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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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nf-core hackathon - Amsterdam site!
by BeNeLux bioinformaticians forum 03 Feb '25

03 Feb '25

Hi everyone, My name is Rayan, and I am part of the Data Team (Joep de Ligt’s team) at the Hartwig Medical Foundation in Amsterdam. >From March 24th to 26th, in collaboration with Google, we will be hosting a local site in Amsterdam at the Google offices for the March edition of the nf-core hackathon! This event is open to everyone who wants to get together in an informal setting work on Nextflow and nf-core related things. Interested? Here’s the registration information https://nf-co.re/events/2025/hackathon-march-2025 Spread the news: https://shorturl.at/DTlpI I hope you can join us! With kind regards, Rayan Hassaïne, MSc Bioinformatician, Data Team [Hartwig Medical Foundation] [signature_129242794]<http://www.ccg2025.eu/> A Science Park 408, 1098 XH Amsterdam T +31 (0)20 226 9700<tel:+31202269700> | +31 (0)6 2391 4885<tel:+31623914885> W hartwigmedicalfoundation.nl<https://www.hartwigmedicalfoundation.nl/> | oncoact.nl<https://oncoact.nl/> N Subscribe to our newsletter<https://mailchi.mp/475bfde5c6f3/nieuwsbrieven-hartwig-medical-foundation> [LinkedIn][Instagram][YouTube][Facebook] It is our mission to realize that every cancer patient with metastatic cancer receives a personalized treatment using a complete DNA test

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Master RNA-Seq & Single-Cell RNA-Seq Data Analysis – In-Person & Online Courses
by BeNeLux bioinformaticians forum 03 Feb '25

03 Feb '25

Dear all, Are you working with RNA-Seq or Single-Cell RNA-Seq data? Gain the skills and confidence to analyse your transcriptomics datasets with our expert-led training courses at Edinburgh Genomics. We offer both in-person and onlineoptions to suit your needs. 🔬 RNA-Seq Data Analysis 📍 In-Person: 17–20 February 2025 (Details & Registration<https://genomics.ed.ac.uk/event/rna-seq-data-analysis-3/>) 💻 Online: 16–19 June 2025 (Details & Registration<https://genomics.ed.ac.uk/event/rna-seq-data-analysis-4/>) Learn how to process and analyse bulk RNA sequencing data, from quality control to differential expression analysis, using widely adopted bioinformatics workflows. 🧬 Single-Cell RNA-Seq Data Analysis 📍 In-Person: 24–26 February 2025 (Details & Registration<https://genomics.ed.ac.uk/event/single-cell-rna-seq-data-analysis/>) 💻 Online: 23–25 June 2025 (Details & Registration<https://genomics.ed.ac.uk/event/single-cell-rna-seq-data-analysis-3/>) Explore cutting-edge single-cell transcriptomics analysis, covering pre-processing, clustering, and interpretation of complex datasets. Why join our courses? ✅ Expert-led instruction from experienced bioinformaticians ✅ Hands-on exercises with real-world datasets ✅ Small class sizes for personalised learning ✅ Flexible in-person and online formats These courses are ideal for researchers, bioinformaticians, and students looking to develop their skills in RNA sequencing data analysis. Spaces are limited—register now to secure your place! For any questions, feel free to get in touch. 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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Extended deadline ECCO'2025 Combinatorial Optimization @Marrakech
by BeNeLux bioinformaticians forum 01 Feb '25

01 Feb '25

************************************************************************************* ECCO'2025 38th Conference of the European Chapter on Combinatorial Optimization 8-10 May 2025 Marrakech, Morocco https://ecco2025.sciencesconf.org ************************************************************************************* The 38th Conference of the European Chapter on Combinatorial Optimization will be held in Marrakech (Morocco) from 8 till 10 May 2025. AIMS The ECCO annual meetings aim to bring together researchers in Combinatorial Optimization to present their work, share experiences, and discuss recent advances in theory and applications. CALL FOR ABSTRACTS We invite all researchers, practitioners, and students interested in the following subject areas to submit an abstract: - Theory and applications of combinatorial optimization - Optimal solution methods, approximation algorithms and metaheuristics for combinatorial optimization problems - Integer programming, global optimization, stochastic integer programming, multi-objective programming, mixed optimization, graph theory and network flows - Application domains include, but are not limited to, logistics and supply chain optimization, manufacturing, energy production and distribution, land consolidation, telecommunications, bioinformatics, finance, discrete tomography, discrete and hybrid dynamical systems. IMPORTANT DATES Extended deadline for abstract submission 28 Feb 2025 Notification of acceptance 14 March 2025 Deadline for early registration 28 March 2025 ABSTRACT SUBMISSION Abstracts must be written in English and contain no more than 1,500 characters in plain text format (no formulas are allowed). Please note that the submission MUST be done by the person who will present the paper. For each submitted paper, ONE unique registration must be submitted (e.g., for two submitted papers, two separate registrations must be submitted). SOCIAL EVENTS Conference Dinner: Friday 9 May at Chez Ali PUBLICATIONS Book of Abstracts Special Issue: A special issue of the Journal of Combinatorial Optimization will be devoted in papers presented in the conference. All articles will be refereed according to the high standards of the journal. Details of the process will be given during the conference. COMMITTEES Conference chair El-Ghazali Talbi (chair), University of Lille, France Program and steering committee Jacek Blazewicz, Poznań University of Technology, Poland Bo Chen, University of Warwick, UK Van-Dat Cung, Université Grenoble Alpes, France Alain Hertz, Polytechnique Montréal, Canada Silvano Martello, Università di Bologna, Italy Greet Vanden Berghe, KU Leuven, Belgium El-Ghazali Talbi (chair), University of Lille and INRIA, France Paolo Toth, Università di Bologna, Italy CONTACT Prof. El-ghazali Talbi email: ecco2025(a)sciencesconf.org -- *********************************************************************** OLA'2025 International Conference on Optimization and Learning (SCOPUS, Springer) April 23-25, 2025, Dubai, https://ola2025.sciencesconf.org *********************************************************************** ********************************************************************** ECCO'2025 EURO Conference on the European Chapter of Combinatorial Optimization May 8-10, 2025, Marrakech, Morocco, http://ecco2025.sciencesconf.org *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS

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Genome Assembly and Annotation Online Course - Few Spaces Remaining
by BeNeLux bioinformaticians forum 27 Jan '25

27 Jan '25

Genome Assembly and Annotation Online Course *NEW* Date: 10-12 February 2025 Time: 10am-3pm Register here<https://genomics.ed.ac.uk/event/genome-assembly-and-annotation/> We have a few spaces left on our exciting Genome Assembly and Annotation Course, taking place online from 10–12 February 2025. If you’ve been considering attending, this is your chance—spaces are filling up, and registration closes soon! This hands-on workshop is perfect for anyone working with long-read sequencing technologies like PacBio or Oxford Nanopore, offering practical skills and insights to advance your research. Key Benefits: * Hands-on learning: Master tools for genome assembly, polishing, and annotation. * Hi-C data integration: Learn techniques to boost genome completeness. * Tailored instruction: Explore both prokaryotic and eukaryotic annotation strategies. * Quality assessment: Evaluate your genome assemblies with confidence. Don’t miss out—secure your spot today! <https://genomics.ed.ac.uk/event/genome-assembly-and-annotation/> Genome Assembly and Annotation – Edinburgh Genomics<https://genomics.ed.ac.uk/event/genome-assembly-and-annotation/> genomics.ed.ac.uk<https://genomics.ed.ac.uk/event/genome-assembly-and-annotation/> [cropped-eg_favicon-180x180.png]<https://genomics.ed.ac.uk/event/genome-assembly-and-annotation/> We hope to see you at this unique and engaging course. 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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