- Bioinfo List - SeqShare Mailing Lists

Reminder: COP tomorrow!!!
by Christa Twyford Gibson 09 Oct '24

09 Oct '24

Dear Colleagues, Just a reminder that our monthly Bioinformatics Community of Practice is TOMORROW 10 October at 13:45 CEST. The Zoom link for the meeting is below! Our colleague Albert Bortey from the Noguchi Memorial Institute for Medical Research will be giving us a demonstration of hARMonize. It should be super interesting! We look forward to seeing you all tomorrow! Christa Christa Gibson is inviting you to a scheduled Zoom meeting. Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 [cid:image001.png@01DB1A4A.165EDF60] Christa Twyford Gibson Project Manager for SeqAfrica Project Fleming Fund Regional Grant SeqAfrica (dtu.dk)<https://www.food.dtu.dk/english/topics/antimicrobial-resistance/seqafrica> chrgi(a)dtu.dk<mailto:chrgi@dtu.dk> +45 53 81 91 15 National Food Institute Research Group for Global Capacity Building Building 204 Henrik Dams Allé 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/>

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Change of date for October Bioinformatics Community of Practice: join us on 10 October
by Christa Twyford Gibson 01 Oct '24

01 Oct '24

Dear Colleagues, Please spread the word- we are moving our monthly Bioinformatics COP to 10 October at 13:45 CEST this month. The Zoom link (below) is the same. Please let your colleagues know of the change! Cheers, Christa Christa Gibson is inviting you to a scheduled Zoom meeting. Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 [cid:image001.png@01DB134E.CBB49D30] Christa Twyford Gibson Project Manager for SeqAfrica Project Fleming Fund Regional Grant SeqAfrica (dtu.dk)<https://www.food.dtu.dk/english/topics/antimicrobial-resistance/seqafrica> chrgi(a)dtu.dk<mailto:chrgi@dtu.dk> +45 53 81 91 15 National Food Institute Research Group for Global Capacity Building Building 204 Henrik Dams Allé 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/>

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Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050
by Marco van Zwetselaar 18 Sep '24

18 Sep '24

FYI, a new (Wellcome and Fleming funded) comprehensive systematic review of historic & future trends in AMR burden. Naghavi M, Vollset SE, Ikuta KS, et al. Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050. The Lancet 2024; 0. DOI:[10.1016/S0140-6736(24)01867-1](https://doi.org/10.1016/S0140-6736(24)0…. Cited as "39 million estimated deaths from AMR between 2025 and 2050" by Wellcome[1] and HealthData.org[2] Best wishes, Marco [1] https://wellcome.org/news/new-forecasts-reveal-39-million-deaths-will-be-di… [2] https://www.healthdata.org/news-events/newsroom/news-releases/lancet-more-3…

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Fwd: Free online course: Strengthen your antimicrobial resistance prediction skills with experts in bacterial genomics
by Marco van Zwetselaar 13 Sep '24

13 Sep '24

FYI -------- Forwarded Message -------- Subject: Free online course: Strengthen your antimicrobial resistance prediction skills with experts in bacterial genomics Date: Thu, 12 Sep 2024 07:01:12 +0000 From: Wellcome Connecting Science learning and training [<coursesandconferences(a)email.wellcomeconnectingscience.org>](mailto:coursesandconferences@email.wellcomeconnectingscience.org) Reply-To: Wellcome Connecting Science learning and training [<re-6Y2C-RJRY-1ODXOW-C1TZY(a)email.wellcomeconnectingscience.org>](mailto:re-6Y2C-RJRY-1ODXOW-C1TZY@email.wellcomeconnectingscience.org) To: Gain free and expert-led training in AMR genomics and data sharing [View in browser](https://email.wellcomeconnectingscience.org/cr/AQj04xMQ3rlOGNDPrjD… [Wellcome Connecting Science logo] Learning and training [Click this header to find out more about this online course on the FutureLearn website](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg… [Blog](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg88C… [LinkedIn](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjA… [X](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg9cCBD_… [YouTube](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg… Free online training to strengthen your AMR genomics expertise! Dear Marco, [Antimicrobial Resistance and Genotype Prediction: Data Sharing and Analysis](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjA… our free online course led by experts in bacterial genomics and data analysis, focusing on how to use relevant tools and databases for the prediction of antimicrobial resistance (AMR). Starting on 30 September 2024, our educators will guide you through everything you need to learn to confidently predict AMR using your own data, understand effective data-sharing, and enhance your expertise in AMR genomics. The course will run live for three-weeks, during which time you will be able to interact with our educators and other learners (through the FutureLearn platform), and exchange ideas and thinking with peers from across the globe. This is an excellent opportunity for early career researchers, healthcare professionals, and public health experts to benefit from free and accessible training in AMR prediction, using genotypic and phenotypic data, and the latest genomics tools and technologies. Sign up for a free place on the FutureLearn website today, and start learning from 30 September. [Find out more about the course](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg4… Key information Start learning: 30 September 2024 Live period: 3 weeks Weekly study expectation: 5 hours Educators Conor Meehan Nottingham Trent University, UK Jane Hawkey Monash University, Australia Kristy Horan AusTrakka platform, Australia Certificate Gain a certificate on successful completion of the course to demonstrate your learning investment. Free online training to strengthen your AMR genomics expertise! Dear Marco, [Antimicrobial Resistance and Genotype Prediction: Data Sharing and Analysis](#anchor31)is our free online course led by experts in bacterial genomics and data analysis, focusing on how to use relevant tools and databases for the prediction of antimicrobial resistance (AMR). Starting on 30 September 2024, our educators will guide you through everything you need to learn to confidently predict AMR using your own data, understand effective data-sharing, and enhance your expertise in AMR genomics. The course will run live for three-weeks, during which time you will be able to interact with our educators and other learners (through the FutureLearn platform), and exchange ideas and thinking with peers from across the globe. This is an excellent opportunity for early career researchers, healthcare professionals, and public health experts to benefit from free and accessible training in AMR prediction, using genotypic and phenotypic data, and the latest genomics tools and technologies. Sign up for a free place on the FutureLearn website today, and start learning from 30 September. [Find out more about the course](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg5… Key information Start learning: 30 September 2024 Live period: 3 weeks Weekly study expectation: 5 hours Educators Conor Meehan Nottingham Trent University, UK Jane Hawkey Monash University, Australia Kristy Horan AusTrakka platform, Australia Certificate Gain a certificate on successful completion of the course to demonstrate your learning investment. Watch the course trailer to discover more about what you will learn with our expert educators https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAgmsyBD6EIU… https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAgmsyBD6EIU… Learn how to: - Explain the genotypic basis of AMR. - Contrast and critique the various ways to predict AMR from linked genotype and/or phenotype data. - Discuss the various AMR databases, and their related benefits and limitations. - Explain how different AMR prediction tools can be applied, as well as how their outputs are interpreted and implemented. - Explain the current limitations of AMR prediction tools. - Describe the process required to create and share FAIR and open AMR data. Other learning and training events that may interest you [Colour photo of two CRISPR conference delegates discussing scientific poster insights | Image credit: Ben McDade photography for Connecting Science] [Conferences](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDP… [Colour photo of two scientists working in a lab, wearing lab coats and safety gloves, whilst using pipettes | Image credit: Ben McDade photography for Connecting Science] [Courses](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg… [Colour photo of a group of drug discovery course participants in Uruguay | Image credit: Wellcome Connecting Science] [Courses outside the UK](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg-cCBD… Other learning and training events that may interest you [Colour photo of two CRISPR conference delegates discussing scientific poster insights | Image credit: Ben McDade photography for Connecting Science] [Conferences](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDP… [Colour photo of two scientists working in a lab, wearing lab coats and safety gloves, whilst using pipettes | Image credit: Ben McDade photography for Connecting Science] [Courses](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg… [Colour photo of a group of drug discovery course participants in Uruguay | Image credit: Wellcome Connecting Science] [Courses outside the UK](https://email.wellcomeconnectingscience.org/c/AQj04xMQ3rlOGNDPrjAg-cCBD… [Unsubscribe](https://email.wellcomeconnectingscience.org/uns/AQj04xMQ3rlOGN… | [Forward to an interested colleague](https://email.wellcomeconnectingscience.org/fw/AQj04xMQ3rlOGNDPr… Image credit: Colour photography by Ben McDade for Connecting Science Wellcome Connecting Science Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Reminder: SeqAfrica September Bioinformatics CoP – Exciting AMRomics demo!
by Pernille Nilsson 04 Sep '24

04 Sep '24

Dear Bioinformatics Community of Practice Members, We hope this email finds you well and thriving in your research endeavors! We are excited to inform you of the upcoming Bioinformatics Community of Practice session, where we will be showcasing the AMRomics workflow. This is a fantastic opportunity to see this tool in action and learn how it can enhance your research projects and AMR work. Date: Thursday 5 September Time: 14.00-14.45 CEST Zoom link: https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 During this session, we will demonstrate the key features and capabilities of the AMRomics workflow and engage in a lively Q&A session/discussion to address all your burning questions. This session promises to be informative and fun and it’s a great chance to connect with fellow community members and share insights. Looking forward to seeing you there with your curiosity and enthusiasm. Best wishes, Pernille [signature_1133531634] Dr Pernille Nilsson Pronouns: she, her Project Manager SeqAfrica National Food Institute Research Group for Global Capacity Building Mob. +45 93 51 16 54 pnil(a)food.dtu.dk<mailto:pnil@food.dtu.dk> Henrik Dams Allé Building 204 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk>

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ONT Knowledge Exchange
by Christa Twyford Gibson 29 Aug '24

29 Aug '24

Hi all, Please see the link below for an upcoming knowledge exchange hosted by ONT. Webinar: sequencing and analysis of nanopore-only microbial isolates (nanoporetech.com)<https://nanoporetech.com/about/events/knowledge-exchange/sequencing-and-ana…> I hope some can join! Cheers, Christa [cid:image001.png@01DAFA58.6AAD76B0] Christa Twyford Gibson Project Manager for SeqAfrica Project SEQAFRICA (antimicrobialresistance.dk)<https://antimicrobialresistance.dk/seqafrica.aspx> chrgi(a)dtu.dk<mailto:chrgi@dtu.dk> +45 935 106 61 National Food Institute Research Group for Global Capacity Building Building 204 Henrik Dams Allé 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/>

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Yet another AMR pipeline: AMRomics
by Marco van Zwetselaar 31 Jul '24

31 Jul '24

AMRomics: a scalable workflow to analyze large microbial genome collections https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-024-10620-8 Two interesting features (vis a vis other pipelines): support for Nanopore reads, and construction of phylogenetic trees from core-genomes of the data. Cheers, Marco

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Reminder: Bioinformatics COP this Thursday!
by Christa Twyford Gibson 30 Jul '24

30 Jul '24

Dear Colleagues, Don't forget this month's SeqAfrica Bioinformatics Community of Practice meeting! We will be discussing new developments in sequencing and bioinformatics tooling for microbial / AMR genomics. The meeting is Thursday (1.8.24) at 14:00 CEST. The zoom link is below. We can't wait to see and hear from you! Please share this invitation with your bioinformatics-curious and interested friends! Kind Regards, Christa Join Zoom Meeting https://dtudk.zoom.us/j/68365887835 Meeting ID: 683 6588 7835 [cid:image001.png@01DAE276.7B716BE0] Christa Twyford Gibson Project Manager for SeqAfrica Project SEQAFRICA (antimicrobialresistance.dk)<https://antimicrobialresistance.dk/seqafrica.aspx> chrgi(a)dtu.dk<mailto:chrgi@dtu.dk> +45 935 106 61 National Food Institute Research Group for Global Capacity Building Building 204 Henrik Dams Allé 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/>

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... and yet another plasmid finder
by Marco van Zwetselaar 30 Jul '24

30 Jul '24

PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning https://doi.org/10.1093/bib/bbae322 Cheers, Marco

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BLAST core_nt to be default from Aug 1st
by Marco van Zwetselaar 24 Jul '24

24 Jul '24

NCBI announces the "better, faster, smaller" core_nt database to become the default from August: From: NLM/NCBI List blast-announce [<blast-announce(a)ncbi.nlm.nih.gov>](mailto:blast-announce@ncbi.nlm.nih.gov) Interested in faster nucleotide BLAST searches with more focused search results? NCBI has been re-evaluating the BLAST nucleotide database (nt) to make it smaller and more efficient. Thanks to your feedback, we have created the core nucleotide database (core_nt), an alternative to the default nt database that contains better-defined content and is less than half the size. Read more at NCBI Insights and try out the new database: https://bit.ly/46d49r8 https://bit.ly/46d49r8

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2026

2025

2024