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ISMB/ECCB 2025 CompMS – Save the date & call for proposals
by BeNeLux bioinformaticians forum 17 Mar '25

17 Mar '25

— ISMB/ECCB 2025 CompMS – Save the date & call for proposals — [https://lh7-rt.googleusercontent.com/docsz/AD_4nXdoqLBMidPuqjJpwNWHbCzeE2Rv…] Dear colleagues, Please join us during the ISMB/ECCB 2025 conference in Liverpool, United Kingdom for the Computational Mass Spectrometry (CompMS) COSI session on July 20–24, 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. A strong scientific and technical program showcases the best international developments in bioinformatics and computational biology, making ISMB/ECCB 2025 a must attend event. Virtual participation options are also available. We are delighted to offer travel fellowships for early-career researchers (ECRs)! Fill out this form<https://forms.gle/EUbckZCV9NuuvZQDA> 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. Date: * ISMB/ECCB: July 20–24, 2025 * CompMS COSI: July 22, 2025 Venue: ACC Liverpool, Kings Dock St, Liverpool L3 4FP, United Kingdom / virtual Website: https://www.iscb.org/ismbeccb2025 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 Call for proposals Abstract submission for ISMB/ECCB 2025 is now open! 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

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Two Job openings at VIB Training & Conferences Program
by BeNeLux bioinformaticians forum 17 Mar '25

17 Mar '25

Dear all, We are very excited to announce that we have two openings in our team. * Project Manager Training & Conferences: https://jobso.id/mh9y * Data Science and AI Trainer: https://jobso.id/mha4 Please spread the announcement in your network as you see fit. Best regards, Alex

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VIB upcoming courses. Invest in your career !!!
by BeNeLux bioinformaticians forum 14 Mar '25

14 Mar '25

[cid:image001.png@01DB9428.BA2F5B30] Chose the next training and invest in your career! The program offered in VIB consists of fundamental learning and trajectories that include: * GENERAL RESEARCH SKILLS Scientific writing & oral presentations Click for registration<https://training.vib.be/all-trainings/scientific-writing-oral-presentations…>, Leuven 03rd April Intellectual Property workshop Click for registration<https://training.vib.be/all-trainings/ip-workshop>, Gent 02nd April Research Data Management (RDM): your ally on the way to your publication Click for registration<https://training.vib.be/all-trainings/biomedical-research-ethics-4>, FREE, Gent 08th May Biomedical research ethics Click for registration<https://training.vib.be/all-trainings/biomedical-research-ethics-4>, FREE, Gent 16th May * PROGRAMMING Gentle hands-on introduction to Python programming Click for registration<https://training.vib.be/all-trainings/gentle-hands-introduction-python-prog…>, Online 29th April * REPRODUCIBILITY Docker and Apptainer for reproducible and automated data analysis Click for registration<https://training.vib.be/all-trainings/docker-and-apptainer-singularity-repr…>, Gent 31st March NextFlow for reproducible and automated data analysis Click for registration<https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d…>, Gent 28th April * DATA ANALYSIS Functional analysis: the biology behind the genes Click for registration<https://training.vib.be/all-trainings/functional-analysis-biology-behind-ge…>, Leuven 4th April Bioimaging data analysis on the HPC Click for registration,<https://training.vib.be/all-trainings/bioimaging-data-analysis-hpc-1> Leuven 22nd May Spatial Omics: - How to start with spatial omics? Click for registration<https://training.vib.be/all-trainings/how-start-spatial-omics-1>, Leuven 30th April - Hands-on introduction to targeted spatial transcriptomics data analysis Click for registration<https://training.vib.be/all-trainings/hands-introduction-targeted-spatial-t…>, Leuven 23rd June - Hands-on introduction to targeted spatial transcriptomics data analysis Click for registration<https://training.vib.be/all-trainings/hands-introduction-spatial-proteomics…>, Leuven 25th June Check all trainings and conferences that are open for registration in our website<https://www.vibtrainingandconferences.be/#/>! VIB Training & Conferences Technologiepark-Zwijnaarde 75, 9052 Ghent – Belgium vibtrainingandconferences.be<https://www.vibtrainingandconferences.be/#/> | elixir-belgium.org/training<https://www.elixir-belgium.org/training> [Graphical user interface Description automatically generated]<https://vib.be/en/technology>

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PhD in Collaborative Metadata Management for Data-Driven Plant Resilience Enhancement
by BeNeLux bioinformaticians forum 10 Mar '25

10 Mar '25

Hi all, We are seeking a highly motivated PhD candidate to join our research team focused on Collaborative Metadata Management for Large Data Repositories supporting data-driven methods and AI models in plant science. The project is part of the CropXR program, a highly collaborative 10-year national initiative of universities and industry, with a mission to grow resilient crops developed by a data-driven design. This PhD project will analyse and address the requirements for establishing effective metadata management in large data repositories. The expected outcomes are innovative technical solutions, systems, and methodologies for metadata elicitation, metadata evolution, and metadata quality management. The goal of these outcomes is to improve the practices of metadata management in plant sciences in accordance with the FAIR principles (Findable, Accessible, Interoperable, Reusable). This will enable our team of interdisciplinary partners to reliably develop, train and deploy complex AI models for improving plant resilience (e.g., plants which are more resilient to temperature changes or drought). More information: https://careers.tudelft.nl/job/Delft-PhD-Position-Collaborative-Metadata-Ma… Deadline: 13 Apr 2025 kind regards, Thomas

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Learn Variant Analysis – Online Course (17–20 March 2025)
by BeNeLux bioinformaticians forum 04 Mar '25

04 Mar '25

Dear all, Want to master variant calling and annotation? Join our Variant Analysis course (17–20 March 2025) and learn how to detect germline & somatic variants using the GATK pipeline. This hands-on, online training covers germline variant calling, genotype refinement, and interpretation of short-read sequencing data. 📅 Dates: 17–20 March 2025 (9:30 AM – 3:30 PM GMT) 💻 Format: Live online, interactive sessions 👩‍🔬 Who should attend? Researchers with basic Linux knowledge 💰 Fees: * £361 – University of Edinburgh staff & students * £380 – Other university or registered charity staff & students * £397 – Industry researchers Spaces are limited—Register now<https://genomics.ed.ac.uk/event/variant-analysis-2/> or contact egtrain(a)ed.ac.uk for more info! 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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Postdoc on genome assemblies of four plant-parasitic nematode species
by BeNeLux bioinformaticians forum 04 Mar '25

04 Mar '25

Dear all, The Laboratory of Nematology at Wageningen University has an opening for a bioinformatics postdoc position on genome assembly. Are interested in genome biology and do you want to help our understanding of nefarious soil-borne parasites? At the laboratory of Nematology at Wageningen University we are looking for a PostDoc on genome assemblies of four plant-parasitic species. Do you have a keen interest in host-parasite interactions? Do you enjoy applying cutting-edge genomics to current agronomical problems? Are you skilled at genome assembly and eager to explore the genomic and genetic diversity in economically important plant-parasitic species? If yes, then we may have the perfect opportunity for you! Post Doc on genome assemblies of four plant-parasitic species - WUR<https://www.wur.nl/en/vacancy/post-doc-on-genome-assemblies-of-four-plant-p…> Dr. M.G. Sterken Assistant Professor Wageningen University and Research Centre, Laboratory of Nematology Droevendaalsesteeg 1 6708 PB Wageningen Mail: mark.sterken(a)wur.nl<mailto:mark.sterken@wur.nl> Website: www.wageningenur.nl/nem<http://www.wageningenur.nl/nem>

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VIB - Strategic use of Generative AI course Brussels - Just 6 days to register
by BeNeLux bioinformaticians forum 26 Feb '25

26 Feb '25

Registration deadline: 5 March 2025 ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ ‌ Strategic use of Generative AI No Images? Click Here<https://vib.emlnk9.com/lt.php?x=3DZy~GDHV6OiEHR.zgDKW.lu2nygj_9ukuVkXnTEUIX…> [VIB conference header] Dear Bruna Piereck Moura, Over the last few months, the rapid establishment of generative AI and Large Language Models (LLM) has opened new frontiers in a variety of domains. VIB offers a hands-on class to teach you a more effective use of this cutting-edge technology in an interdisciplinary way! You can join us for half day, and learn about the general uses of Gen AI, good practices, ethics and ownership. This session is aimed to anyone interested in using genAI! When you stay with us for the full day you can extend your knowledge about the use for research. The upcoming training takes place in Brussels on 12 March. Register before 5 March and don't miss out! [Register here]<https://vib.emlnk9.com/lt.php?x=3DZy~GDHV6OiEHR.zgDKW.lu2nygj_9ukuVkXnTEUIX…> [https://stripo.cluster.app-us1.com/api/v1/images/tpM3kOUYclzH2Flrx3iIjsG02v…] The class aims to show participants how to effectively integrate new generative AI tools within their work and research workflow. AI tools are not intended as substitutes, but rather as tools to support brainstorming, exploration, analysis and synthesis processes. Objectives include: * Providing a background of the evolution of generative AI models * Providing an overview of the features and capabilities of genAI * Analysing prompt engineering techniques for different purposes * Exploring several applications of genAI in academic research (afternoon session) * Providing hands-on experience with using different genAI tools for work and research purposes * Critically evaluating the AI generated outcomes The trainers are: [https://vib.activehosted.com/cdn-cgi/image/width=650,dpr=2,fit=scale-down,f…] [https://vib.activehosted.com/cdn-cgi/image/width=650,dpr=2,fit=scale-down,f…] Bruna Piereck, VIB / ELIXIR-BE Alexander Botzki, VIB / ELIXIR-BE You can register via vibtrainconf.be<https://vib.emlnk9.com/lt.php?x=3DZy~GDHV6OiEHR.zgDKW.lu2nygj_9ukuVkXnTEUIX…>. During the registration process you will be able to select the project code of your group on which the registration fee for the workshop can be booked. Please do not hesitate to reach out to us<mailto:trainingandconferences@vib.be>, if you would encounter any problems. We look forward to seeing you there! Kind regards, Bruna and Alexander [Upcoming VIB Conferences] [Twitter]<https://vib.emlnk9.com/lt.php?x=3DZy~GDHV6OiEHR.zgDKW.lu2nygj_9ukuVkXnTEUIX…> [Linkedin]<https://vib.emlnk9.com/lt.php?x=3DZy~GDHV6OiEHR.zgDKW.lu2nygj_9ukuVkXnTEUIX…> [Website]<https://vib.emlnk9.com/lt.php?x=3DZy~GDHV6OiEHR.zgDKW.lu2nygj_9ukuVkXnTEUIX…> [Email]<mailto:team@vibconferences.be> Do you have any questions about VIB Training, make sure to check the FAQ page<https://vib.emlnk9.com/lt.php?x=3DZy~GDHV6OiEHR.zgDKW.lu2nygj_9ukuVkXnTEUIX…>. You are receiving this email because you are active in this specific conference topic. Not interested? Click here to unsubscribe<https://vib.emlnk9.com/proc.php?nl=45&c=1654&m=1703&s=4fc9f876f589360040050…> VIB, Suzanne Tassierstraat 1 , 9052 Ghent, Belgium Read your privacy settings here<https://vib.emlnk9.com/lt.php?x=3DZy~GDHV6OiEHR.zgDKW.lu2nygj_9ukuVkXnTEUIX…>

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BioSB HotTopics Symposium - Data representation of small molecules and their application
by BeNeLux bioinformaticians forum 26 Feb '25

26 Feb '25

BioSB is happy to invite you to the next BioSB HotTopics symposium: Data representation of small molecules and their application It will take place in the afternoon of March 25 in Amsterdam and you can register here for free: https://www.dtls.nl/data-representation-of-small-molecules-and-their-applic… Programme: 12:30 – 13:00 Registration 13:00 – 13:05 Introduction BioSB 13:05 – 13:40 Daniel Probst (WUR): Molecular representations: The good, the useful, the weird 13:40 - 14:15 Gabriel Vogel (TU Delft): From Small Molecules to Synthetic Polymers: Adapting Representations and Algorithms for AI-Guided Discovery 14:15 - 14:45 Coffee 14:45 – 15:20 Denise Slenter (Maastricht University): Including more chemistry in metabolomics pathway analysis 15:20 - 15:55 Gerard van Westen (Leiden University): Title TBA 15:55 - 16:20 Discussion 16:20 – 17:00: Drinks

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New Hands-On Genomics Courses – RNA Library Prep & Full-Length 16S Sequencing!
by BeNeLux bioinformaticians forum 24 Feb '25

24 Feb '25

Dear all, We are super excited to announce two new hands-on training courses at Edinburgh Genomics! 🎉 After the success of our recent lab courses (see photo!), we are expanding our offerings with: 🔬 RNA Library Preparation – Lab Course 🧬 Full-Length 16S rRNA PacBio Sequencing & Bioinformatics Analysis (covering both lab work and analysis!) To maximize hands-on experience, we are limiting each course to just 12 participants – spaces are expected to go quickly, so register ASAP to avoid disappointment! ________________________________ 📌 RNA Library Preparation – Lab Course 📅 Dates: 26th – 27th March 2025 📍 Location: Edinburgh Genomics, Ashworth Laboratories, The King’s Buildings, University of Edinburgh, EH9 3FL 🔗 Register here: RNA Library Prep Course<https://genomics.ed.ac.uk/event/rna-library-preparation-lab-course/> What You’ll Learn: Gain practical experience in producing directional mRNA sequencing libraries using the NEBNext UltraExpress® RNA Library Prep Kit. This streamlined, 1-day workflow enables efficient library production from total RNA. ✅ Introduction to Sequencing ✅ Library Preparation & QC ✅ Edinburgh Genomics Lab Tour ✅ MiSeq Loading Demo & QC Discussion ________________________________ 📌 Full-Length 16S rRNA PacBio Sequencing & Bioinformatics Analysis(Lab + Bioinformatics) 📅 Dates: 🔬 Lab Sessions: 8th – 9th April 2025 💻 Bioinformatics Sessions (Online): 15th – 16th April 2025 📍 Location: Edinburgh Genomics, Ashworth Laboratories (Lab) & Online (Bioinformatics) 🔗 Register here: Full-Length 16S Course<https://genomics.ed.ac.uk/event/full-length-16s-sequencing/> What You’ll Learn: This course provides an overview of a workflow for full-length 16S rRNA sequencing using PacBio technology, covering both lab work and data analysis. Participants will: ✅ Explore the advantages of full-length 16S sequencing over short-read approaches, focusing on amplicon generation, library preparation, sequencing, data quality, and analysis workflows. ✅ Learn about primer structure and usage for full-length 16S rRNA amplification. ✅ Compare different approaches to sample barcoding, including PacBio’s Kinnex chemistry for higher-throughput studies. ✅ Understand sequence annotation strategies and how to analyze taxonomic classifications. 🔬 In the Lab: ✔️ Introduction to PacBio Sequencing ✔️ Library Preparation & SMRTbell ligation ✔️ Edinburgh Genomics Lab Tour ✔️ Library QC & Revio Loading Demo ✔️ QC Discussion 💻 In Bioinformatics: ✔️ Introduction to R for sequencing data analysis ✔️ Processing results in SMRT Link ✔️ Sequencing QC & DADA2 pipeline ✔️ Taxonomic annotation & data visualization ________________________________ 📢 Limited spaces – register now to secure your place! For any questions, feel free to contact us at egtrain(a)ed.ac.uk<mailto:egtrain@ed.ac.uk> We look forward to welcoming you to Edinburgh Genomics! Kind 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. ======================================================== [IMG_4525.jpeg] 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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BioSB 2025 - CALL for ABSTRACTS - HURRY!
by BeNeLux bioinformaticians forum 18 Feb '25

18 Feb '25

Dear Colleagues, On behalf of the BioSB 2025 Programme Committee, I cordially invite you to the 11th edition of our annual BioSB Conference! BioSB 2025 will take place on 20&21 May in Baarlo, NL. Read all about it on our BioSB 2025 website<https://www.aanmelder.nl/biosb2025>. This is also a great opportunity for our colleagues in Bioinformatics and System Biology from Belgium, Germany and Luxembourg: Baarlo is in the south of the Netherlands and easy to reach for scientists from accross the Dutch borders. Come over and meet your colleagues! Important note: The deadline for Abstract Submission is on 24 February! Submit your abstracts via this link<https://www.aanmelder.nl/biosb2025/abstract-submission>. BioSB is a great place to be if you want to discuss the latest research developments in bioinformatics, systems and computational biology and their broad applications in life sciences & health, agriculture, food & nutrition. Experienced scientists, entrepreneurs and (PhD) students/colleagues who are just starting their careers come together to share knowledge and to network. This year we have three great scientist programmed to give keynote lectures: * Emma Schymanski<https://www.aanmelder.nl/biosb2025/emma-schymanski> (Luxembourg Centre for Systems Biomedicine LCSB) Exposomics: Where Systems Biology meets Chemistry * James Briscoe<https://www.aanmelder.nl/biosb2025/james-briscoe> (The Francis Crick Institute, London) The Dynamics of Spinal Cord Development * Jan Korbel<https://www.aanmelder.nl/biosb2025/jan-korbel> (European Molecular Biology Laboratory EMBL, Germany) Investigating origins of de novo chromosomal aberration by systematically coupling imaging and genomics This conference is also likely to be of great interest to industrial partners. Please check the sponsor page<https://www.aanmelder.nl/biosb2025/sponsoring> for more information. For example, there are sessions called 'Industrial challenges awaiting academic solutions' and 'Meet your future employer!'. To sum up, check our website<https://www.aanmelder.nl/biosb2025/welcometobiosb2025> for more information, submit your abstract<https://www.aanmelder.nl/biosb2025/abstract-submission> of your talk or poster, and register for BioSB 2025<https://www.aanmelder.nl/biosb2025/registration>! I hope to see many of you in Baarlo! Best regards, Petra -- Petra Aarnoutse BioSB community manager Office: Health-RI @HI-FIVE✋Beatrixgebouw, Jaarbeursplein 6 , Utrecht Working days: Mon-Thu [cid:part1.IqQL0vM6.dOcfTnTq@health-RI.nl]

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