February 2025 - BBClist - maillist.psb.ugent.be

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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Snakemake Course – Register Now!
by BeNeLux bioinformaticians forum 17 Feb '25

17 Feb '25

Are you looking to automate and streamline your data analysis workflows for next-generation sequencing (NGS) data? Join our Snakemake for Bioinformatics course to learn how to create scalable, reproducible workflows for RNA-seq analysis, variant calling, bacterial genome assembly, and more! Course Dates: 24-27 March 2025 Location: Online (Cloud-based Linux environment provided) Register here: https://genomics.ed.ac.uk/event/snakemake-2/ Why Snakemake? Snakemake is a powerful, Python-based workflow management system that allows you to define and execute complex bioinformatics workflows efficiently. It avoids redundant computation and seamlessly scales from a personal workstation to high-performance computing (HPC) environments. What You’ll Learn: * Automate NGS data analysis with Snakemake * Create modular, scalable workflows * Integrate external tools and handle dependencies * Optimise workflow performance and share workflows online Who Should Attend? This course is designed for researchers who need to automate bioinformatics pipelines. A working knowledge of the Linux BASH command line is required (our Linux for Bioinformatics course provides a suitable background). No prior Python experience is needed. New to Linux? If you're unfamiliar with the Linux command line, consider attending our Linux for Bioinformatics course first. This one-day workshop provides the essential skills needed to confidently navigate and operate within a Linux environment, preparing you for workflow automation with Snakemake. More details are available here: Introduction to Linux for Genomics<https://genomics.ed.ac.uk/event/introduction-to-linux-for-genomics-4/>. Interested in Variant Analysis? We also offer a dedicated Variant Analysis course that covers essential methods for detecting and interpreting genetic variants in NGS data. Learn more and register here: Variant Analysis<https://genomics.ed.ac.uk/event/variant-analysis-2/>. Register Now! Spaces are limited, so secure your place today. For more details and registration, visit https://genomics.ed.ac.uk/event/snakemake-2/ 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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Enhance your bioimaging data analysis skills – join our VIB courses on Fiji and QuPath in March/April
by BeNeLux bioinformaticians forum 14 Feb '25

14 Feb '25

Dear all, Exciting opportunities for bioimaging data analysis are on the offering of VIB Training and Conferences! Whether you're new to image processing or looking to enhance your skills, we have two hands-on courses introducing important bioimaging data analysis techniques. Basic Image Processing using Fiji March 6, Ghent Master the fundamentals of image processing with Fiji (ImageJ), a powerful and widely used open-source tool. This course provides a solid foundation in image analysis, helping you transition from capturing images to extracting meaningful data. What you'll learn: • The basics of image processing and Fiji's capabilities • How to perform essential image operations • Using advanced plugins for enhanced analysis • Creating automated analysis pipelines using ImageJ macros • Best suited for microscopy researchers with little to no experience Just a laptop with the required software pre-installed—no prior knowledge needed. Registration Deadline: 27 February - https://training.vib.be/all-trainings/basic-image-processing-using-fiji-5 QuPath: Quantitative Pathology & Bioimage Analysis March 7, Ghent or April 11, Leuven Take your bioimage analysis to the next level with QuPath, an open-source software designed for working with slide scanner images. This workshop covers essential techniques and provides practical training in image annotation, classification, and scripting. What you'll learn: • Managing images and annotations in QuPath • Cell segmentation and pixel classification techniques • Extracting features and performing object classification • Basics of scripting for batch image processing • Hands-on practice with your own dataset (optional) Just a laptop with the required software pre-installed—no prior knowledge needed. Registration deadline: 27 February - https://vib.emlnk9.com/lt.php?x=3TxtmrUFUqPUT55qA3P3WOOf1aIpvgLvjMljjXXMIXa… The trainers for both courses are: Benjamin Pavie, Amanda Gonçalves, Jérémy Verbeke of the VIB Bioimaging Core. Limited spots available! Secure your place now and take your bioimaging skills to the next level. Best wishes, Alex

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(synthetic biology) Open positions at Western University, Canada: Syntato project
by BeNeLux bioinformaticians forum 10 Feb '25

10 Feb '25

> reply to Bogumil Karas <bkaras(a)uwo.ca <mailto:bkaras@uwo.ca>> >> Hi everyone, >> >> I will have several openings in my lab at Western University starting as soon as April 1st for the following positions: >> >> 1 Research Associate >> 1 Postdoctoral Fellow >> 1 PhD Student >> >> The "Syntato" project aims to create synthetic genomes, similar to the synthetic diatom project, but focusing on engineering and delivering synthetic potato chloroplast genomes. >> >> I am looking for passionate researchers with expertise in plant tissue culture, particularly potato protoplast isolation and regeneration into full plants. >> >> If you know someone who might be interested, please encourage them to contact me. I would greatly appreciate any referrals! >> >> Thank you >> >> Bogumil >> >> >> >> Bogumil J. Karas >> Assistant Professor >> Western University >> Department of Biochemistry, MBL 374 >> London, ON, N6A 5C1, Canada >> Cell: 519-719-0340 ================================================================== Stephane Rombauts Principal Scientific staff Bioinformatics & Systems Biology Division Tel:+32 <tel:+32> (0)9 331 38 21 fax:+32 (0)9 3313809 VIB-UGent Center for Plant Systems Biology, Ghent University Technologiepark 71, 9052 Gent, BELGIUM strom(a)psb.vib-ugent.be <mailto:strom@psb.vib-ugent.be> http://bioinformatics.psb.ugent.be/ ==================================================================

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Join Us for the NSBM Spring Meeting 2025
by BeNeLux bioinformaticians forum 09 Feb '25

09 Feb '25

Dear Colleagues, On behalf of the Netherlands Society on Biomolecular Modelling (NSBM), we are pleased to invite you to the NSBM Spring Meeting 2025, taking place on 1–2 April, at the University Library Utrecht Science Park. This meeting serves as a dynamic forum for students and researchers to explore recent developments in structural bioinformatics and biomolecular modelling. Meeting Themes Recent breakthroughs in highly accurate predicted structures of biomolecules have shifted the focus to the exploration of biomolecular flexibility and conformational changes. These dynamic aspects are pivotal for unravelling biomolecular interactions, function, and activity, and can be effectively investigated through innovative AI methodologies. While the primary focus of this meeting aligns with the themes listed below, we welcome submissions on any relevant topic within the field of structural bioinformatics as we aim to remain inclusive. 1. Conformational Dynamics Investigate the transitions and intrinsic flexibilities that govern biomolecular function and activity. 2. Biomolecular Interactions Explore AI-based predictions of ligand, protein, and peptide interactions, their binding poses and affinities. 3. Geometric AI in Bioinformatics Discover how cutting-edge deep learning techniques are deployed in the field to achieve unprecedented accuracy and precision. 4. Translational Applications Leverage bioinformatics and data-driven insights to accelerate drug discovery and the development of targeted therapies. We encourage contributions that integrate experimental methods, computational tools, and theoretical insights to advance the field. Key Details * Date and Time: April 1–2, 2025 * Location: Boothzaal M0.3, Mezzanine, University Library Utrecht Science Park * Registration: Free for all participants Registration and Abstract Submission We invite Master’s students, PhD candidates, postdoctoral researchers, and senior scientists to submit abstracts for oral and poster presentations. Please note that submitting an abstract is not mandatory for participation; however, registration is required for everyone attending. * Abstract Deadline: March 15, 2025 * Abstract Length: Approximately 300 words (including title, authors, and affiliations) * Registration: Please register and submit your abstract here<https://forms.gle/mv48FYpmWSnTJQMA9> [https://lh3.googleusercontent.com/OVMchxAMUZe-zDVCeTVbSsiwGwyoAXK5fE_FK7ZR5…]<https://forms.gle/mv48FYpmWSnTJQMA9> NSBM 2025 Registration<https://forms.gle/mv48FYpmWSnTJQMA9> Event Date: 1st - 2nd April 2025 Event Address: Mezzanine, University Library Utrecht Science Park Contact: nsbm25(a)outlook.com forms.gle Why Participate? * Gain insights from keynote presentations by leading experts in structural bioinformatics and AI-driven research. * Present your work to an engaged, knowledgeable audience. * Network and foster collaborations in a multidisciplinary setting. * Enjoy free registration for all participants. For further details and updates, please visit our website: https://www.nsbm.nl/about For any inquiries, feel free to contact us at: nsbm25(a)outlook.com We look forward to welcoming you at the NSBM Spring Meeting 2025. Kind regards, The NSBM Organizing Committee

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Register for the up-coming VIB courses - Git & Gitub, Containers on the HPC and Nextflow for reproducibleand automated data analysis
by BeNeLux bioinformaticians forum 08 Feb '25

08 Feb '25

Dear all, I’d like to draw your attention to a series of courses where you can learn strengthen your skills about reproducible data analysis. Learn about version control, containers, pipelines, and data analysis reproducibility. This will steer you towards the reproducibility of your research, as well as the impact and reliability of research findings and methods. Moreover, using the methods introduced here you can collaborate and experiment in ways that allow reproducibility and creativity to coexist and thrive. You have several opportunities to join us: Micro-credentials: a mini diploma to prove you can make reproducible data analysis https://studiekiezer.ugent.be/2024/micro-credential-reproducible-data-analy… This first session will take place in Ghent 28th February. More details on the announcement of UGent. Or follow each module individually with a certificate of attendance: Reproducibility in practice https://training.vib.be/all-trainings/reproducibility-practice Ghent 28th February Introduction to Git & GitHub https://training.vib.be/all-trainings/introduction-git-github-13 Ghent 10th March Docker and Apptainer for reproducible and automated data analysis https://training.vib.be/all-trainings/docker-and-apptainer-singularity-repr… Ghent 31st March NextFlow for reproducible and automated data analysis https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d… Ghent 28th April You will have the guidance of your VIB and ELIXIR trainers and plenty of opportunities to ask questions and discuss. Looking forward to welcoming you in any of these sessions! Best regards, Alex

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PhD & ML engineer positions in AI & Bioinformatics – University of Antwerp (deadline: March 3, 2025)
by BeNeLux bioinformaticians forum 04 Feb '25

04 Feb '25

Dear colleagues, Our lab at the University of Antwerp is hiring for positions in AI-driven bioinformatics and computational mass spectrometry: * PhD position(s) – Develop cutting-edge deep learning models for molecular data analysis, with applications in proteomics, immunopeptidomics, and metabolomics. Details & apply<https://www.uantwerpen.be/en/jobs/vacancies/academic-staff/?q=3822>. * Machine learning engineer – Build scalable ML software, translate research into high-impact bioinformatics tools, and optimize HPC infrastructure. Details & apply<https://www.uantwerpen.be/en/jobs/vacancies/administrative-and-technical/?q…>. Join our lab! * World-class research environment: Collaborate with experts in AI, bioinformatics, and life sciences in a dynamic and internationally connected research community. * High quality of life: Affordable living, rich cultural heritage, and a thriving international atmosphere in the heart of Europe. * Strong academic ecosystem: Work in a top research university with access to cutting-edge computational resources and interdisciplinary collaboration. 📅 Application deadline: March 3, 2025. Please share with strong candidates! Best, Wout Bittremieux Assistant Professor University of Antwerp

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