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A newly certified AIRR-compliant software tool: The Immcantation Framework

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The AIRR Community is excited to announce that the Immcantation Framework has been certified as compliant with the AIRR-C v1.0 standard for AIRR-Seq software tools.

In an effort to enable rigorous and reproducible immune repertoire research at the largest scale possible, the AIRR-C Software Working Group has established a standard to validate software tools using the AIRR-C Standards and meeting a series of interoperability and quality criteria. Developers interested in certifying their tools should complete the checklist and submit it to the AIRR-C Software Working Group for evaluation and ratification by its members.

More details can be found at the website AIRR Software WG – Guidance for AIRR Software Tools.

All compliant tools will be issued a badge and listed on the website AIRR Software WG – List of Tools Certified as Compliant.

Successful AIRR Community Meeting V

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The fifth AIRR Community meeting (#AIRRC5) was held virtually Dec 8–10, 2020. The theme of this meeting was “Zooming in to the AIRR Community” connecting the global AIRR research community despite the pandemic for a series of Working Group & Sub-committee presentations, scientific sessions, interactive poster sessions, software tool demonstrations and networking events.

AIRR Community meetings are the premier event for research on adaptive immune-receptor repertoires. They are also the primary location where the AIRR-Community’s Working Groups and Sub-committees come together in one location to discuss how to push standardization in AIRR-sequencing (AIRR-seq) data and analysis forward.  All video recordings can be found here https://www.youtube.com/airrcommunity. All presentations can be found in the AIRR Community Resources section of the website. 

Just as the biology of AIRR is high-dimensional, this meeting’s success was as well!  We gathered some of the numbers that best describe the success of the #AIRRC5 meeting.

  • 1 Keynote speaker: Ignacio Sanz (Emory University School of Medicine, USA)
  • 3 Basic Science Presentations, 3 Biomedical Science Presentations
  • Attendees from 18 countries and 6 continents
  • 161 Registrants 
  • 5 Sponsors 
  • 6 Invited Speakers 
  • 2 Judging Panels 
  • 4 Short Talk Presenters 
  • 28 Poster Presenters 
  • 4 Software Demonstrators 
  • 9 Moderators 
  • 19 Community Presenters 
  • This was the second time a twitter hashtag was used for an AIRR Community Meeting (#AIRRV)
  • We achieved the milestone of more than 100 subscribers for the AIRRC YouTube channel thus enabling a custom YouTube URL: https://www.youtube.com/airrcommunity 
  • In addition to the main meeting, two free pre-meetings were held with over 175 participants
    • Pre-meeting 1: “AIRR-seq in the Pandemic” co-hosted by the AIRR Community and Tsinghua University in China which took place on December 5th/6th
    • Pre-meeting 2 “AIRR-seq Biological Standards and Workflows“ which was hosted by the Biological Resources Working Group on December 7th.

AIRR-dedicated Issue in the journal Current Opinion in Systems Biology 

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Ramit Mehr edited an issue on Systems immunology & host-pathogen interaction Current Opinion on Systems Biology to which many AIRR-C scientists have contributed. The issue encompasses eight original articles on the following topics: 

  1. Development of adaptive immune cells and receptor repertoires from infancy to adulthood, (2) Antigen discovery tools for adaptive immune receptor repertoire research
  2. The adaptive immune receptor repertoire community as a model for FAIR stewardship of big immunology data 
  3. Tools for adaptive immune receptor repertoire sequencing 
  4. Beyond bulk single-chain sequencing: Getting at the whole receptor 
  5. Disease susceptibility genes hidden in plain sight? 
  6. Mining adaptive immune receptor repertoires for biological and clinical information using machine learning 
  7. T cell repertoire sequencing as cancer’s liquid biopsy—can we decode what the immune system is coding? 

Read all articles here: https://www.sciencedirect.com/journal/current-opinion-in-systems-biology/vol/24/suppl/C.

AIRR Community and PrecisionFDA COVID-19 Precision Immunology App-a-thon

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The AIRR Community is helping to lead the PrecisionFDA COVID-19 Precision Immunology App-a-thon.  

This is part of the “precisionFDA Challenges” program, which is designed to engage and improve software that analyzes NGS (next generation sequencing data) through community challenges. There were 68 bioinformaticians pre-registered for the Precision Immunology Challenge, and more are expected to join as the app-a-thon continues.  These “citizen scientists” will form teams to design software that will make AIRR-seq data more available and accessible for immunologists to realize the promise of immunological big data for improved diagnostics and therapeutics in immunotherapy.

The Precision Immunology Challenge uses AIRR-seq repertoire data from COVID-19 patients downloaded from the AIRR Data Commons (VDJServer and iReceptor Public Archive) through the iReceptor Gateway. These data sets have been carefully chosen to include data on patient demography and clinical outcome in order to illuminate the relationship between personalized adaptive immunity molecular data and COVID-19 disease variables.

The AIRR Community Diagnostics Working Group published a blog post as part of this effort, explaining the possible uses of AIRR-seq data in the clinic in the near future.

The app-a-thon runs through February 2021 at which time the apps will be judged for usability, impact and innovation.

 

Announcing the new AIRR Community Executive Sub-committee!

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As part of the recent AIRR-C Meeting V the Executive Sub-committee election results were announced. Thank you to all nominees for their interest and for letting their names stand and to the many community members that took the time to vote.
We would like to thank Nina Luning Prak for her excellent and tireless work as Chair these past 18 months.  We would also like to recognize Steve Kleinstein for his many years on Exec and for his long standing commitment to the AIRR Community.
Please welcome the new Executive:
Lindsay Cowell, University Texas Southwestern, USA – Chair
Nina Luning Prak, University of Pennsylvania, USA – Past Chair
Victor Greiff, University of Oslo, Norway – Chair-elect
Felix Breden, Simon Fraser University, Canada – Elected Member
Christian Busse – DKFZ, Germany – Elected Member
Encarnita Mariotti-Ferrandiz, – Sorbonne Universite, France – Elected Member