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
REGISTER

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.

Get Noticed at ABRF 2017!

The ABRF 2017 Program Committee is looking for your cool and exciting images to be displayed throughout the ABRF 2017 meeting space at the Town and Country Resort & Convention Center in San Diego, CA this March.

If your image is selected, it will be professionally printed (16” X 20”) and mounted.  As an added incentive for submitting, after the ABRF 2017 Annual Meeting your mounted prints will be mailed to your lab compliments of the ABRF!

Technical details:

  • Resolution 300 DPI at 16” X 20”
  • CMYK production, all color specifications will be matched to the closest 4-color process. Images without call-outs will be produced using the CMYK values contained in the digital file.

Formats:

  • Photoshop (.psd)
  • Encapsulated Postscript (.eps)
  • TIFF (.tif )
  • JPEG (.jpg)

Please email images by February 20 to richard.cole@health.ny.gov.

*If images are too large for email, contact Rich Cole for Dropbox instructions.

 

Take FASEB’s Shared Research Resources Survey and share your perspective as a user or provider!

The Federation of American Societies for Experimental Biology (FASEB) wants to learn about your experiences with shared research resources. Please complete this survey by March 2, 2017.

The questions in this 10-15 minutes survey focus on the following topics: (1) resource utilization and unmet needs; (2) the role of facilities in providing access to resources; (3) sources of funding and support for resources; (4) careers in resource provision and development as well as training on best practices. Your feedback will help inform FASEB’s policy positions and recommendations.

Please share this survey link widely with other biological researchers! FASEB is collecting responses from resource users and providers in the US. Survey link: http://www.surveygizmo.com/s3/3244931/FASEB-s-Shared-Research-Resources-Survey

ABRF Announces Executive Board Election Results

ABRF Members turned out in record numbers to elect two new members for the Executive Board.

Rich Cole, Research Scientist V, Director, Advanced Light Microscopy & Image Analysis Core, Wadsworth Center and Research Assistant Professor, Department of Biomedical Sciences, School of Public Health State University of New York and Nancy C. Fisher, PhD, Director, UNC Flow Cytometry Core Facility and Professor of Microbiology & Immunology, University of North Carolina at Chapel Hill were elected to serve a term of four (4) years on the Executive Board of ABRF. Their terms will commence immediately following the ABRF 2017 Annual Meeting in San Diego, California. Congratulations, Rich and Nancy!

The terms of Bill Hendrickson, President, and Paula Turpen, Treasurer, will conclude after the ABRF 2017 Annual Meeting. Thank you Bill and Paula for your outstanding leadership, hard work, and dedicated service to the ABRF and its membership.

A ‘New Nerds’ Insight on NERLSCD

Written by Jeffery A. Nelson, Instrumentation Specialist
Harvard University, Bauer Flow Cytometry Core Facility

Although I’ve been in the field of Flow Cytometry for a while, I am new to the Boston area and for the first time, had the opportunity to attend the Northeast Regional Life Sciences Core Directors meeting (NERLSCD or NERD). Unlike most of the meetings I attend, which focus mainly on flow cytometry and imaging, the NERLSCD meeting was multidisciplinary, covering a wide range of specialties, including; Flow Cytometry, Imaging, Genomics, Proteomics,14615825_1199490510114686_6519811918853205566_o  Bioinformatics, High Throughput Screening, Antibodies and Administration. The meeting format consisted of; numerous pre-meeting satellite events prior to the opening reception (various meetings and tours of local core facilities), excellent daily keynote speakers, followed by break-out sessions covering a wide variety of ‘Technical Tracks’ and finally a poster session and vendor / colleague networking opportunity to finish out the evening.
Prior to the opening reception, since our core facility was one of the host facilities giving the tour, I attended the New England Cytometry Users Group meeting (another local scientific meeting that coincided perfectly with the NERD meeting schedule). Once the NERLSCD meeting started, I particularly thought the keynote speakers were very good each day and I loved the 14753444_1199487126781691_5931631331088966043_odiverse Technical Track sessions! Since I work in a flow cytometry core facility helping researchers optimize their flow experiments, I thought it was extremely cool to see how the cells I sort for someone could be used in the latest downstream technologies. I also like keeping current with some of the new administrative and regulatory challenges that face various core facilities so enjoyed hearing from core leaders and administrators. I also really enjoyed the poster session where I got to see a wide variety of research, both within and outside my primary field of interest. Lastly, I always enjoy visiting the vendor booths to keep current with the latest technology. Specifically, I loved the vendor booth experience at the NERD meeting, because I learned about some of the technologies that researchers are looking to use in conjunction with flow cytometry and learned a lot!

Overall, I think the NERD meeting was awesome! I think the wonderfully diverse, but correlated technologies represented at the NERD meeting allowed me to see the whole picture. Not only did I get to see how flow cytometry fits in with the newest downstream technologies but also administratively within an institution. By seeing what users are doing downstream of sorting, I am able to better optimize their sorting experience and to provide suggestions for their sort to better accommodate their downstream goals.
Finally, I want to end with a funny meeting experience. On the first day, I arrived at the hotel and was immediately greeted by a nice lady. I was so impressed with the personal greeting and was wondering how she knew my name. I thought then she would give me my name tag and direct me to the meeting, but instead, she said; “The bus is waiting for you, so whenever you are ready you can start the tour” – I guess some other guy with my name was giving a Boston tour. Things were more realistic when I found the NERD staff, who were also very friendly but not as overwhelmingly excited as the first lady I met and I had to give them my name-LOL. So, if I wasn’t so new to Boston, the NERD meeting could have also given me the opportunity to add ‘giving a Boston tour’ to my resume!

November 15 Webinar: The ABRF NGS Study, Phase 2: DNA Sequencing Platforms

 

 

Date: November 15th
Time:
1:00 pm ET
REGISTER

 

Don Baldwin
Co Founder,
MSK,dx LLC

Christopher Mason
Associate Professor,
Weill Cornell Medical College

Scott Tighe
Manager, Massively Parallel Sequencing Facility, University of Vermont Cancer Center

 

 

 

 

 

 

 

 

 

This webinar will provide an update on Phase 2 of the ongoing ABRF Next Generation Sequencing Study, an effort to evaluate the performance of NGS platforms and to identify optimal methods and best practices. Phase 1 of the study focused on RNA sequencing, while Phase 2 is focusing on genomic DNA samples.

In particular, Phase 2 of the ABRF NGS study aims to address three questions applicable to most technologies being used for deep sequencing of genomic DNA: 1) for a typical combination of sample preparation method and sequencing instrument (a “platform”), what levels of intra- and inter-laboratory variation should be expected; 2) how is a platform affected by DNA exposed to formalin fixation ; and 3) how is a platform affected by DNA that contains a skewed nucleotide composition? Sequencing for the study is being performed by independent academic service laboratories not affiliated with reagent or instrument vendors. The use of well-characterized, publicly available reference samples and uniform protocols within each platform will generate baseline data sets against which alternative methods, hardware upgrades, and any sequencing lab’s performance can be compared.

 

 

MWACD from a Marketer’s Eye: Keep the Core Tours Coming

A group of MWACD attendees head out to the core tours to kickoff the conference.

A group of MWACD attendees head out to the core tours to kickoff the conference.

Since becoming an ABRF member in 2013, I continue to be amazed at how different each experience is at the national and chapter conferences. As the marketing specialist for the Biomedical Research Core Facilities at the University of Michigan, I’m a member of the Midwest Association of Core Directors (MWACD). A few days out from #MWACD ’16, and I am still working through everything I learned in Cincinnati.

Confession: Cincinnati is my hometown, so I was even more excited than usual to being able to share one of my favorite cities with coworkers. The first item on our agenda was of course to introduce my Michiganders to one of my favorite local haunts: Skyline Chili!

After a great lunch, we arrived in the host hotel downtown and the real party started. Our gracious hosts at Cincinnati Children’s Hospital went above and beyond in every aspect of the event.

The conference kicked off with high energy as we toured the cores at Cincinnati Children’s. This is always one of my favorite parts of the annual MWACD meeting. Every year, we learn so much by having  the opportunity to meet with core facilities around the Midwest who are dealing with similar issues, challenges and successes that we have here at Michigan.
20161005_Nikon A1R upright multi-photonI’ve been with the Biomedical Research Core Facilities at U-M for five years, and the breadth and scope of what it takes to make a core facility successful – depending on facility and institution – never ceases to amaze me.
Cincinnati is certainly no exception. Seeing firsthand how the cores at Cincinnati Children’s collaborate through their divisions, learning about their workflow processes, and seeing some of their impressive equipment generated a lot of discussion throughout the conference.

The Midwest Association of Core Directors may cover only one region of the United States, but the variety of sizes, service offerings, financial models, and solutions that work for a many different organizations and universities is invaluable to hear about.

I can’t recommend the core tours enough. The opportunity to learn about other institution’s service contracts, relationships with vendors, most-used equipment, interactions with customers, is invaluable. The openness and collaboration between members is what you’d expect from passionate professionals focused on research and knowledge. Everyone seems to enjoy hearing about one another’s experience, and more importantly, everyone wants to share and help others succeed.2016_10_CC_BMR_Facility

I had the great fortune of touring multiple facilities at Cincinnati Children’s, including:

  • Confocal Microscopy Core (a Nikon Center of Excellence),
  • Flow Cytometry Core,
  • DNA Sequencing and Genotyping Facility,
  • NMR-Based Metabolomics Core, and
  • Transgenic Animal and Genome Editing Core Facility.

Oftentimes, it can feel like core facilities are isolated and on their own at their home institutions. We aren’t like other departments or centers or units. We don’t have the same goals as administrators for faculty or student-focused groups, or corporations. ABRF and its chapter organizations serve as the best reminder that we are not alone, and the unique research and business of cores can be found across the world.

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Claudius Mundoma, Ph.D., Director of the Physical Biochemistry Facility, at Florida State University, gives the keynote Friday morning on establishing core facilities in Africa, another highlight of the conference for me.

You can see more photos from MWACD 2016 on the ABRF Facebook page. Fellow MWACD attendees, what was your favorite part? Share your story in the comments, or email blog@abrf.org.

ABRF Announces November 1 Webinar: CRISPR/Cas9 Editing in Human Cell Lines and Animal Models

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This webinar will outline new strategies for genome editing in mammalian cells using CRISPR/Cas9, with talks focused on point mutation repair in human cell lines and the design of knock-in animal models.

Dr. Eric Kmiec Director, Gene Editing Institute, Christiana Care Health System’s Helen F. Graham Cancer Institute & Research Center

 Dr. CB Gurumurthy Director, Transgenic Core Facility, University of Nebraska Medical Center

During this webcast, Dr. Eric Kmiec will discuss a new approach to the correction of point mutations using single-stranded oligonucleotides and a partially synthetic form of CRISPR/ Cas9, a ribonucleotideprotein (RNP) complex. The experimental design, including the process of RNP assembly and the workflow, will be presented.

Dr. Kmiec will share details of a case study in which a point mutation in an integrated copy of the mutated eGFP gene in a human cell line is corrected using this approach, and a reaction pathway that is likely distinct from that of homology-directed repair. The use of short single-stranded oligonucleotides may be a strategy of choice when the desired endpoint is correction of point mutations in chromosomal genes.

Our second speaker, Dr. CB Gurumurthy, will discuss the latest trends and CRISPR tools available for animal genome editing, with a particular emphasis on strategies for increasing the homology-directed repair mechanism to enable insertion of longer sequences at the Cas9 cut sites. A few examples of designing knock-in animal models and the workflow of generating the models will be presented.

This webinar is the second on gene editing under the GenomeWeb/ABRF 2016 Webinar Series. The first webinar in the series is available on demand here.