August 2025 - Bioinfo List - SeqShare Mailing Lists

Share Your Feedback - SeqAfrica Bioinformatic Community of Practice Member Survey
by Pernille Nilsson 29 Aug '25

29 Aug '25

Dear SeqAfrica Bioinformatic Community Members, We invite you to participate in tthe SeqAfrica Bioinformatic Community of Practice - Member Survey 2025. This survey aims to assess member satisfaction with the SeqAfrica Community of Practice and gather input for sustaining the network beyond March 2026, when the project concludes. Your feedback is vital to solidifying the impact and shaping the future of the community. 📝Take the survey here: https://forms.gle/YaJH26nhgCr5QfPF6 The survey will only take a few minutes to complete, and your responses will be treated confidentially. Thank you for your continued engagement and support! Warm regards, Pernille [http://www.dtu.dk/-/media/DTU_Generelt/Andet/mail-signature-logo.png] Dr Pernille Nilsson Project Manager SeqAfrica Pronouns: she, her Mob. +45 22 13 75 50 pnil(a)food.dtu.dk<mailto:pnil@food.dtu.dk> National Food Institute Research Group for Global Capacity Building Henrik Dams Allé Building 204 2800 Kgs. Lyngby www.food.dtu.dk<http://www.food.dtu.dk/>

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You are invited: webinar on DTU's Genomic Proficiency Test 30 September 13:00 CEST
by Christa Twyford Gibson 28 Aug '25

28 Aug '25

Dear Colleagues, Please find attached a flyer for our upcoming webinar on the results and findings from the DTU Genomic Proficiency Test in Europe and Africa. This session will cover the results of the DTU Genomic Proficiency Tests from 2020-2022. The session will be held on Zoom at: https://dtudk.zoom.us/j/66908008515?pwd=6GZlVRai9TjKfMpQmQZJhnnJe0HGqJ.1 If anyone would like me to add them to the calendar invite, please let me know. Thank you for your consideration! Kind regards, Christa [cid:image001.png@01DC1831.45DCBAB0] 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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FW: Master AMR Detection in Bacteria: Apply by 3 November 2025
by Christa Twyford Gibson 27 Aug '25

27 Aug '25

Dear Colleagues, Please see below an upcoming course that we thought might be of interest to some of your labs. Kind regards, Christa From: Wellcome Connecting Science learning and training <coursesandconferences(a)email.wellcomeconnectingscience.org<mailto:coursesandconferences@email.wellcomeconnectingscience.org>> Sent: Wednesday, 27 August 2025 14:00 To: Anthony Smith <anthonys(a)nicd.ac.za<mailto:anthonys@nicd.ac.za>> Subject: Master AMR Detection in Bacteria: Apply by 3 November! Course dates:7–13 March 2026 | Free course in Africa View in browser<https://email.wellcomeconnectingscience.org/cr/AQj04xMQt9CRAhiajKIq12akC6eB…> [Image removed by sender. Wellcome Connecting Science logo] Learning and training 2025 [Image removed by sender.]<https://email.wellcomeconnectingscience.org/c/AQj04xMQt9CRAhiajKIqINrJihnYG…> [Image removed by sender.]<https://email.wellcomeconnectingscience.org/c/AQj04xMQt9CRAhiajKIqILa3iBkOy…> [Image removed by sender.]<https://email.wellcomeconnectingscience.org/c/AQj04xMQt9CRAhiajKIqILe3iBl-J…> [Image removed by sender.]<https://email.wellcomeconnectingscience.org/c/AQj04xMQt9CRAhiajKIqILi3iBky_…> [Image removed by sender.]<https://email.wellcomeconnectingscience.org/c/AQj04xMQt9CRAhiajKIqILm3iBlF3…> [Image removed by sender.]<https://email.wellcomeconnectingscience.org/c/AQj04xMQt9CRAhiajKIqILq3iBkO4…> Learn genomic approaches for understanding AMR in bacterial pathogens! Dear Anthony, Join us in collaboration with the National Institute for Communicable Diseases (NICD), for our 2026 Antimicrobial Resistance (AMR) of Bacterial Pathogens course.<https://email.wellcomeconnectingscience.org/c/AQj04xMQt9CRAhiajKIqINvJihkDD…> Course dates: 7-13 March This free training course is designed for researchers and clinicians, based in Africa, interested in applying genomics approaches to address regionally specific AMR challenges. Through a series of lectures and hands-on laboratory and computational practical sessions, you will learn best practice methods for the detection of AMR in bacteria. There will also be a focus on multi-pathogen-based approaches for use in low-resource settings. Topics will cover: * Epidemiology of AMR pathogens and national surveillance programmes. * The clinical importance of AMR. * The causes and biological mechanisms of resistance in Gram-positive and Gram-negative bacteria. * Antimicrobial susceptibility testing (AST) methods. * Understanding of breakpoints and AST reporting, QC/QA. * Antibiotic use policies and stewardship. * Tackling AMR using a One Health approach. * Whole genome sequencing (WGS) techniques. * Web-based and command line tools for pathogen genome analysis. * Genomic surveillance of AMR. Across the week, you will have opportunities to network and form new professional relationships, supporting the potential for forming long-term partnerships and collaborations. A limited number of bursaries are available to support with travel and accommodation costs. Apply by 3 November to be considered for a free place! [Apply for a place] [Image removed by sender.] Key date Application deadline: 3 November [Image removed by sender.] Instructors Beth Blane University of Cambridge, UK Vindana Chibabhai Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), and National Institute for Communicable Diseases (NICD), South Africa Francesc Coll I Cerezo Instituto de Biomedicina de Valencia, Spain Ewan Harrison Wellcome Sanger Institute, UK Fahad Khokar University of Cambridge, UK Collins Kigen Kenya Medical Research Institute(KEMRI), and Walter Reed Army Institute of Research (WRAIR), Africa Cebile Lekhuleni National Institute for Communicable Diseases (NICD), South Africa Caroline Maluleka Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), and National Institute for Communicable Diseases (NICD), South Africa Fahima Moosa National Institute for Communicable Diseases (NICD), South Africa Anthony Smith National Institute for Communicable Diseases (NICD), South Africa Learn genomic approaches for understanding AMR in bacterial pathogens! Dear Anthony, Join us in collaboration with the National Institute for Communicable Diseases (NICD), for our 2026 Antimicrobial Resistance of Bacterial of Bacterial Pathogens course.<https://email.wellcomeconnectingscience.org/c/AQj04xMQt9CRAhiajKIqIN3JihkPi…> Course dates: 7-13 March This free training course is designed for researchers and clinicians, based in Africa, interested in applying genomics approaches to address regionally specific AMR challenges. Through a series of lectures and hands-on laboratory and computational practical sessions, you will learn best practice methods for the detection of AMR in bacteria. There will also be a focus on multi-pathogen-based approaches for use in low-resource settings. Topics will cover: * Epidemiology of AMR pathogens and national surveillance programmes. * The clinical importance of AMR. * The causes and biological mechanisms of resistance in Gram-positive and Gram-negative bacteria. * Antimicrobial susceptibility testing (AST) methods. * Understanding of breakpoints and AST reporting, QC/QA. * Antibiotic use policies and stewardship. * Tackling AMR using a One Health approach. * Whole genome sequencing (WGS) techniques. * Web-based and command line tools for pathogen genome analysis. * Genomic surveillance of AMR. Across the week, you will have opportunities to network and form new professional relationships, supporting the potential for forming long-term partnerships and collaborations. A limited number of bursaries are available to support with travel and accommodation costs. Apply by 3 November to be considered for a free place! Apply for a place<https://email.wellcomeconnectingscience.org/c/AQj04xMQt9CRAhiajKIqIN7JihkD4…> [Image removed by sender.] Key date Application and bursary deadline: 3 November [Image removed by sender.] Instructors Beth Blane University of Cambridge, UK Vindana Chibabhai Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), and National Institute for Communicable Diseases (NICD), South Africa Francesc Coll I Cerezo Instituto de Biomedicina de Valencia, Spain Ewan Harrison Wellcome Sanger Institute, UK Fahad Khokar University of Cambridge, UK Collins Kigen Kenya Medical Research Institute(KEMRI), and Walter Reed Army Institute of Research (WRAIR), Africa Cebile Lekhuleni National Institute for Communicable Diseases (NICD), South Africa Caroline Maluleka Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM), and National Institute for Communicable Diseases (NICD), South Africa Fahima Moosa National Institute for Communicable Diseases (NICD), South Africa Anthony Smith National Institute for Communicable Diseases (NICD), South Africa Learn how to: * Carry out standard laboratory methods for antimicrobial susceptibility testing, including disc diffusion testing and MIC determination. * Describe the principles and practice of quality assurance and control in AMR surveillance techniques, antimicrobial susceptibility testing and reporting. * Discuss the range of control strategies for AMR in human and veterinary medicine (including antimicrobial stewardship, infection control and use policies). * Use appropriate software tools to analyse WGS data for assembly of bacterial genomes, detect resistant variants and conduct phylogenetic analysis. * Analyse and interpret genomics data for AMR surveillance. Other learning and training events that may interest you [Image removed by sender. 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/AQj04xMQt9CRAhiajKIqILu3iBnRQ…> [Image removed by sender. 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/AQj04xMQt9CRAhiajKIqILy3iBkkg…> [Image removed by sender. 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/AQj04xMQt9CRAhiajKIqIL23iBnMh…> [Image removed by sender. 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/AQj04xMQt9CRAhiajKIqILu3iBnRQ…> [Image removed by sender. 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/AQj04xMQt9CRAhiajKIqILy3iBkkg…> [Image removed by sender. 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/AQj04xMQt9CRAhiajKIqIL23iBnMh…> Unsubscribe<https://email.wellcomeconnectingscience.org/uns/AQj04xMQt9CRAhiajKIq12akC6e…> 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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Fwd: Applications Now Open for African Bioinformatics Institute Group Leaders
by Marco van Zwetselaar 11 Aug '25

11 Aug '25

Dear all, FYI, the African Bioinformatics Institute (to be) invites applications for the role of ABI Group Leaders. Kind regards, Marco -------- Forwarded Message -------- Subject: Applications Now Open for African Bioinformatics Institute Group Leaders Date: Fri, 08 Aug 2025 17:05:48 +0000 From: Nicola Mulder [<nicola.mulder(a)uct.ac.za>](mailto:nicola.mulder@uct.ac.za) Reply-To: Nicola Mulder [<nicola.mulder(a)uct.ac.za>](mailto:nicola.mulder@uct.ac.za) To: Dear colleagues, On behalf of the Interim Council of the African Bioinformatics Institute (ABI), we are pleased to invite applications for Group Leaders. These prestigious positions are open to senior scientists based in Africa who are leading independent research, training, or service groups in bioinformatics at a university, research institute, public health agency, or similar institution. Group Leaders will contribute to ABI’s mission by advancing excellence in their institutions, mentoring the next generation, and engaging in collaborative initiatives across the continent. Applicants must have a strong track record in publications, mentorship, contribution to the field of bioinformatics (e.g. bioinformatics research, software or resource development), grant acquisition, and collaborative work in the field of bioinformatics. Institutional support is essential, as each Group Leader’s host institution becomes an official ABI site. While no remuneration is offered, ABI provides non-financial support including strategic visibility, networking opportunities, and administrative support for collaborative grant proposals. Group Leaders will be part of a dynamic, pan-African network, with opportunities to contribute to ABI’s training programs, research agenda, and governance. The term of appointment is three years, renewable. Applicants must complete an online form and submit a CV and an institutional letter of support. Applications will be reviewed on a rolling basis, with a first review deadline of 19 September 2025. Please read the full details of the call first (attached or [here](https://bioinformaticsinstitute.africa/sites/default/files/ABI_Request_for_Applications_Group_Leaders.pdf)). Apply online here: https://redcap.link/dgg60u9fFor any enquiries, please contact: info(a)bioinformaticsinstitute.africa. We encourage applications from all regions of Africa and look forward to building this community together. If you are not yet an established bioinformatics scientist and thus not eligible to apply as a Group Leader, there are other opportunities to join the ABI or to get involved with ABI activities, see more opportunities here: https://www.bioinformaticsinstitute.africa/about-organization. We will open applications for Associate Group Leaders and Fellows in due course. Regards Nicky On behalf of the ABI Interim Council

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Sustainability of the SeqAfrica Monthly Bioinformatics Community of Practice
by Christa Twyford Gibson 07 Aug '25

07 Aug '25

Dear Colleagues, Thank you again to Sade for a great presentation today! I look forward to seeing how the fungal pipeline develops. Please reach out to Sade at sadem(a)nicd.ac.za<mailto:sadem@nicd.ac.za> if you would like to test the pipeline for her. Per our conversation today regarding the sustainability of our COP after the end of the Fleming Fund, I’ve attached the TOR for the ABI COP on AMR and Pathogen Genomics. I would love to hear your thoughts regarding the idea of merging our COP into the ABI one- or if you’d like to continue our COP under new leadership once Niamh, Pernille and I are gone. We can discuss this at future meetings as well, but please also feel free to reach out by email if you have any ideas. Warm regards, Christa [cid:image001.png@01DC07A2.745A17B0] 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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SeqAfrica Monthly Bioinformatics Community of Practice tomorrow (7 August) at 12:30 CEST
by Christa Twyford Gibson 06 Aug '25

06 Aug '25

Dear Colleagues, We are so excited to invite you to our August Bioinformatics Community of Practice meeting tomorrow at 12:30 CEST. Our colleague from the South African National Institute for Communicable Disease will be presenting on a new pipeline she is creating. Please see the summary below. Likewise, please see the Zoom link for tomorrow’s meeting below. We look forward to seeing you all tomorrow! Warm regards, Christa Antifungal resistance is an emerging global health threat, particularly affecting immunocompromised populations. In Africa, the situation is exacerbated by high burdens of HIV, limited diagnostics, and increasing resistance in key fungal pathogens like Candida auris, Aspergillus fumigatus, and Cryptococcus neoformans. Resistance is driven by overuse of antifungals, poor infection control, and environmental pressures. To combat this, bioinformatic pipelines offer scalable tools for species identification and resistance gene detection. Our pipeline begins by identifying SPAdes genome assemblies, then uses BLAST against a custom fungal database for species assignment. It extracts reference accession numbers, downloads corresponding genomes, organizes data by species, and uses tools like ChroQueTas to detect antimicrobial resistance (AMR) genes. These methods can be applied in African public health labs to improve surveillance, support diagnostics, and inform treatment decisions — but require investment in sequencing capacity, training, and infrastructure. Topic: SeqAfrica Bionformatics Community of Practice (recurring invitation) Time: Every month on the First Thursday Join Zoom Meeting https://dtudk.zoom.us/j/68532308758?pwd=AK8CRJQaskd7BvavJZ8RapDJ63baCg.1 Meeting ID: 685 3230 8758 Passcode: 210273 --- One tap mobile +31207946519,,68532308758#,,,,*210273# Netherlands +31207946520,,68532308758#,,,,*210273# Netherlands --- Dial by your location • +31 20 794 6519 Netherlands • +31 20 794 6520 Netherlands • +31 20 794 7345 Netherlands • +31 707 006 526 Netherlands • +31 20 241 0288 Netherlands • +31 20 794 0854 Netherlands Meeting ID: 685 3230 8758 Passcode: 210273 Find your local number: https://dtudk.zoom.us/u/ccOdRjxrFb --- Join by SIP 68532308758(a)109.105.112.236<mailto:68532308758@109.105.112.236> • 68532308758(a)109.105.112.235<mailto:68532308758@109.105.112.235> --- Join by H.323 • 109.105.112.236 • 109.105.112.235 Meeting ID: 685 3230 8758 Passcode: 210273 Dear Colleagues, We are so excited to invite you to our August Bioinformatics Community of Practice meeting tomorrow at 12:30 CEST. Our colleague from the South African National Institute for Communicable Disease will be presenting on a new pipeline she is creating. Please see the summary below. Likewise, please see the Zoom link for tomorrow’s meeting below. We look forward to seeing you all tomorrow! Warm regards, Christa “Antifungal resistance is an emerging global health threat, particularly affecting immunocompromised populations. In Africa, the situation is exacerbated by high burdens of HIV, limited diagnostics, and increasing resistance in key fungal pathogens like Candida auris, Aspergillus fumigatus, and Cryptococcus neoformans. Resistance is driven by overuse of antifungals, poor infection control, and environmental pressures. To combat this, bioinformatic pipelines offer scalable tools for species identification and resistance gene detection. Our pipeline begins by identifying SPAdes genome assemblies, then uses BLAST against a custom fungal database for species assignment. It extracts reference accession numbers, downloads corresponding genomes, organizes data by species, and uses tools like ChroQueTas to detect antimicrobial resistance (AMR) genes. These methods can be applied in African public health labs to improve surveillance, support diagnostics, and inform treatment decisions — but require investment in sequencing capacity, training, and infrastructure.” Topic: SeqAfrica Bionformatics Community of Practice (recurring invitation) Time: Every month on the First Thursday Join Zoom Meeting https://dtudk.zoom.us/j/68532308758?pwd=AK8CRJQaskd7BvavJZ8RapDJ63baCg.1 Meeting ID: 685 3230 8758 Passcode: 210273 --- One tap mobile +31207946519,,68532308758#,,,,*210273# Netherlands +31207946520,,68532308758#,,,,*210273# Netherlands --- Dial by your location • +31 20 794 6519 Netherlands • +31 20 794 6520 Netherlands • +31 20 794 7345 Netherlands • +31 707 006 526 Netherlands • +31 20 241 0288 Netherlands • +31 20 794 0854 Netherlands Meeting ID: 685 3230 8758 Passcode: 210273 Find your local number: https://dtudk.zoom.us/u/ccOdRjxrFb --- Join by SIP 68532308758(a)109.105.112.236<mailto:68532308758@109.105.112.236> • 68532308758(a)109.105.112.235<mailto:68532308758@109.105.112.235> --- Join by H.323 • 109.105.112.236 • 109.105.112.235 Meeting ID: 685 3230 8758 Passcode: 210273 Dear Colleagues, We are so excited to invite you to our August Bioinformatics Community of Practice meeting tomorrow at 12:30 CEST. Our colleague from the South African National Institute for Communicable Disease will be presenting on a new pipeline she is creating. Please see the summary below. Likewise, please see the Zoom link for tomorrow’s meeting below. We look forward to seeing you all tomorrow! Warm regards, Christa “Antifungal resistance is an emerging global health threat, particularly affecting immunocompromised populations. In Africa, the situation is exacerbated by high burdens of HIV, limited diagnostics, and increasing resistance in key fungal pathogens like Candida auris, Aspergillus fumigatus, and Cryptococcus neoformans. Resistance is driven by overuse of antifungals, poor infection control, and environmental pressures. To combat this, bioinformatic pipelines offer scalable tools for species identification and resistance gene detection. Our pipeline begins by identifying SPAdes genome assemblies, then uses BLAST against a custom fungal database for species assignment. It extracts reference accession numbers, downloads corresponding genomes, organizes data by species, and uses tools like ChroQueTas to detect antimicrobial resistance (AMR) genes. These methods can be applied in African public health labs to improve surveillance, support diagnostics, and inform treatment decisions — but require investment in sequencing capacity, training, and infrastructure.” Topic: SeqAfrica Bionformatics Community of Practice (recurring invitation) Time: Every month on the First Thursday Join Zoom Meeting https://dtudk.zoom.us/j/68532308758?pwd=AK8CRJQaskd7BvavJZ8RapDJ63baCg.1 Meeting ID: 685 3230 8758 Passcode: 210273 --- One tap mobile +31207946519,,68532308758#,,,,*210273# Netherlands +31207946520,,68532308758#,,,,*210273# Netherlands --- Dial by your location • +31 20 794 6519 Netherlands • +31 20 794 6520 Netherlands • +31 20 794 7345 Netherlands • +31 707 006 526 Netherlands • +31 20 241 0288 Netherlands • +31 20 794 0854 Netherlands Meeting ID: 685 3230 8758 Passcode: 210273 Find your local number: https://dtudk.zoom.us/u/ccOdRjxrFb --- Join by SIP 68532308758(a)109.105.112.236<mailto:68532308758@109.105.112.236> • 68532308758(a)109.105.112.235<mailto:68532308758@109.105.112.235> --- Join by H.323 • 109.105.112.236 • 109.105.112.235 Meeting ID: 685 3230 8758 Passcode: 210273 [cid:image001.png@01DC06C0.63370570] 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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2025

2024

Bioinfo List August 2025