- BBClist - maillist.psb.ugent.be

Enhance your bioimaging data analysis skills – join our VIB courses on Bioimaging analysis on HPC, Fiji and QuPath in May and June 2025
by BeNeLux bioinformaticians forum 21 Apr '25

21 Apr '25

Dear all, We are happy to announce another suite of bioimaging data analysis courses in May and June 2025. Bioimaging data analysis on the HPC https://training.vib.be/all-trainings/bioimaging-data-analysis-hpc-1 Image Processing using Fiji https://training.vib.be/all-trainings/basic-image-processing-using-fiji-6 QuPath: Quantitative Pathology & Bioimage Analysis Software https://training.vib.be/all-trainings/qupath-quantitative-pathology-bioimag… The trainers for these courses are: Tatiana Woller and Sebastian Munck, Benjamin Pavie and Bob Asselbergh. Additional courses can be found at: https://vibtrainconf.be. Best regards, Alex

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VIB-SIB Machine Learning and AI summer school: application deadline April 29th
by BeNeLux bioinformaticians forum 16 Apr '25

16 Apr '25

Dear all, A kind reminder regarding the announcement of the the 𝗠𝗮𝗰𝗵𝗶𝗻𝗲 𝗟𝗲𝗮𝗿𝗻𝗶𝗻𝗴 𝗮𝗻𝗱 𝗔𝗜 𝗦𝘂𝗺𝗺𝗲𝗿 𝗦𝗰𝗵𝗼𝗼𝗹, a collaborative initiative by VIB<https://www.linkedin.com/company/vib/> and SIB Swiss Institute of Bioinformatics<https://www.linkedin.com/company/sib-swiss-institute-of-bioinformatics/>, taking place from August 24–29, 2025, near Diest, Belgium. This week-long, hands-on training is designed for researchers with an intermediate background in machine learning and experience using Python. Participants will explore four core topics: • Protein language models • Spatial omics data analysis • Data integration and large language models • Deep learning for protein structure prediction The #MLAI25<https://www.linkedin.com/search/results/all/?keywords=%23mlai25&origin=HASH…> program includes around 20 hours of practical, group-based work in a hackathon-style format, supported by experienced instructors. In addition to the technical sessions, participants will attend talks on current developments in machine learning and AI in the life sciences. We’ve also included a midweek social activity to create space for informal connection and exchange. Tickets include accommodation and meals. The application deadline is Tuesday, April 29. Submit your motivation here: https://www.vibconferences.be/events/machine-learning-and-ai-summer-school Best regards, Alex

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Course material of the spatial omics data analysis course powered by the ELIXIR Single-Cell Omics community available on GitHub
by BeNeLux bioinformaticians forum 16 Apr '25

16 Apr '25

Dear all, We are excited to share the success of our recently delivered course on spatial omics data analysis – a collaborative effort powered by the ELIXIR Single-Cell Omics (SCO) Community. Spatial omics is revolutionizing bio/medical research by offering unprecedented insights into the spatial context of gene expression. However, with these exciting opportunities comes the challenge of analyzing increasingly complex datasets. This hands-on training brought together 14 expert trainers from across Europe (from ELIXIR-BE, ELIXIR-CH, ELIXIR-DE, ELIXIR-GR, ELIXIR-ES, ELIXIR-NL, and ELIXIR-SE) to empower data analysts with the skills needed to harness the full potential of spatial omics data analysis. Thanks to the support from the ELIXIR Staff Exchange, the event was not only a success in knowledge sharing but also a really nice example of international collaboration. Participants appreciated the balanced mix of theory and hands-on practicals – with one attendee noting, “Thank you for an excellent, extremely useful course! All of the trainers were friendly and answered questions very clearly. I would recommend this course to colleagues.” This positive feedback reinforces the value of a well-organized, safe and collaborative training environment that truly supports data analysts in the field. All course materials are now freely available and reusable on GitHub<https://elixir-europe-training.github.io/ELIXIR-SCO-spatial-omics/>, including videos on the SIB Training YouTube channel<https://www.youtube.com/playlist?list=PLxHnvy2HZSYlnFo0LhxO1irgDby6hV-On> as well. Whether you are a researcher, student, or trainer keen on exploring the rapidly evolving world of single-cell and spatial omics, these resources are for you! We invite you to dive into the course content, share your thoughts, and join our ELIXIR Single-Cell Community<https://elixir-europe.org/communities/single-cell-omics>, to continue building a sustainable spatial omics data analysis training capacity. Best regards, Alex On behalf of the ELIXIR Single-Cell Community

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TransMed COSI announcement
by BeNeLux bioinformaticians forum 15 Apr '25

15 Apr '25

Dear TransMed community, Don’t forget to submit your abstracts<https://www.iscb.org/ismbeccb2025/call-for-submissions/abstracts> for a talk or poster for the TransMed COSI track at ISMB/ECCB 2025 in Liverpool, UK! 🗓️ Deadline: 17 April We’re thrilled to announce our TransMed keynote speakers this year: Dr. Melanie Schirmer, Microbiome and systems biology expert, Technical University of Munich, Germany Dr. Jonathan Carlson, Managing Director, Microsoft Health Futures Please also mark your calendars for several exciting activities related to Translational Medicine at ISMB/ECCB: * TransMed COSI track: Tuesday, 22 July, featuring talks and posters on translational and systems medicine. * ISCB Academy Webinar<https://www.iscb.org/cms_addon/academy/history?year=2025>: Tune in this spring for a dedicated session on cutting-edge advances in Translational Medicine—details coming soon! * Conference Dinner – Come Together: A Night of Networking & Fun Wednesday, 23 July, 19:00–21:00 at Punch Tarmey’s Confirm your participation by Thursday, 17 April We can’t wait to see you in Liverpool or online for this inspiring event. Please share this information with your colleagues and networks! If you have any questions, feel free to reach out to us at TransMed-organizers(a)uni.lu Kind regards, The TransMed COSI Organizing Committee

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Summer School on Microbial Community Data Integration, Leuven 24-25th Sep 2025
by BeNeLux bioinformaticians forum 14 Apr '25

14 Apr '25

Dear colleagues, We are pleased to announce our summer school on data integration with microbial networks and community models taking place in Leuven from 24-25th September 2025. The school will introduce students at the Master and PhD level to different data integration methods to derive biological hypotheses from sequencing data of microbial communities. These methods include black-box approaches that do not require a mechanistic understanding (e.g. association networks, machine learning) and white-box approaches that do (mathematical models). The latest developments in the field will be covered through research talks, while tutorials will give participants hands-on experience with selected methods. For more information and registration, please visit: http://msysbiology.com/microbialdataintegration/ Kind regards, The organising team Karoline Faust & Haris Zafeiropoulos

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Postdoc position: cross-species translation of gene regulation modules in plants
by BeNeLux bioinformaticians forum 10 Apr '25

10 Apr '25

Dear all, The Wageningen Bioinformatics Group has a vacancy for a postdoctoral researcher on an exciting project that is part of CropXR, a national public-private initiative that aims to develop more resilient crops. Are you looking for a research position at the intersection of plant biology and computer science? Are you interested in developing new, machine learning-based bioinformatics methods, in close collaboration with a large team of modellers and experimentalists? If so, this postdoc position may be for you. Please find more information and an application link (deadline May 12, 2025) here: https://www.wur.nl/en/vacancy/postdoc-position-on-cross-species-translation… Dick de Ridder Bioinformatics Group, Wageningen University

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ISMB/ECCB 2025 CompMS – Abstract submission deadline (April 17, 2025)
by BeNeLux bioinformaticians forum 10 Apr '25

10 Apr '25

— ISMB/ECCB 2025 CompMS – Abstract submission deadline (April 17, 2025) — [https://lh7-rt.googleusercontent.com/docsz/AD_4nXcGQGaugZxhKBw668A-zDcWk1EX…] We would like to remind you that the abstract submission deadline for the Computational Mass Spectrometry (CompMS) session at the ISMB/ECCB 2025 conference is April 17, 2025. This is also the deadline to apply for an early-career researcher travel fellowship! We encourage you to submit your abstract today and join us during the ISMB/ECCB 2025 conference in Liverpool (or virtually) on July 20–24, 2025. ⏰ We are delighted to offer travel fellowships for early-career researchers (ECRs). Fill out this form<https://forms.gle/6hz43G3ZNQuVxwhn8> to apply for one of the $300 travel fellowships. Eligibility criteria include being an early career researcher (undergraduate student, graduate student, postdoctoral researcher, or equivalent) and having submitted an abstract to the CompMS track. Key dates April 17, 2025: Abstract & travel fellowship submission deadline May 13, 2025: Talk/poster acceptance notifications May 15, 2025: Late poster submission deadline May 22, 2025: Late poster acceptance notifications July 20–24, 2025: ISMB/ECCB conference * July 22, 2025: CompMS COSI * Venue: ACC Liverpool, Kings Dock St, Liverpool L3 4FP, United Kingdom / virtual * Website: https://www.iscb.org/ismbeccb2025 Abstract submission deadline The abstract submission deadline for ISMB/ECCB 2025 is fast approaching! Submit your abstract to ISMB/ECCB to present your work at the leading bioinformatics/computational biology conference. Attend the CompMS session to learn about the latest algorithmic advances in computational mass spectrometry. Please remember to select the CompMS COSI as your session of interest upon submitting your abstract. Call for abstracts: https://www.iscb.org/ismbeccb2025/call-for-submissions/abstracts ECR travel fellowship application: https://forms.gle/EUbckZCV9NuuvZQDA We look forward to seeing you at ISMB! The CompMS organizing committee. Wout Bittremieux Isabell Bludau Marie Brunet Lindsay Pino Timo Sachsenberg More information about ISMB/ECCB 2025: Combining the annual Intelligent Systems for Molecular Biology (ISMB) and the European Conference on Computational Biology (ECCB), this is the world’s largest bioinformatics/computational biology conference. Every year it brings together scientists from computer science, molecular biology, mathematics, statistics, and related fields and provides an intense multidisciplinary forum for disseminating the latest developments in bioinformatics/computational biology. The conference fosters fresh dialogues, collaboration and learning opportunities, and is a gathering which shapes the future of the field. At the heart of the scientific program are ISCB’s Communities of Special Interest (COSIs), enabling community involvement and bolstering ISMB/ECCB’s reputation as the leading conference in the field. The CompMS COSI promotes the efficient, high-quality analysis of mass spectrometry data through dissemination and training in existing approaches and discussion of new, innovative approaches. The CompMS initiative aims to exploit synergies between different mass spectrometry-based application domains, in particular proteomics, metabolomics, and lipidomics.

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Inquiry to post two job opportunities at a biotechnology start-up company
by BeNeLux bioinformaticians forum 10 Apr '25

10 Apr '25

Dear Sir/Madam, Good morning! This is Xin Zhang ( https://www.linkedin.com/in/xin-zhang-20717b259/) who was a PhD student with Berend Snel and Michael Seidl from Utrecht University. I have been following the BBC list for a long time and enjoy the information you share. Currently, I am working at a start-up biotechnology company, Novobiom (https://www.linkedin.com/company/novobiom/) in Belgium, and we are happy to hire two permanent positions. Could you please let me know if it's possible to post the hiring information on the BBC list? I have attached the two job descriptions here. Many thanks! Xin Zhang Lead Computational Mycologist +31 0645902772 Avenue Jean Monnet 1 1348 Louvain-la-Neuve, Belgium

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Bioinformatician - BaseClear B.V.
by BeNeLux bioinformaticians forum 09 Apr '25

09 Apr '25

🚀 We're hiring - Bioinformatician wanted Are you passionate about data-driven discovery and eager to apply your skills to real-world commercial projects? We're looking for a Bioinformatician to join our team! In this varied and impactful role, you’ll: 🔍 Analyze data for commercial projects 🧫 Maintain and improve our internal (meta)genomics and transcriptomics pipelines and databases 🧪 Collaborate with our Product Development team on exciting new products ✅ Be a key player in ensuring the quality and performance of our bioinformatics tools We're seeking someone with: 🎓 A Bachelor’s or Master’s degree in Bioinformatics 💻 Strong experience in bioinformatics, programming, and DNA sequence analysis 🌟 A proactive mindset and enthusiasm for working across diverse projects 📍 Location: Leiden Bio Science Park If you're looking to grow in a dynamic environment where your work truly makes a difference, we’d love to hear from you. 📩 If you’re interested in this position, please apply via the website: https://www.baseclear.com/career-jobs/bioinformatician/ Met vriendelijke groet, Kind regards, Mark Bessem Manager Bioinformatics [cid:image001.jpg@01DBA949.E815A140] General: +31 (0)715 23 39 17 www.baseclear.com<https://www.baseclear.com/> [cid:image002.png@01DBA949.E815A140]<https://www.linkedin.com/company/baseclear/> Please consider the environment before printing this email. Disclaimer<https://www.baseclear.com/disclaimer>

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Courses in Long-read bioinformatics and Metagenomics
by BeNeLux bioinformaticians forum 08 Apr '25

08 Apr '25

Dear all, We are excited to announce two upcoming online courses designed to advance your expertise in bioinformatics: 1. Introduction to Long-read Bioinformatics * Dates: 28 April – 1 May 2025 * Time: 10:00 AM – 3:00 PM BST (including a 1-hour lunch break) * Venue: Online * Registration Fee: * £371 – University of Edinburgh staff/students * £390 – Other university or registered charity staff/students * £408 – Industry staff This course offers a comprehensive introduction to long-read sequencing technologies, focusing on Oxford Nanopore and PacBio platforms. Participants will engage in hands-on tutorials covering data pre-processing, genome assembly, structural variant detection, and base modification analysis. 2. Metabarcoding and Metagenomics * Dates: 6–9 May 2025 * Time: 10:00 AM – 3:30 PM BST (including a 1-hour lunch break) * Venue: Online * Registration Fee: * £390 – University of Edinburgh staff/students * £410 – Other university or registered charity staff/students * £428 – Industry staff This course delves into the principles of metabarcoding and metagenomics, providing practical experience with both short and long-read data analysis. Participants will learn to use tools such as Qiime2, NanoClust, MetaPhlAn, HUMAnN, MEGAHIT, CheckM, and GTDB-Tk for taxonomic and functional annotation, as well as metagenome-assembled genome creation. Registration Details: Each course is limited to 20 participants. To secure your place, please register at the links below: * Introduction to Long-read Bioinformatics: Register Here<https://genomics.ed.ac.uk/event/introduction-to-long-read-bioinformatics-3/> * Metabarcoding and Metagenomics: Register Here<https://genomics.ed.ac.uk/event/metabarcoding-and-metagenomics/> Upon registration, our finance team will contact you to arrange payment. Your place will be confirmed once payment is received. For further information, please contact our training team at egtrain(a)ed.ac.uk. Best regards, Dr Kathryn Campbell Genomics and Bioinformatics Training Coordinator - Edinburgh Genomics School of Biological Sciences University of Edinburgh Email: kcampb2(a)ed.ac.uk [C0537FE1-6FA3-49DE-BC61-6312CF32C502.png] ======================================================== Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender. ======================================================== The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th’ ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336.

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