An International Symposium of the Association of Biomolecular Resource Facilities

Core Administration Oral Presentations

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Session Type: Innovative Topics

  • Informatics Core: Adding value to Data Produced in Core Facilities
    Claudia Neuhauser University Of Minnesota
    In 2014, the University of Minnesota Informatics Institute (UMII) was founded to foster and accelerates data-intensive research across the University system in agriculture, arts, design, engineering, environment, health, humanities, and social sciences through informatics services, competitive grants, and consultation. Listening to researchers across the University and in design thinking workshops, it became clear that increasingly data management and analysis are becoming a major bottleneck in research labs. Core facilities in genomics, proteomics, and imaging are producing large amounts of data that are usually delivered to users without much prior processing. With bioinformatics being a fast moving field, it is increasingly difficult for labs to stay on top of the latest analysis tools. Furthermore, quality control of data and basic analysis are in need to become more standardized. To aid researchers in the management and analysis of their data, UMII hired analysts to run workflows and a data wrangler to help with the data management. Over the past year, UMII became part of Research Computing, which includes the Minnesota Supercomputing Institute and U-Spatial. These three institutes provide a full range of services that transform raw data into usable products through standardized workflows and research collaborations.
    Session Type: Innovative Topics

Session Type: Workshop

  • Combining Tools to Enhance Scientific Research
    Cheryl Kim La Jolla Institute For Allergy And Immunology (LJI)
    Core facilities at the La Jolla Institute (LJI) provide scientists with powerful technologies necessary to understand more about the cells of the immune system and their function in a wide range of diseases. While each technique has it’s own advantages, combining these tools can provide comprehensive details about the immune system as a whole. In this brief talk, we will present a few different projects involving multiple core facilities and techniques, including Sequencing, Microscopy and Cytometry, to enhance scientific research. In the first project, we will discuss the methods used to improve cell sorting of rare immune cell populations, such as antigen specific T cells, and subsequent global gene expression analysis by RNASeq. In another project, we will discuss deeper profiling and characterization of immune cell subsets by combining imaging, cytometry and transcriptomics.
    Session Type: Workshop
  • A Balanced Approach to Return on Investment (ROI) for Research Core Facilities
    Justine Karungi, MBA, FACHE Hoglund Brain Imaging Center, University Of Kansas Medical Center
    In these times of economic constraint and increasing research costs, shared resource cores have become a cost effective and essential platform for researchers who seek to investigate complex translational research questions. Cores produce significant value that cannot be captured using traditional financial metrics. Benchmarking studies conducted by ABRF and other organizations indicate that most research cores do not fully recover operating expenses. As such, these “operational losses” represent institutional investment which, if well planned and managed, produce future returns for the institution’s research community that extend far beyond subsidized pricing. Current literature indicates that there is no single measure that can provide an accurate representation of the full picture of the returns on research investments. This presentation attempts to provide instruction and examples using the Balanced Score Card (BSC), (Kaplan and Norton), as a tool for assessing the Return on Investment (ROI) on research core facilities. The BSC supplements traditional financial measures with criteria to measure performance in three additional areas - customers, internal business processes and learning and growth. The presenters will also discuss and share their experiences and good practices on how they have utilized these ROI approaches to streamline their core operations and make sound investment decisions and strategies to further the mission of their institutions and to meet the expectations of their various investors and key stakeholders.
    Session Type: Workshop
  • Communicating Science to the Public: Break on through to the other side
    Hudson Freeze FASEB And SBP Medical Discovery Institute
    That important topic and The Doors rhythmic answer may not be so far-fetched. Practicing is not simple; it’s time consuming, plus there’s a foreign language requirement. A few perspectives will be offered, but solutions will come from your own efforts outside the laboratory.
    Session Type: Workshop
  • Management for Scientists, Part 2: Core Business Problem Solving
    Robert Carnahan Vanderbilt University
    How will Kurt handle his BIG core getting BIGGeR? That is the focus of this hands-on problem-solving workshop. Come prepared to work! This session will begin with an overview of problem-solving strategies for organizations. Attendees will then be divided into teams and be guided through a case study that incorporates the types of pressures and decisions that commonly face core facilities. The goal is to use this exercise to develop and refine systematic approaches that can be applied to nearly any problem.
    Session Type: Workshop
  • Cross core collaborations; building bridges between resources
    Matthew Cochran University Of Rochester
    Broad ranging research projects often require input and collaboration from multiple Shared Resource laboratories. While occasionally these cross over projects go on without the knowledge of the core personnel involved it should be a goal of shared resources to promote these collaborative efforts in order to provide the best advice and service possible. In this workshop we are going to discuss cross core collaborations in three different ways. First we’ll discuss the administrative perspective on promoting collaborations and encouraging interaction between cores. Second, from the core directors perspective, we’ll discuss potential issues and ideas to improve workflow between labs. Lastly, the implementation of the Polaris from Fluidigm in a shared resource will be discussed as an example of new instrumentation meant to bridge the gap between core technologies.
    Session Type: Workshop

Session Type: Satellite Workshop

  • Core Operations Reporting: Generating Operational Tools for Specific Stakeholder Groups
    Jay Fox University Of Virginia School Of Medicine
    There is a critical need to understand core operations to ensure successful and efficient delivery of value to stakeholders. Different stakeholders, such as staff, core directors, departmental chairs and deans have different perspectives of core operations and different interpretations of how those operations impact their individual domains. Most core have the benefit of access to ample data that when harvested and presented appropriately have offer a clear assessment of core operations that is tailored to the specific needs and view points of various stakeholder groups. The the University of Virginia Office of Research Core Operations (ORCA) we have complied a number of specific reporting tools tailored to the needs of core staffs, clients and those with institutional oversight over core operations. In this presentation we will present examples of these reporting tools, describe how they are compiled, and how the information in the tools is of value to specific stakeholders.
    Session Type: Satellite Workshop

Session Type: Scientific Session

  • Rigor and Reproducibility
    AMY WILKERSON Session Organizer, The Rockefeller University
    Independent verification of research results is essential to scientific progress and to public trust of the scientific method. Growing concern over increasing reports of the lack of transparency and reproducibility in biomedical research has led to increased scrutiny of scientific publications and a general call for development of best practices for generating and reporting research findings. Specific examples of how the science community is responding include the NIH guidelines for addressing rigor and reproducibility in grant applications and progress reports, the consensus “Principles and Guidelines in Reporting Preclinical Research, and efforts to further strengthen quality controls and data reporting and retention practices by core facilities. During this session, experts in sponsored program administration, scientific publishing, and core facility management will provide information about how each sector is addressing the call for increased rigor and reproducibility in biomedical science. In addition, each presenter will provide suggestions on how core facilities can support researchers in addressing new funding agency requirements and for enhancing rigor and reproducibility overall.
    Session Type: Scientific Session
  • Research Development & Core Facilities Infrastructure
    Karin Scarpinato Florida Atlantic University
    Core facilities are laboratories in academic institutions that provide state-of-the-art instrumentation and world-class technical expertise whose costs are shared by researchers on a fee-for-service basis, and/or supported by the institution. As such, core facilities enable the researchers to obtain access to services/instrumentation that otherwise are too expensive to have in their own labs. To that end, core facilities extend the scope of research programs and accelerate scientific discoveries. Historically, core facilities have not taken a key role in research development. However, over time, academic institutions and federal funding agencies have recognized the importance of shared resources, and are re-evaluating best practices for operations and efficiency. In the systematic evaluation of core facility operations and its infrastructure, many principles of research development are recognized which lends to the suggestion that RD offices can add value to strategic development of individual core facilities and the network of core facilities infrastructure institutionally, regionally and nationally. Principles that govern core facilities that can be enhanced by RD include, but are not limited to strategic planning, interdisciplinary team building, grant writing, seed funding programs and limited submissions management. This panel discussion will provide examples of how RD principles apply to the development of core facilities infrastructure, and how RD offices can assist in improving operations of such facilities. These examples will be followed by an open discussion and exchange of ideas with the audience. By supporting core facilities, RD offices expend their impact in promoting research beyond the single-investigator/research teams. In turn, these services enhance the office outputs: new initiatives, collaborations, grant applications and outreach
    Session Type: Scientific Session
  • Realizing Commercial Value from Product Opportunities that Arise from Academic Research: An Introduction to the SBIR/STTR Programs
    Ron Orlando UGA And GlycoScientific
    An objective of basic scientific research is the acquisition of knowledge, typically without the obligation to apply it to practical ends. Often during this endeavor, scientists will make a discovery with inherent commercial worth. The value of this work is difficult to ascertain since the technology may be un-validated, may lack intellectual property protection, and has an unknown market potential. These and other vulnerabilities often cause the technology to be undervalued and make it too risky to attract funding from the typical early stage investment strategies, particularly angel investors/venture capitalists. Hence, the potential value is often not realized. The US government has established two grant/contract programs that can be used to bridge this gap between academic concept and commercial product. These are the Small Business Initiated Research (SBIR) and the Small Business Technology Transfer (STTR) programs, which provide over $3 Billion in funding annually. These initiatives intended to help small businesses conduct research and development and aim to increase private sector commercialization of innovations derived from Federal research expenditures. NIH also provides market insight, through the Niche Assessment Program, that can be used to help small businesses strategically position their technology in the marketplace. These and other programs are put inplace to invigorate small buisness growth. This presentation will discuss how to leverage these opportunities to commercialize academic research. Particular attention will be paid on how to obtain capital from these funding mechanisms, compare SBIR to STTR programs, and describe how to decide which program to utilize at each stage of company and idea development. The presenter will draw on his experience to provide examples of how SBIR/STTR funding can be used to create commercial hardware, software, and research reagents. This presentation will also describe a strategy to extract value from product opportunities that arose from academic studies.
    Session Type: Scientific Session
  • Bioinformatics of TMT Multiplex Data, UNR-Style
    Karen Schlauch University Of Nevada Reno
    Recent advances in mass spectrometry using the Thermo Scientific Orbitrap Fusion Tribrid Mass Spectrometer allow for the identification and multiplex quantification of many proteins across larger and larger sample sizes. Managing variation across sample protein abundances is not (yet) as standard as with microarrays or RNA-seq platforms. The Nevada INBRE Bioinformatics Core at the University of Nevada, Reno offers several specific methods of analyzing TMT multiplex data run on the Orbitrap Fusion and extracted using Proteome Discoverer at our adjoining Nevada Proteomics Core. A pilot study run in our Cores measured the biological variability in protein abundance of 3000 identified proteins across ten human tissue samples; our Core uses these measures as baseline variability for quality control in human tissue experiments. To further manage intra-cohort variability of protein abundances, our Core developed a technique to identify outliers per protein and per cohort that controls variation without excluding data from entire proteins or samples. We show that our method notably decreases the coefficient of variation of abundance measures (by 2-fold or more) within cohorts and thus leads to more statistically powerful hypothesis tests across cohorts. Our Core performs statistically sound hypothesis tests on these processed data to identify differentially expressed proteins or peptides at either the protein level or the peptide level; tests are specifically based on data distribution and experimental hypotheses. For studies involving post-translational modifications, statistical tests are applied only on unique modified peptides of each post-translational modified protein to take into consideration that abundances of modified peptides make up only a portion of each modified protein’s abundance (sometimes as low as < 10%). We show that our technique offers stronger statistical tests across cohorts for post-translational modifications. To conclude, our Bioinformatics and Proteomics Cores offer novel and specific techniques for TMT data on one or many mutiplex experiments.
    Session Type: Scientific Session

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