institutionally funded time dedicated to these INBRE activities.

Faculty and students from any Idaho INBRE institution continue to use facilities at whichever INBRE research institutions (UI, ISU, BSU) is appropriate for their project, or to use multiple facilities for different types of analysis, via our high speed telecommunications infrastructure. Key personnel continue to meet regularly online and in person to share expertise, tools, and best-practices. Each institution retains faculty and staff specialists for data management and analysis. These facilities have received COBRE (UI) or instrumentation (BSU, ISU) awards, substantial material support from each university administration, and support from individual NIH and NSF research
awards.

James A. Foster, PhD, continues to serve as the INBRE Bioinformatics Director (for the 12th year) and is responsible for overall bioinformatics planning and reporting. Each research institution has retained their current Bioinformatics Director, who is responsible for the scientific and technological operations of the local bioinformatics facilities and will report directly to the INBRE Bioinformatics Director (Foster). These are: James A. Foster, PhD, at UI; Michael Thomas, PhD, at ISU; and Julie Oxford, PhD, at BSU. Each research institution also retained their Bioinformatics Coordinator, who is responsible for local scientific advice and training, and for coordinating bioinformatics education and training in their geographic region. These are: Celeste Brown (UI), PhD, for Northern Idaho; Laura Bond for Southwestern Idaho; Michael Thomas (ISU), PhD, for Southeastern Idaho. Each other participating institution has retained a Bioinformatics Liaison who is responsible for implementing bioinformatics activities at their local institutions and for reporting progress to their regional Bioinformatics Coordinator. These are: Barry Myers, PhD at NNU; Amy Doetsch at CSI; Ann Koga at College of Idaho; Todd Kelson, at BYUI; Rhena Cooper, at NIC; and Matt Johnson, at LCSC. Each of these individuals is serving in the described capacity in the current INBRE. We have been very fortunate to retain so much experience and high-level expertise for the first year of this project.