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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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upcoming training opportunity
by Christa Twyford Gibson 22 Jul '25

22 Jul '25

HI Colleagues, I wanted to share an upcoming training opportunity with you all. DTU will organise a virtual training on “Molecular Epidemiology and Global Transmission of Cholera” on 27th August and 3rd September 2025 from 9:00 to 12:30 CEST. Through this webinar, participants will gain insights into analyzing and interpreting single-nucleotide polymorphism (SNP) matrices and maximum parsimony trees to study the population genetics of Vibrio cholerae. They will also learn to link AMR and virulence profiles to epidemiological data. You can already register for this training: Course: GenEpi-BioTrain - Virtual training 19 - Molecular Epidemiology and Global Transmission of Cholera. To register for the course, you will need to create a login on the ECDC Learning portal here: https://sso2.ecdc.europa.eu/saml20/idp/sso Warm regards, Christa [cid:image001.png@01DBFB16.270DCDF0] 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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Got 10 minutes? Share your work at our next Bioinformatics CoP!
by Pernille Nilsson 30 Jun '25

30 Jun '25

Dear Bioinformatics Community, We have an open spot for a presentation at our next CoP session on 7 August. If you or someone you know would like to give a 10-minute presentation we would love to hear from you! As a reminder, the SeqAfrica Bioinformatic Community of Practise has a monthly meet-up for everyone passionate about bioinformatics. Each session features a stand-up round where participants share their current projects, followed by a "Soapbox" segment showcasing scientific talks, tool demonstrations or discussions of new developments in the field. Previous sessions have encompassed tool demonstrations of AMRomics and hARMonize, a presentation on Marburg virus outbreak investigations in Rwanda, and a script presentation for SNP detection in V. cholerae. Looking forward to hearing from you! Kind 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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Reminder: SeqAfrica Bioinformatics CoP June
by Pernille Nilsson 24 Jun '25

24 Jun '25

Dear Bioinformatics Community of Practise Members, This is a gentle reminder that we have our June session coming up on Thursday! Sade Magabotha will be presenting her script which looks for SNPs in Vibrio cholerae datasets. The github page is here https://github.com/Shaedeycool/Vibrio_SNPs. The script is set to look for SNPs with 90% similarity to the sequences in the database covering 90% of the entire length of the sequences of interest for biotype and serotype. Join us to learn more about this script! Date: Thursday 26 June 2025 Time: 12:30 CEST Zoom link: https://dtudk.zoom.us/j/68532308758?pwd=AK8CRJQaskd7BvavJZ8RapDJ63baCg.1 Meeting ID: 685 3230 8758 Passcode: 210273 We look forward to seeing you there! Best wishes, 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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New date: SeqAfrica June Bioinformatic CoP - Presentation of SNP script for Vibrio cholera
by Pernille Nilsson 27 May '25

27 May '25

Dear Bioinformatics Community of Practice Members, We are happy to announce our upcoming Bioinformatics Community of practice session! This event promises to be an enlightening experience, featuring a presentation by Sade Magabotha on her script which looks for SNPs in Vibrio cholera datasets. If you are interested in exploring the details of the script in advance of the meeting, you can find the github page here: https://github.com/Shaedeycool/Vibrio_SNPs Please note the change in date from June 5th to June 26th! Date: Thursday 26 June 2025 Time: 12:30 CEST Zoom link: https://dtudk.zoom.us/j/68532308758?pwd=AK8CRJQaskd7BvavJZ8RapDJ63baCg.1 Meeting ID: 685 3230 8758 Passcode: 210273 We look forward to seeing you there! Best wishes, 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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Reminder: metadata expert elicitation tomorrow
by Christa Twyford Gibson 19 May '25

19 May '25

Dear Colleagues, This is a gentle reminder that our metadata expert elicitation will take place tomorrow at 14:15 CEST. The Zoom link to join is below. We look forward to seeing you tomorrow! Kind regards, Christa ────────── Christa Twyford Gibson is inviting you to a scheduled Zoom meeting. Join Zoom Meeting https://dtudk.zoom.us/j/67066262671?pwd=yqMv6duCXRDaSZz6ytH7hVxcV8G3U0.1 Meeting ID: 670 6626 2671 Passcode: 432088 --- One tap mobile +4589883788,,67066262671#,,,,*432088# Denmark +4532701206,,67066262671#,,,,*432088# Denmark --- Dial by your location • +45 89 88 37 88 Denmark • +45 32 70 12 06 Denmark • +45 32 71 31 57 Denmark • +45 32 72 80 10 Denmark • +45 32 72 80 11 Denmark • +45 47 37 25 75 Denmark Meeting ID: 670 6626 2671 Passcode: 432088 Find your local number: https://dtudk.zoom.us/u/cdW8yWGZ3y --- Join by SIP 67066262671(a)109.105.112.236<mailto:67066262671@109.105.112.236> • 67066262671(a)109.105.112.235<mailto:67066262671@109.105.112.235> --- Join by H.323 • 109.105.112.236 • 109.105.112.235 Meeting ID: 670 6626 2671 Passcode: 432088 ────────── [cid:image001.png@01DBC8A2.9A799CC0] 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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New date: SeqAfrica May Bioinformatics CoP - Outbreak Response using Genomics
by Pernille Nilsson 12 May '25

12 May '25

Dear Bioinformatics Community of Practice Members, We are thrilled to announce our upcoming Bioinformatics Community of practice session! This event promises to be an enlightening experience, featuring a presentation by Raissa MUVUNYI on "Outbreak Response Using Genomics: The case of the Marburg Outbreak in Rwanda". This session is a fantastic opportunity to delve into the transformative power of genomics in outbreak detection and response, as demonstrated by real-world efforts on the ground. Please note the change in date from May 1st to May 15th! Date: Thursday 15 May 2025 Time: 12:30 CEST Zoom link: https://dtudk.zoom.us/j/68532308758?pwd=AK8CRJQaskd7BvavJZ8RapDJ63baCg.1 Meeting ID: 685 3230 8758 Passcode: 210273 We look forward to seeing you there! Best wishes, 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 to an expert elicitation on metadata for LMICs 20 May at 14:15 CET
by Christa Twyford Gibson 24 Apr '25

24 Apr '25

Dear Colleagues, We are pleased to invite you to an upcoming Metadata Expert Elicitation Session on May 20 2025, at 14:15 CEST. This event is a follow-up to our engaging webinar series last fall, where a presentation on metadata sparked strong interest in further discussion—especially around applications in LMIC settings. This 90-minute session will begin with a brief introduction to key metadata concepts relevant to risk assessments, surveillance, and outbreak response. Following this, participants will join breakout discussions focused on current practices, opportunities for enhancement, and practical challenges in different contexts. The session can be joined by Zoom at: https://dtudk.zoom.us/j/67066262671?pwd=yqMv6duCXRDaSZz6ytH7hVxcV8G3U0.1 Meeting ID: 670 6626 2671 Passcode: 432088 Please email me if you would like me to add you or any of your colleagues to the meeting invite. Warm regards, Christa [cid:image001.png@01DBB518.635D19D0] 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