ABRF Announces September 13 Webinar: Advancing Clinical Metagenomics Via CLIA/CAP Accreditation



Clinical metagenomics is still in its infancy, and maturation of the field requires an appropriate accreditation program to ensure quality testing and patient safety. Please join J. Russ Carmical, PhD, Assistant Professor, Baylor College of Medicine & Sequencing Director, Alkek Center for Metagenomics & Microbiome Research and Nadim J. Ajami, PhD, Assistant Professor, Alkek Center for Metagenomics & Microbiome Research on September 13 at 1:00 pm ET for an overview of how one metagenomics lab — the Alkek Center for Metagenomics & Microbiome Research (CMMR) at Baylor College of Medicine — is pursuing CLIA/CAP accreditation.


J. Russ Carmical PhD


Nadim J. Ajami PhD

An integral component of the accreditation process is proficiency testing (PT), which utilizes pre-established criteria, or measurement standards, for inter-laboratory comparisons. To date, commercially available metagenomic PT offerings are not available, which puts the burden on individual laboratories to develop an alternative assessment. In order to address the need for PT in metagenomics, the CMMR utilized a combination of previously sequenced samples (e.g. “blinded generous donor samples”), synthetic DNA standards, and mock communities to evaluate microbial DNA extraction, library preparation, and sequencing. In addition to developing PT specific to metagenomic analyses, the CMMR developed a quality system with standard operation procedures (SOPs), competency testing, a laboratory information management system (LIMS), and asset management software in compliance with CLIA/CAP standards. This webinar is the second on metagenomics under the GenomeWeb/ABRF 2016 Webinar Series. The first webinar in the series is available on demand here.

Trifecta! Registration now open for three ABRF Chapters.

The Western Association of Core Directors (WACD), Midwest Association for Core Directors (MWACD) and Northeast Regional Life Sciences Core Directors (NERLSCD) officially announce registration for their meetings is now OPEN!

Each chapter has something to offer.  From Keynote lectures on Zika, to  sessions on developing strong scientific staff and learning about core facility interactions each conference has something to offer for everyone in scientific and administrative positions.  Seats are hot, topics are lively, and colleagues are friendly.  Register soon before prices go up!  See the details and conference agenda below.

We hope to see you at an ABRF chapter near you!


6th annual WACD Conference

Sustainable Core Facilities Through Science and Service

Sept 22- Sept 23, 2016
Alexandria Conference Center in Torrey Pines, Ca – near the UC San Diego campus

Register Now!
See the Conference Schedule


MWACDOctober 5-7, 2016

Kingsgate Marriott! in Cincinnati, OH

 2016 Meeting Information

Register Now


Reflections on SEASR

Written by Robert Carnahan and David Blum

The fourth annual meeting of the Southeastern Association of Shared Resources (SEASR) was held at the Emory Conference Center in Atlanta June 22-24, 2016.  There was a total of 133 registrants including academic, government and industrial attendees.  The attendees represented a wide range of institutions across the Southeast including Emory University, Vanderbilt University, the University of Georgia, the University of Florida, the University of Tennessee, Georgia Tech, Morehouse School of Medicine and others.

The conference started out with tours of the Centers for Disease Control and Prevention Museum followed by the opening reception and bowling tournament at Wisteria Lanes in the Emory Conference Center with both being big hits among attendees.  On Thursday, June 23rd, the opening keynote focused on problem-solving strategies and it led directly into a 90 minute hands-on problem-solving workshop.  Both sessions were led by Joe Rando (Vanderbilt).   Friday, June 24th began with a double-header keynote with 2 sessions focused on crisis management using the Ebola epidemic as the theme. Aneesh Mehta, one of the attending physicians at Emory discussed how teamwork was used to manage the treatment of several US based infected individuals.  This session was followed by a joint session by Erika James, Dean of the Emory-Goizueta Business School and Inger Damon, Director of the CDC’s Division of High-Consequence Pathogens and Pathology.  They presented on “Leading Under Pressure” which continued the Ebola theme and focused on leadership qualities.

The significant focus on lab management continued throughout each day of the meeting with breakouts sessions on topics such as managing staff in lean times, writing a business plan, “speaking business”, and a discussion of the role of Cores in  education, training and outreach.   Each day also included vendor-sponsored sessions with workshops by Swift Bioscience, Agilent and HTG Molecular, Pall-Forte-Bio and 3Scan.  The conference concluded with a workshop of Lean principles and included using LEAN principles in a hands-on activity to make paper airplanes as a group.  The initial survey results have been very positive and we look forward to seeing everybody next year in Tampa!

Meet FASEB’s New President, Hudson Freeze


Hudson H. Freeze, PhD

On July 1, the Federation of American Societies for Experimental Biology (FASEB) welcomed its new President, Hudson H. Freeze, PhD. Dr. Freeze is Professor of Glycobiology and Director of the Human Genetics Program at the Sanford-Burnham-Prebys Medical Discovery Institute in La Jolla.

“I am honored to lead FASEB—the policy and advocacy voice of 125,000 scientists. Today, we have extraordinary opportunities to communicate with the most receptive Congress in 15 years. Our message has connected, we’ve turned a corner, but now it’s our responsibility to speak out even more strongly. We must advocate for research because we know it benefits all citizens in all districts,” Dr. Freeze said.

For the last 20 years, Freeze’s research has focused on the identification and understanding of Congenital Disorders of Glycosylation (CDGs), genetic errors in the way sugars attach to proteins and lipids. He contributed to the discovery of 18 of the more than 110 known CDGs. Dr. Freeze collaborates closely with physicians, families, and their support organizations and regularly consults on cases while still tracking the genetic basis of multiple patients with unknown glycosylation defects.

Beginning with his postdoctoral work, Freeze has earned nearly 40 years of continuous funding from the National Institutes of Health (NIH). As FASEB President, he will lead initiatives to advocate for increased funding for NIH and other federal agencies that fund scientific research.

“The most important thing is to get it [funding] for NIH, which is the crown jewel of federal agencies,” Dr. Freeze told San Diego’s KUSI. “We hear a lot of talk about ‘Let’s make America great again,’ but, in fact, in medical research, we are great. What we have to do is sustain that,” said Freeze.

Among his priorities during his year as FASEB president is increasing communication with FASEB member societies. “One thing is fundamental: FASEB represents scientists. From postdocs to Society leaders, I want us to have an open dialog—scientist to scientist—about how FASEB can better serve its members and the scientific community,” Freeze said.

Prior to his election as President, Dr. Freeze served as FASEB’s Vice President for Science Policy. He is a Past President of the Society for Glycobiology and its first representative to the FASEB Board of Directors. Dr. Freeze is also a member of the American Society for Biochemistry and Molecular Biology (ASBMB) and The American Society for Human Genetics.

In 2013, Dr. Freeze shared the Golden Goose Award  with microbiologist Thomas Brock, PhD, for identifying Thermus aquaticus (Taq), an “extremophile” bacteria capable of thriving in extreme heat. Freeze was an undergraduate research assistant in 1966 when he and Brock found Taq in the hot springs of Yellowstone National Park. By identifying an organism with DNA machinery that could survive near-boiling temperatures, their discovery opened the door to the development of polymerase chain reaction and other technologies that would revolutionize biomedical research.

This introduction to science led Dr. Freeze to advocate tirelessly on behalf of basic research. “New cures for devastating diseases and exciting advances in medicine are all rooted in federally funded basic research,” Dr. Freeze wrote in a San Diego Union-Tribune op-ed after his Golden Goose win. “Today’s benefits came from yesterday’s investment. Tomorrow’s cures depend on today’s decisions.”

To help ensure that message gets national attention, he urges scientists to engage with public audiences as often as possible. To that end, Freeze worked with ASBMB to organize an exhibition of BioArt winning images in a brewery during the Experimental Biology meeting.

As President of FASEB, Freeze aims to ensure that policymakers hear the views of researchers and that researchers recognize those legislators who are champions for science. “Congressional leaders assured us that the $2billion increase for NIH funding in 2016 will not be a one hit wonder,” said Freeze. “Let’s help keep that pledge on track with continuing advocacy for greater investment in research. Go make a difference; we can make a difference,” he said.

FASEB is made up of 30 scientific member societies, representing over 125,000 researchers from around the world. ABRF is a member society of FASEB, and ABRF’s members receive the full benefits of FASEB membership.

Strengthening and Promoting the ABRF LMRG network at the FOM2016 meeting

By Erika (Tse-Luen) Wee, ABRF Light Microscopy Research Group (LMRG) Chair, McGill University

Recently, Erika (Tse-Luen) Wee, ABRF Light Microscopy Research Group (LMRG) Chair, traveled to a conference in Taipei, Taiwan.  There, she presented a poster on research efforts being made within her ABRF research group.  In turn, she found and generated interest in what it means to be an ABRF member.  Below is her story.

The Focus on Microscopy 2016 Conferencewas recently held in Taipei, Taiwan, and organized by Prof. G.J. (Fred) Brakenhoff from the University of Amsterdam, and Prof. Fu-Jen Kao from the National Yang-Ming University. This annual conference series was started in 1988 by Andres Kriete in Giessen, Germany, and has over the years welcomed a growing number of researchers, principal investigators, core facilities managers, and exhibitors from all over the world.

The theme of the meeting this year was brain imaging, as well as a special focus on correlated light and electron microscopy. Other topics included super-resolution, fluorescence probes, light sheet, image processing/analysis, new developments in confocal, non-linear optics and lasers, all of which are hot topics and in high demand in light microscopy core facilities today.

The focus of the FOM2016 meeting had strong relevance to current LMRG studies. Being the current LMRG Chair, I had a poster presentation on the current LMRG study (#3), as well as the previous two studies conducted by the LMRG from previous years. The poster presentation was very well received, and stimulated a lot of discussion about LMRG and most importantly, the ABRF.Untitled.1

These interactions provided a great opportunity to increase awareness of the ABRF and to demonstrate how the Association provides a forum for networking and sharing. I was very surprised to see many Canadians and Australians attending the conference alongside the more common European attendants and microscopy vendors from Asia and Europe. It was a very nice opportunity to network with microscopists from around the world, and to promote membership with the ABRF in an effort to bridge the gap between Asia, Europe and the US communities. Several individuals at the conference, including participants from Singapore, Italy, Japan, and Germany expressed their interests in participating in the LMRG study and joining the ABRF, and we very much look forward to future discussions.

One of the main highlights was the invitation talk “Challenges and Tradeoffs in Modern Fluorescence Imaging Methods” from Eric Betzig, the Nobel Prize Winner in 2014. This is one of the best presentations I have attended recently; it was truly insightful and educational. The main focus of his talk was to compare the strengths and weaknesses of different microscopy modalities as applied to different biological problems and how to avoid artifacts caused by labeling, fixation, specimen motion, and image processing. This presentation content echoed perfectly with the LMRG mission: “To promote scientific exchange between researchers, define & improve relative testing standards that will assist core managers and users in the maintaining their microscopes for optimal operation”.

UntitledIn the end, I am very thrilled to see that FOM2016 had taken place in my home town of Taipei, Taiwan, and very honored to be able to represent ABRF here. Taipei is one of the political, economic, and cultural hubs of Asia. As a global city, it has great dynamics, diversity, and insightfulness in regards to culture, politics, high-end technologies, and impressive research programs. And of course, the food was amazing!

This trip would not have been possible without the generous support of ABRF and McGill University.  I would like to thank ABRF Executive Board members Peter Lopez and Frances Weis-Garcia for their amazing assistance and support of LMRG, and I also would like to thank Claire Brown and Rich Cole for their mentorship and guidance.

ABRF Announces August 4 Webinar: A Hypothesis-Driven Lean Management Tool for Core Labs



Jay W. Fox, Professor of Microbiology, Immunology & Cancer Biology, University of Virginia School of Medicine

Sean Jackson, Chief Information Officer, University of Virginia School of Medicine & Physicians Group

This online seminar will provide an overview of A3 problem solving, a lean management tool that can be used to improve efficiencies in life science core labs. 

Developing a culture of continuous improvement in the core lab involves winning the hearts and minds of researchers and administrators and aligning their efforts around delivering value to the customer as quickly, cost-effectively, and flawlessly as possible. Along the way, performance gaps present themselves. The A3 lean approach — so-called because it limits all documentation to a single piece of 11 x 17 inch, or A3, paper — offers a consistent and effective means by which to address these gaps.

Using a hypothesis-driven approach, the A3 tool guides inquiry into the root cause of performance gaps, and the identification of proposed countermeasures and targets to improve. It also serves as a means by which to monitor progress toward goals and share results with others so that all may benefit from what has been learned.

Please join Jay W. Fox, Professor of Microbiology, Immunology & Cancer Biology, University of Virginia School of Medicine and Sean Jackson, Chief Information Officer, University of Virginia School of Medicine & Physicians Group on August 4 at 11:00 am EDT for this webinar, during which they will describe how the A3 tool works, and how your organization can benefit from its adoption and use.


ABRF Announces Next Webinar: The Emergence of Gene Editing


This online seminar, part of the GenomeWeb/ABRF 2016 Webinar Series, will cover the history of gene editing methods like TALENs and CRISPR/Cas and provide an overview of various gene editing technologies.

Please join Eric Kmiec, Ph.D., of Christiana Care Health System’s Helen F. Graham Cancer Center & Research Institute and Channabasavaiah Gurumurthy of the University of Nebraska Medical Center July 19 at 1:00 pm EDT US for their discussion on some of the origins of gene editing and how the field emerged from a series of basic science observations to the dynamic fast-paced field dominating research journals today.

Kmiec and Gurumurthy will also discuss some of the factors that can influence the frequency and efficacy with which gene editing takes place, including cell cycle progression, and the introduction of specific double-strand breaks at specified sites relative to the target.

The second part of the webinar will focus on latest developments in genome editing technologies: specifically, different genome editing technologies will be compared with a special emphasis on the CRISPR/Cas system.

For more information and to register, please click HERE.

Educating Johannesburg on the Benefits of Core Facilities in Research.


This post was adapted from a Florida State University Press Release.

Dr. Claudius Mundoma, from Florida State University, Institute of Molecular Biophysics, and an ABRF Member, was awarded a fellowship by the Carnegie African Diaspora Fellowship Program to travel to South Africa to work with University of Johannesburg and Profs. Charles Mbohwa and Willie Oldewage on “Sharing Research Equipment – Towards a Sustainable Model of Interdisciplinary Collaborative Research”.  This fellowship allows for Mundoma to work with researchers in Africa and educate them with his intimate knowledge on how core facilities in particular can benefit interdisciplinary research and collaboration.  Especially with limited resources and funding for research available.


Dr. Mundoma teaching to students in Johannesburg, South Africa.

Our recognition that scientific research resources are not only the heart of discovery and productivity but also the catalyst to innovation underpins this effort. Equipment sharing is a common practice but there is need for an understanding of the benefits and barriers to greater equipment sharing as a response to reduced capital funding. To maintain economic competitiveness, it is critical to sustain gains in scientific investments made over the past decade through efficient use of available resources.  It is with this focus that Dr. Claudius Mundoma is collaborating with the University of Johannesburg to come up with a comprehensive strategy to managing the research assets at University of Johannesburg that will focus on efficiency as a very first step towards innovation.

The need is addressed in three ways:

(1) By equipment-sharing and better scientific resource management principles we strengthen Africa’s collaboration networks. By creating a searchable equipment portal and a sharing management system, the university can be able to stretch scarce research funds to serve a wider research community. The sharing portal brings visibility to research capabilities across the university and enhances efficiency by optimizing redundancies and increasing equipment access. It is also important to note that not all equipment is shareable.

P1010735(1) 2) Centralization has advantages of economies of scale, which allows the university to better manage the full life cycle cost of its equipment, i.e., from acquisition to retirement or re-purposing.


Learning the ‘ropes’ on equipment.

(3) Providing management training options for the equipment managers through adoption of best practices and joining professional organizations. Equipment managers should be able to cross-train on various instruments and increase their value to the university community thus extending training to graduate students and faculty in their departments.

The University of Johannesburg project is one of 57 projects that will pair African Diaspora scholars with higher education institutions in Africa to collaborate on curriculum co-development, research, graduate teaching, training and mentoring activities.  Dr. Claudius Mundoma is one of 59 African Diaspora scholars who have been awarded fellowships to travel to Africa beginning in May 2016 to conduct a wide range of projects across disciplines, from agroforestry to e-learning modules for nursing, and from ethnomusicology to military mental health. The program has now selected and approved a total of 169 Fellows since its inception in 2013.


Enjoying an afternoon high tea in the break room.

The Carnegie African Diaspora Fellowship program facilitates engagement between scholars born in Africa who are now based in the United States or Canada and scholars in Africa on mutually beneficial academic activities.  The Advisory Council selected forty-one African universities to host the Fellows, based on collaborative project proposals submitted by faculty members and administrators at the African universities, to meet specific needs at their universities. This innovative program is managed by the Institute of International Education (IIE) in collaboration with United State International University-Africa (USIU-Africa) in Nairobi, through Dr. Paul Tiyambe Zeleza, who chairs the Advisory Council, and is funded by the Carnegie Corporation of New York.


MAD SSCi 2016: The Corpse in the Conservatory

-Written by Roxann Ashworth, MAD SSCi Secretary, JHU

The fourth annual MAD SSCi conference was held at the beautiful William Pitt Union on the urban campus of the University of Pittsburgh.  Pittsburgh welcomed 95 delegates, representing BioNano, Biorepository, Flow Cytometry, Imaging and Molecular Technology facilities.  Core directors, administrators, managers and staff were able to interact and form or renew fruitful relationships that will lead to future collaboration.  We were very happy to be joined by the ABRF Executive Director Susan DeCourcey.

“Wonderful opportunity to meet and interact with colleagues working in Core Facilities.  I enjoyed the Quality Assurance Workshop which generated good discussions.  The presentations on Biorepositories were informative and created topics for us to discuss in our Core.”  –Lori Kelly, U. Pitt, New Core Director, First Time Attendee

Accreditation: CMU Field Robotics Center

Accreditation: CMU Field Robotics Center

Attendees from universities and institutions around the Mid-Atlantic, and as far away as Texas and Tennessee, kicked off the conference with a reception at the Phipps Conservatory and a talk from Dr. Alan Waggoner of Carnegie Mellon University.  Dr. Waggoner described the development of a roving biosensor and fluorescent dyes that may one day be deployed to look for life on Mars.  Earthbound testing took place in the hostile, but striking Atacama Desert, Chile.

Romero – thankfully not a scratch and sniff picture!

Romero – thankfully not a scratch and sniff picture!


The highlight of the evening was the once in a lifetime opportunity to see (and smell) the blossoming of the Corpse Flower known as “Romero.”  When we walked in that evening, we all thought it was pretty cool, and maybe noticed a slight aroma.  When we walked out at the end of the evening past the now fully open flower, we all understood how the plant got its name!

Thursday and Friday brought presentations on topics ranging from A(dministration) to Z(ika).

A Dynamic David Dilts Acceditation: Kunjie Hua, UNC

A Dynamic David Dilts Acceditation: Kunjie Hua, UNC




David Dilts of OHSU provided an entertaining and thought provoking talk on how to define the value that our core facilities provide to our investigators and the universities we serve.  Our closing talk was a fascinating look at the possible mechanisms and explanations for why the Zika virus, which has been around since 1947, has suddenly become a devastating disease now that it has reached South America.  Between these keynotes, delegates had the opportunity to attend vendor workshops on a variety of topics, go to concurrent sessions on topics as diverse as Biorepositories, Genome Editing, Light Sheet Microscopy and Project management, and to pick each other’s brains for solutions to common problems in the “What’s your Core?” round table discussion.


Gene Editing Session Accreditation: Roxann Ashworth, JHU

Gene Editing Session
Accreditation: Roxann Ashworth, JHU

Lans Taylor gave an interesting overview of how the University of Pittsburgh is integrating systems biology and 3D cultured organs on a chip to develop methods for cheaper and more efficient drug discovery. Rebecca Davies placed the provision of QA training and infrastructure at the center of assuring accurate and repeatable data.  She argued for the development of best practices within the research community.  Describing the collaborative, centralized approach she has championed at the University of Minnesota, Dr. Davies gave our attendees much to discuss regarding the role of core facilities in assuring reproducibility.

“The conference felt personal due to the size and background and those that attended…[The] other managers…were insightful with how to handle instrument usage, advertisements, etc. Overall a good conference to attend, especially being new to managing a facility.”  — Greg Donohoe, Ph.D., BioNano Research Facilities Manager, Shared Research Facilities, West Virginia University

Corey Lipchick Accreditation: Roxann Ashworth, JHU

Corey Lipchick
Accreditation: Roxann Ashworth, JHU

Corey Lipchik from the National Surgical Adjuvant Breast and Bowel Project, Allegheny Health Network won the poster travel award for: FFPE Tissue and the HTG Oncology Biomarker Panel: a Low-Input, Extraction-Free Gene Expression Pilot Study.  He will receive $500 to attend either the national meeting or next year’s MAD SSCi meeting.  Michael Chua of the UNC Michael Hooker Microscopy Core Facility won a free ABRF membership kindly donated by ABRF Ambassadors.

“[The MAD SSCi conference is] small enough and regional to make the networking particularly fruitful.”— Paul Wood, University of Pittsburgh

Next year MAD SSCi 2017 will be held in Morgantown, WV hosted by West Virginia University.  We have many ideas for content, and plan to develop more staff focused technical and networking sessions that will compliment the excellent administrative and management focus of recent years.  Watch our website to see what we are up to!  Our new President, Trina Wafle, has some exciting new ideas and will continue our tradition of wonderful entertainment and fabulous science!

JBT Publishes a Special Issue on Core Management


This issue of the Journal of Biomolecular Techniques is devoted to the business of cores, from developing performance standards and metrics for evaluating core performance to implementing product lifecycle management for core operation improvement, all while creating disaster response and business continuity plans. We thank Ron Orlando, JBT Editor-in-Chief, and the ABRF Executive Board for supporting this special issue of JBT. It is our hope that readers will find these articles useful for developing approaches that will benefit their cores and institutions.