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On AIRR Podcast Episode 12 Now Available!

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In the latest episode of the On AIRR – An AIRR-C Podcast Series, Dr. Ulrik Stervbo and Dr. Zhaoqing Ding speak with Dr. Charlotte Deane (Professor of Structural Bioinformatics in the Department of Statistics in University of Oxford (UK) and head of the Oxford Protein Informatics Group) about the relevance of including protein structure to study and design antibodies, and the availability of such data. 

You can subscribe and listen in your favorite podcasting app or check out all of the On AIRR episodes here at http://onairr.airr-community.org or on the AIRR YT Channel. If you share podcast-related content in social media, please remember to use the hashtag #onairr!

 

On AIRR Podcast Episode 11 Now Available!

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In the latest episode of the On AIRR – An AIRR-C Podcast Series, Dr. Ulrik Stervbo and Dr. Zhaoqing Ding speak with Dr. Xenophon Papademetris (Professor of Radiology and Biomedical Imaging, and Biomedical Engineering at Yale University) about the typical regulatory process for software classified as a medical device.

You can subscribe and listen in your favorite podcasting app or check out all of the On AIRR episodes here at http://onairr.airr-community.org. If you share podcast-related content in social media, please remember to use the hashtag #onairr!

 

partis is now certified as AIRR-compliant

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The AIRR Community is excited to announce that partis has been certified as compliant with the AIRR-C v1.0 standard for AIRR-Seq software tools. partis is an HMM-based framework for B- and T-cell receptor sequence annotation, simulation, clonal family and germline inference, and affinity prediction. It is built on top of the ham HMM compiler and ig-sw set of Smith-Waterman annotation tools. partis is free software under the GPL v3.

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. The list currently includes CompAIRR, Dandelion, Immcantation, ImmuneDB, ImmuneML, Scirpy, SONAR and TRUST4 in addition to partis.

Announcing the AIRR Community Seminar Series!

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Join the AIRR Community for a 90 minute “lab-style” virtual seminar.  Each month an established and an early career scientist will discuss their AIRR-seq related research. Seminar time will be 16:00 – 17:30 Central European Time (CET), typically on the 4th Thursday of the month.  Most talks will be recorded and posted on the AIRR Community YouTube channel.  In the spirit of open science collaboration we want to give credit where credit is due – this seminar series is modelled after and a follow-up to the highly successful iReceptor Plus Seminar Series: Theories and Applications of Immune Repertoires which ran from 2020-2022. Check out their website for many scientifically related talks!

Register today for the April 27th talks presented by Hashem Koohy from Oxford University and Marcos Vieria from University of Chicago.

Check out the seminar series web page for upcoming seminars and registration links.

 

TRUST4 is now certified as AIRR-compliant

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The AIRR Community is excited to announce that TRUST4 has been certified as compliant with the AIRR-C v1.0 standard for AIRR-Seq software tools. TRUST4 (Tcr Receptor Utilities for Solid Tissue 4) is a tool for assembling BCRs and TCRs from bulk and single-cell RNA-Seq data.

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. The list currently includes SONAR, ImmuneDB, Scirpy, Immcantation, CompAIRR, ImmuneML and Dandelion in addition to TRUST4.