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

 

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 Next Webinar: Experimental and Computational Standards in Metagenomics

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This online seminar, part of the GenomeWeb/ABRF 2016 Webinar Series, will provide an overview of experimental and computational standards for metagenomics that have been developed as part of the Genomes in a Bottle standards consortium.

Please join Christopher Mason of Weill Cornell Medical College and Scott Tighe of the University of Vermont on June 7 at 1:00 pm EDT US for an overview of metagenomics standards that leverage a titrated mixture of known bacteria and eukaryotes. These have been sequenced across multiple next-generation sequencing platforms and characterized with ten different algorithms for taxonomic classification. The consortium members have also aggregated a set of 30 control samples for additional classification.

Dr. Mason and Dr. Tighe will report on a number of findings from the project, including the fact that sites of cross-algorithm agreement can lead to the most accurate estimate of the number of species from a new sample. They will also present an online resource for these tools, methods, and data sets; all of which are freely available. These methods and standards can help the many large-scale metagenomics projects around the world (and even some in space).

For more information and to register, please click HERE.

Metagenomics Research Group Gains White House Attention

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Recently the ABRF Metagenomics Research Group (MGRG) was represented  at the recent White House meeting on the National Microbiome Initiative by three members of the MGRG; Samantha Joye from the University  of Georgia, Nick Greenfield of One Codex, Rita Colwell of the University of Maryland.. While our  involvement with the NMI is small, we are working especially hard to be recognized as a leader in advancing the science and techniques of metagenomics and microbiome analysis. Represented through discussion with Nick Greenfield of One Codex, one of the Extreme Microbiome Project (XMP) corporate partners, the ABRF MGRG, the XMP, and Chris Mason’s Metasub International consortium were highlighted as well recognized study groups.  It should be noted that the MGRG is somewhat different from other ABRF groups because of the affiliation with the XMP which engages participants from corporate, academia, and government and members from around the world. The RG has approximately 25 members and growing.

The National Microbiome Initiative is exciting as the US government recognizes the magnitude of metagenomics and microbiome research. There has been over 100 million dollars dedicated by several US  agencies as well a dozens of other institutes dedicating additional resources to study all aspects of metagenomics research  from collection techniques to bioinformatics tools.

You can read more about this initiative here.

ABRF Executive Board Seeks Members as Consultants for Research Group Study Proposals

Under current ABRF policy, all Research Group Study Proposals are reviewed by the Executive Board prior to implementation. Over the past ten years, ABRF has expanded to include a wider array of technologies. As a result, situations may arise where the current EB members have limited backgrounds in a specific research technology area, making a comprehensive scientific review difficult. To ensure each Research Group Study Proposal receives a well-rounded review, the Executive Board would like a pool of consultants from which to solicit opinions during the approval process. All ABRF members interested in being added to the list can do so by sending an email to abrf@abrf.org with the following information:

Subject line:  RG Study Proposal Consulting List
Body of the email:
– Your name
– Organization
– Title
– General area of expertise (genomics, proteomics, light microscopy, flow, etc.)
– Specific area of expertise (NGS, MS, confocal microscopy, iCRISPR, etc.)

Thank you in advance for making yourself available on an RG Study Consultant list.

Sincerely,
ABRF Executive Board
William Hendrickson, President
Paula Turpen, Treasurer
Frances Weis-Garcia, President-Elect
Christopher Colangelo, Treasurer-Elect
Julie Auger
Allis Chien
Andrew Chitty
Peter Lopez

 

ABRF 2015 Program Highlights and Features

The ABRF 2015 Program Committee is proud to announce a few highlights for the 26th Annual Meeting being hosted in St. Louis, MO beginning on Saturday, March 28th.

Check out the pre-conference workshops! Don’t miss the opportunity to expand your knowledge and learn the latest from the experts. There is something for everybody! The first workshop, “Experimental Design and Sample Collection: Best Practices for Metabolomics and Proteomics”, will focus on identifying sample collection methods that may be more compatible for ‘omics technologies.

The second workshop, “Image Processing and Analysis with open Source FIJI/ImageJ”, will be highly interactive, with exercises following each topic. It will focus on workflows for specific biological assays with some detail on the underlying image processing steps.

And last but not least, the third workshop “Next Generation Sequencing of Microbial Communities”, will focus on many of the current strategies being applied to microbial community analysis in regards to project design, sequencing execution, and analysis utilizing QIIME. Remember to register early to ensure your seat!

Each of these workshops will be featured on Saturday, March 28th.  Be sure to register early as these events fill up quickly!  More information about these satellite workshops and details on registration can be found at http://conf.abrf.org/workshops.

 

The 2015 ABRF Conference Program also features 6 different tracks for attendees to follow or design their own itinerary.  Featured tracks include: Administrative, Imaging,       Proteomics, Genomics, MultiTrack, Research Group Topics.  Below are a few highlights from some of the featured tracks.  Be sure to visit our Conference website for more details and information on each offering.  http://conf.abrf.org/program

Administrative:

  • Cost analysis and rate setting
  • Lean enterprise practices in the operation of cores
  • Building a sustainable portfolio of core facilities
  • Inter-core partnerships
  • Trending core business challenges and how to overcome them.

Genomics:

  • Single-cell genomics
  • Fast and low cost NGS sample preparation
  • Metagenomics
  • Large-Scale RNA-Seq analysis, normalization and Interpretation
  • Gene Editing

The Metagenomics content of the program is strong and starts with our distinguished plenary speaker, Susannah Green Tringe, PhD, from the Joint Genome Institute.  There is also a metagenomics scientific session led by Samantha Joye, University of Georgia and a Metagenomics Research Group presentation.  The meeting content is complimented by Saturday’s Satellite Workshop: Next-Generation Sequencing of Microbial Communities: Strategies for Project Design, Execution and QIIME Analysis.

Imaging track:

  • Correlative Light and Electron Microscopy (CLEM)
  • Sample Clearing Methods
  • Challenging Sample Preparations
  • Watching Biology in Action – Live Cell Imaging
  • Live Cell Imaging Tips and Tools
  • New Horizons for Light Microscopy

The imaging track team is also excited about our plenary speaker, John Condeelis, a leader in the field of in vivo imaging. And we are thrilled that the ABRF award is going to go to John White and Brad Amos, who developed confocal microscopy. This last part is a bit tricky, because the award has not been officially announced, and I wouldn’t want the blog to be the first place.

Proteomics and Mass Spectrometry:

  • Antibody Discovery and Characterization
  • Top-down Sequencing of Intact Proteins
  • Single Cell Mass Spectrometry
  • Quantitative Proteomics
  • Metabolomics

We are also excited about our plenary speaker, Daniel Liebler, an internationally recognized expert in proteomics and cancer research.

Other Tracks of Interest:

  • Bioinformatics Cores as a Business
  • Use of Galaxy in multiple frameworks
  • Setting up References in a Clinical Lab
  • Antibody Validation for ChIP- Seq Applications
  • Education and Instrument Standardization in Flow Cytometry

 

The New ABRF’s Metagenomic Research Group (MGRG) and the Extreme Microbiome Project

By Scott Tighe, MGRG ChairMicrobiome Project

Metagenomics and microbiome studies seem to be popping up everywhere. In response to this rapidly growing field, the ABRF has organized a new research group called the Metagenomics Research Group, or MGRG, for short. The group is chaired by Scott Tighe from the University of Vermont who previously served as Chair of the NARG, FCRG, and coordinator for the ongoing NGS study. The current membership of the MGRG is impressive to say the least, with backgrounds in microbiology, genetics, bioinformatics, oceanography, climate research, and more.   ”With such a dynamic multidisciplinary field, I decided to go for the gusto and get the best members I could find; in fact a large percentage of the membership have been involved with microbiome studies for up to two decades.”  Said Scott.  The current  members include  Scott Tighe (Univ of Vermont), Kelley Thomas (UNH), Matt Settles (Univ of Idaho), Ken McGrath (AGRF-Brisbane Australia), Shawn Levy (Hudson Alpha), Nathan Biven (Univ of Missouri), Chris Mason (Weill Cornell), Darryl Reeves (Weill Cornell), Stefan Green (UIC), Natalia Reyero (Mississippi St.), Russ Carmical (BCM), Don Baldwin (Pathonomics), Samantha Joye (Univ of Georgia), Nadim Ajami (BCM), Ebrahim Afshinnekoo (Weill Cornell), Jodie Lee (ATCC) and Tim Hunter (Univ of Vermont),  is the executive board liaison.

Two projects are presently underway by the new MGRG.  The first is an effort to create a cellular-based bacterial standard and the second is the Extreme Microbiome Project (XMP). The development of the bacterial standard builds off of previous work by the nucleic acids research group (NARG) in 2013 which assembled an ethanol-fixed intact microbial community standard with known numbers and types of bacteria used for DNA extraction efficiency studies. Although the MGRG is assembling a similar standard, it will be more refined and include fewer microbial species of varying GC content and Class I genomes. Standards with Class II and Class III genomes will be developed at a later time. The development of the bacterial standard was encouraged by our collaborator Marc Salit from NIST, with input from Jodie Lee at the American Type Culture collection (ATCC).Metagenomics Blog Nov 2014 Continue reading

The ABRF Flow Cytometry Research Group (FCRG)

By:  Peter Lopez, ABRF FCRG

The ABRF Flow Cytometry Research Group was formed in 2012 as a result of the constant encouragement of Michelle Detwiler (then at Roswell Park) with input from Scott Tighe (Vermont Cancer Center). Peter Lopez (NYU Langone Medical Center), following up on his work while at Cytomation (manufacturer of the MoFlo cell sorter), was prompted by a poster at the ISAC’s “CYTO” international flow cytometry congress  by Monica DeLay (Cincinnati Children’s Hospital Medical Center), to come up with the idea for the multi-center study that seeks to answer the question—does cell sorting produce cells that are perturbed in any way? Monica had shown in her poster that dendritic cells purified by cell sorting may have compromised antigen presentation capabilities, depending on cell sorting conditions. With Scott’s help to craft the genomics side of the group’s study, the FCRG study was started. While Scott initially co-chaired the group with Peter, Monica is the co-chair at this time, and the group currently has 10 members, with many others in the flow cytometry community looking to join.

http://www.abrf.org/index.cfm/group.show/FlowCytometryResearchGroup%28FCRG%29.76.htm

Surprisingly, in the long history of mainstream flow cytometry and cell sorting , vanishingly few papers have addressed the condition of cells after cell sorting. Investigators were just happy to get viable cells out of the process (which is most often the case), and then followed up with downstream applications using these sorted cells. Cell sorting condition tailoring or guidelines do exist, but are rarely published. Word-of-mouth best-practice scenarios exist that most core labs follow, such as if more than half the cells are dead before sorting, the resulting sorted cells often had a lower overall viability, even when  viability markers are used to ensure only sorting viable cells. Continue reading