Data Management 101: Best Practices for Storing and Protecting Research Data

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Date: December 7, 2017

Time: 1:00 pm ET

This online seminar will help lab directors and administrators gain a 101 understanding of file naming, data storage, and data management.

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Our panelists will discuss protocols for how to name your files, how to manage the storage of data – especially large file sizes – and how to protect research data. The seminar will include an update on the National Institutes of Health’s policies on data management.

Panelists:

EFogartyErin Fogarty
Information Security Specialist
Case Western Reserve University

 

 

Daniel Timmons
IT Director
University of Colorado Boulder
BioFrontiers Institute

 

 

Matthew Fenchel
Manager, Biostatistical Consulting Unit
Cincinnati Children’s Hospital Medical Center

 

 

This webinar will help lab managers understand the basics (and challenges) of managing data in a research environment and will demonstrate some of the best practices that work well for specific institutions.

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More information on the GenomeWeb/ABRF 2017 Webinar Series is available here.  
Scheduling conflict? You can still participate! All registrants will receive a link to view an on demand recording of the event. 

 Questions? Contact genomewebinars@genomeweb.com    

GenomeWeb and the Association of Biomolecular Resource Facilities (ABRF) have partnered for a second year to produce a series of online seminars highlighting methods, techniques, and instrumentation that support life science research. Special thanks to the series sponsor, PerkinElmer

 

 

A Balanced Approach to Assessing Return on Investment for Research Core Facilities

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Date: November 14, 2017
Time: 1:00 pm ET

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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 the Association of Biomolecular Resource Facilities (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.

Presenters:

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Sheenah Mische, PhD
Senior Director of the Division of Advanced Research Technologies (DART) and
Associate Professor of Pathology at NYU Langone Health
New York, NY

 

 

 

Justine Karungi, MBA, FACHE
Assistant Director at the Hoglund Brain Imaging Center (HBIC) at the
University of Kansas Medical Center
Kansas City, KS

 

 

Current literature indicates that there is no single measure that can provide an accurate representation of the full picture of the return 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 for 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 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.

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Questions? Contact genomewebinars@genomeweb.com

GenomeWeb and the Association of Biomolecular Resource Facilities (ABRF) are partnering for the second year to produce a series of online seminars highlighting methods, techniques, and instrumentation that support life science research. Special thanks to the series sponsor, PerkinElmer

Ask the Experts: Ensuring High-Quality Proteomic Studies with Core Lab Resources

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Date: October 10, 2017
Time: 1:00 pm Eastern Time

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This online, interactive seminar will answer researchers’ most pressing questions about how to gain outstanding research results from proteomic studies. Researchers and clinicians are increasingly adopting proteomics as a go-to method for gaining biological insights and direction. Proteomic core labs are shared resources with the expertise and instrumentation to carry out these specialized studies. Collaboration between researcher and proteomic core combines the expertise and leverages the strengths of both parties. This webinar will provide building blocks on which to jumpstart or strengthen this key relationship.

From study design and sample preparation through data analysis, result interpretation, and overall reproducibility, our panelists will answer your essential questions about setting up and carrying out high-quality proteomic studies. This practical insider info will help researchers and cores to work together and effectively move research forward.

Presenters:

Emily Chen, PhD
Director of Proteomics Shared Resource
Herbert Irving Comprehensive Cancer Center
Assistant professor of Dept. Pharmacology
Columbia University Medical Center, New York, NY

Brett Phinney, PhD
Director, Genome Center Proteomics Facility
University of California, Davis, CA

Scott Shaffer, PhD
Director, Proteomics and Mass Spectrometry Facility
Research Professor, Biochemistry and Molecular Pharmacology
University of Massachusetts Medical School, Shrewsbury, MA

David L. Tabb, PhD
Professor, Division of Molecular Biology and Human Genetics
Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, South Africa

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Questions? Contact genomewebinars@genomeweb.com

GenomeWeb and the Association of Biomolecular Resource Facilities (ABRF) are partnering for the second year to produce a series of online seminars highlighting methods, techniques, and instrumentation that support life science research. Special thanks to the series sponsor, PerkinElmer

Press Release: The Nobel Prize in Chemistry 2017

Cool microscope technology revolutionizes biochemistry

We may soon have detailed images of life’s complex machineries in atomic resolution. The Nobel Prize in Chemistry 2017 is awarded to Jacques Dubochet, Joachim Frank and Richard Henderson for the development of cryo-electron microscopy, which both simplifies and improves the imaging of biomolecules. This method has moved biochemistry into a new era. Read more about this year’s prize…

New FASEB Report: Leveraging Shared Resources to Improve Research

A new report from the Federation of American Societies for Experimental Biology (FASEB), “Maximizing Shared Research Resources,” identifies the challenges encountered by shared research resources providers and users, and makes recommendations for improvement.

Shared research resources – from core facilities to living collections and national laboratories – make efficient use of funds and broaden researchers’ access to advanced technologies and materials. But shared resource providers face difficulties that limit their ability to offer cutting-edge services.

FASEB surveyed shared resource users and providers and identified four key areas for improvement:

Create better business models for shared resource facilities;

  1. Enhance funding programs that support facilities;
  2. Increase national awareness of shared resources;
  3. Connect researchers with institutional resources.

Click here to view the full report including the survey instrument and analysis of findings. For more information, contact Bethany Drehman, FASEB Senior Science Policy Analyst.

Cores: Part of the solution to experimental irreproducibility

Experimental reproducibility is rooted in many things; one of them being poorly validated antibodies. Numerous scientists have highlighted this problem for quite a few years, with this weakness making it into the public arena.  The NIH has taken a step forward by requiring a plan to authenticate key biological and/or chemical resources, among which are antibodies, as part of their research grant and mentored career development applications, but it is the scientific community that needs to develop and implement solutions. Several groups have taken up the charge to facilitate a cultural shift among the many players, among them, Global Biological Standards Institute (GBSI) and Biocompare. Last fall, GBSI ran a workshop entitled “Antibody Validation: Standards, Policies, and Practices” where key stakeholders from academia, industry, funding entities, and journals came to share perspectives and contribute to real and feasible solutions for validating antibodies. The ABRF was proud to sponsor and represent core facilities during these productive discussions of challenges. Participants worked together to map out a path forward through working groups to create a series of antibody validation guidelines for each of the seven most commonly used techniques. This summer, Biocompare stepped up to the plate by producing a very well framed and thought-provoking documentary on the role antibodies play in reproducible scientific endeavors, in which the ABRF was honored to participate.

Core facilities are particularly well positioned to expedite the process towards a better appreciation for this particular biological reagent class as well as to support researcher through a robust validation process. The scientists in core facilities can actively participate in moving antibodies off the list of irreproducibility contributors because they are the “boots on the ground”, working daily with scientists in research labs. We would like to use this blog post to facilitate a conversation within our network of how ABRF can be part of the solutions.  Reading the GBSI workshop report or viewing the Biocompare documentary are great starting points to begin thinking about the role of core facilities in the solution.  Then come back to the blog to share your thoughts and participate in our collective discussion, one that will hopefully lead to action within ABRF.

ABRF WIN2017 Phase 2 Study: Developing Procedures to Optimize Inter-Laboratory Reproducibility of LC-MS/MS-based Proteomic Analyses

June 30, 2017

Dear Colleague:

The 2017 ABRF Workflow Interest Network (WIN) is pleased to announce initiation of Phase 2 of a study to promote inter-laboratory reproducibility of quantitative proteomic LC-MS/MS analyses. Past studies of proteomic performance metrics have focused on the retrospective evaluation of collected data.  In this study we seek to identify data processing tools, including ID-free quality metrics, to support a proactive approach.

Participating laboratories will receive 2 samples: a mixture of peptide internal standards and a HeLa cell lysate digest.  A detailed protocol on how to run these samples will be provided when the samples are shipped.  We estimate it should take no more than 24 hours to complete the analysis.  Participating laboratories will submit raw files and complete a questionnaire of self-reporting parameters according to our instructions.  Results derived from the raw data will be de-identified to maintain the anonymity of the participating laboratories. Each participant will receive a unique identification number allowing them to compare their results with those of other participating laboratories.

The timeline for the study is as follows:

  • Sample requests accepted until August 1, 2017
  • Samples ship to participants starting August 1, 2017
  • Raw data files uploaded to the online repository by October 31, 2017
  • Results and analysis presented at the ABRF 2018 conference April 22-25, 2018, in Myrtle Beach, South Carolina, USA, then posted on the ABRF website.

To request a sample, please go to https://www.surveymonkey.com/r/H8XVSF3 and provide your shipping information before August 1, 2017. The WIN is eager to obtain data from a variety of different laboratories and mass spectrometry platforms, and encourages all mass spectrometry laboratories with an interest in proteomics and data quality metrics to participate.  However, because sample preparation and shipping involve a significant investment of time and money, Phase 2 is limited to 40 participants. The research group asks that you only request a sample if you are confident that you will be able to provide your raw files by the end of October.  We thank you for your support of the ABRF and look forward to your participation in this study.

Sincerely,

Sincerely,

The ABRF Workflow Interest Network
Emily Chen (chair), Achim Treumann, Alex Campos, LeeAnn Higgins, Sheng Zhang, Theresa McLaughlin, and Allis Chien (EB liaison)

 

ABRF Announces June 29 Webinar: Cross-Kingdom Standards in Genomics, Epigenomics, and Metagenomics

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Date: June 29, 2017
Time: 2:00 pm ET
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Christopher Mason Weill Cornell Medical College

Christopher Mason – Weill Cornell Medical College

GenomeWeb and the Association of Biomolecular Resource Facilities (ABRF) are partnering for the second year to produce a series of online seminars highlighting methods, techniques, and instrumentation that support life science research. Special thanks to the series sponsor, PerkinElmer

The first in the series of online seminars, Cross-Kingdom Standards in Genomics, Epigenomics, and Metagenomics, will provide an overview of current standardization efforts in genomics, epigenomics, and metagenomics, with a focus on practical implementation considerations for researchers and labs. Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single cells, RNA profiling, and metagenomics. Technical artifacts and contaminations can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous. Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data.

In this webinar, Christopher Mason of Weill Cornell Medical College will review work to develop standards and their applications in genomics, including the ABRF-NGS Phase II NGS Study on DNA Sequencing; the FDA’s Sequencing Quality Control Consortium (SEQC2); metagenomics standards efforts (ABRF, ATCC, Zymo, Metaquins), and the Epigenomics QC group of the SEQC2. The webinar will also review the computational methods for detection, validation, and implementation of these genomic measures.

More information on the GenomeWeb/ABRF 2017 Webinar Series is available here.

Scheduling conflict? You can still participate! All registrants will receive a link to view an on demand recording of the event.

Questions? Contact genomewebinars@genomeweb.com

ABRF Recognizes Volunteers During National Volunteer Week and Encourages All Members to Volunteer

Dear ABRF Members:

In recognition of National Volunteer Week, and on behalf of your Executive Board and Executive Director, Susan DeCourcey, I thank every one of our members for their continued commitment to the ABRF and all the volunteer work you do to support the advancement of core and research biotechnology laboratories. Your contributions of time, expertise and enthusiasm ensure the continued success of fulfilling on the ABRF’s mission, vision and goals. The work of the ABRF would not be possible without you!

If you are not currently active in the ABRF, one great way to network with your fellow ABRF members and to further develop your career is to participate in one of the various activities undertaken by your association.  Given the breadth of things we do, you will no doubt find something that aligns well with your interests.  Please look over the partial list of topics below. However, the best way to find something fulfilling is to send me an email indicating what you would be interested in doing with your colleagues. It can be related to any of the topics listed below or something developed organically. Also, the amount of time you choose to commit is totally up to you. You can participate in a discrete project with a defined end point, join a committee with a broader impact, or drive a research study.

Do any of these broad topics excite you?  Are there others?

  • Promote career development opportunities for our members
  • Develop educational opportunities, at and outside the annual meeting
  • Join with colleagues in your discipline to tackle common hurdles by joining a Research  Group
  • Be a voice for science advocacy
  • Build relationships between ABRF and like-minded organizations
  • Bring our journal JBT to the next level
  • Make the role of cores in Scientific Rigor and Reproducibility stronger and more prominent
  • Ask and answer technology-related questions through Research Group and Interest Network studies
  • Be a technical reviewer for journals
  • Strengthen and broaden ABRF-vendor relationships
  • Broaden our membership
  • Develop administrative resources
  • Keep your peers informed and engaged through social media and our website
  • Manage annual meeting logistics

I look forward to hearing from you.

Frances Weis-Garcia, ABRF President

frances.weis-garcia@my.abrf.org

 

Participate in the Core Rigor and Reproducibility Survey

The Association of Biomolecular Resource Facilities (ABRF) Committee on Core Rigor and Reproducibility (CCoRRe) is conducting a global worldwide survey to learn how scientific cores or other shared resource facilities generate transparent, rigorous and reproducible research data.  The results of this survey will help the committee implement its mission to support shared resource facilities and their commitment to reproducible research. To participate use this web link, https://www.surveymonkey.com/r/CCoRRe_2017.

We encourage you to forward this survey to other groups who may be interested in participating.  All responses will be anonymized. The survey results will be presented at the ABRF 2017 Annual Meeting in San Diego, March 25-28. We hope you can join us to discuss this important topic.