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

Last call for Version control with Git/Github course 9-10 October 2025 as start of the reproducible data analysis track
by BeNeLux bioinformaticians forum 30 Sep '25

30 Sep '25

Dear all, I’d like to draw your attention to the last call for our course about version control using Git and Github. Version control with Git/GitHub https://training.vib.be/all-trainings/introduction-git-github-14 – 9 and 10 October 2025 If you are interested in the follow-up courses of the reproducible data analysis track, register via the link below: Introduction to High Performance Computing https://training.vib.be/all-trainings/introduction-high-performance-computi… – 17 October 2025, PM Containerisation with Docker and Apptainer https://training.vib.be/all-trainings/introduction-docker-and-apptainer-rep… – 23 and 24 October 2025 Automated pipelines with Nextflow https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d… – 27 and 28 November 2025 We are looking forward to seeing you at one of these courses. Best regards, Alex Dr. Alexander Botzki VIB Training & Conferences | Suzanne Tassierstraat 1 | 9052 Ghent | Belgium ELIXIR Belgium | Suzanne Tassierstraat 1 | 9052 Ghent | Belgium Tel. +32 9 244 66 11<tel:+3292446611> VIB has flexible working hours, so while it suits me to send this e-mail now, please note that I do not expect a reply or action outside of your working hours. Website<https://www.vibtrainingandconferences.be/> | LinkedIn<https://www.linkedin.com/showcase/vibtrainconf/> | Bluesky<https://bsky.app/profile/vibtrainconf.bsky.social> [Image]<https://www.vibtrainingandconferences.be/> [Hx1KyM2Q09lnAAAAAElFTkSuQmCC]

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open post-doc position in bioinformatics / machine learning in Montpellier
by BeNeLux bioinformaticians forum 24 Sep '25

24 Sep '25

Dear colleagues, please feel free to share the offer below for a 18 months post-doc in Bioinformatics/Machine Learning at the IGMM (CNRS) in Montpellier (France). ** *Postdoctoral Position – Mixed Effects Neural Networks for Genome Interpretation* * We are looking for a motivated postdoctoral researcher to join the AI for Genome Interpretation (AI4GI <https://www.igmm.cnrs.fr/team/ia-pour-linterpretation-du-genome/>) group at the IGMM (CNRS, Montpellier) for 18 months. The project is a collaboration between IGMM and IMAG, at the interface of genetics, bioinformatics, statistics, machine learning and deep learning. The projectInterpreting the genome means modeling the relationship between genotype and phenotype, which is the fundamental goal of biology. Achieving this could revolutionize genetics, medicine, and agricultural technology, leading for example to the development of better crops, able to face the challenges posed by global warming._Objectives:_ This project is an interdisciplinary effort at the frontier between Biology (Genetics, Genomics), Bioinformatics, Artificial Intelligence (Neural Networks) and Statistics (LMMs). The aim is to join the Bioinformatics expertise of Dr. Raimondi on the development of GI NN methods and their application to relevant biological problems with the expertise of Dr. Bry and Dr. Trottier on the statistical inference of Linear Mixed Models (LMMs). The project’s goal is to develop a new breed of Mixed Effects Neural Networks (MENN) for Genome InterpretationI that take the best from both worlds, merging the flexibility and power of NNs with the ability of LMMs to robustly learn from structured and noisy (non i.i.d.) data, applying them on the prediction of both plantsand humanphenotypes. These models will combine the flexibility of neural networks with the statistical robustness of linear mixed models to tackle one of biology’s most fundamental questions: how do genetic variants determine phenotypes? The postdoc will: * Start by familiarizing with existing research and methods for genome interpretation (GI NNs, LMMs, GWAS). * Familiarize with the sequencing data * Develop and benchmark MENN prototypes on sequencing datasets (WES/WGS), starting first from model organisms and then working on disease risk prediction in humans. _Candidate profile:_We are looking for a motivatedand curious candidate, with a strong passion for scienceand for scientific discovery through the use and creation of new neural networks and machine learning methods. Bioinformatics and Genome Interpretation are multi-disciplinary and rapidly evolving fields. Therefore, the candidate is expected to 1) be eager to continuously learnnew skills, methods and concepts, and 2) to enjoy finding new solutionsin the face of new and unforeseen difficulties. The ideal candidate has very good 1) python programming skills, 2) understanding of the mathematical foundations and principles of Machine Learning, Linear Algebra(vectorial and matricial operations, optimization), with a particular focus on Neural Networks, 3) problem solving skills, 4) familiarity with GNU/Linuxenvironment. A good understanding of the basic concepts of Bioinformatics is not necessary but welcome. The project will consist in developing un-orthodox Neural Network models with Pytorch. At least the B2 level of English is required. Skills requiredWe are looking for someone with: * Strong backgroundin neural networks, machine learning, linear algebra and an understanding of statistics. * Solid programming skills in Pythonand in scientific computing(PyTorch, scikit-learn, numpy, etc). * Familiarity with GNU/Linux. * Problem solving skills. * Good communication and teamwork skills. * Knowledge of linear/mixed models is a plus. * Familiarity with GWAS, population genetics, or bioinformatics pipelines are a plus. * Experience with the processing of genomic biological data (whole exome or genome sequencing) is a plus _Practical details_ * Location: IGMM, Montpellier (with joint supervision at IMAG). * Duration: 18 months. * Starting date: flexible, but the candidate must be selected beforethe end of 2025. If you’re interested in working at the crossroads of AI, statistics, and genomics—and in developing new methods rather than just applying existing ones—we’d like to hear from you. You can apply from this link * emploi.cnrs.fr Portail Emploi CNRS - Offre d'emploi - Postdoctoral Researcher – Mixed-Effects Neural Networks for Genome Interpretation (M/F) <#> 🔗 https://emploi.cnrs.fr/Offres/CDD/UMR5535-SARADE-091/Default.aspx?lang=EN <https://emploi.cnrs.fr/Offres/CDD/UMR5535-SARADE-091/Default.aspx?lang=EN> -- Daniele Raimondi, PhD Chaire de Professeur Junior CNRS AI for Genome Interpretation group Institut de Génétique Moléculaire de Montpellier (IGMM) 1919 Route de Mende 34090 Montpellier, France - obscurum per obscurius -

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CFP OLA'2026 Optimization & Learning @Crete (Greece)
by BeNeLux bioinformaticians forum 16 Sep '25

16 Sep '25

Apologies for cross-posting. Appreciate if you can distribute this CFP to your network. **************************************************************************************** OLA'2026 International Conference on Optimization and Learning 28-30 April 2026 Chania, Crete, Greece http://ola2026.sciencesconf.org/ SCOPUS Springer Proceedings **************************************************************************************** OLA is a conference focusing on the future challenges of optimization and/or machine learning methods and their applications. The conference OLA'2025 will provide an opportunity to the international research community in optimization and learning to discuss recent research results and to develop new ideas and collaborations in a friendly and relaxed atmosphere. OLA'2026 welcomes presentations that cover any aspects of optimization and/or machine learning research such as big optimization and learning, optimization for learning, learning for optimization, optimization and learning under uncertainty, deep learning, new high-impact applications, parameter tuning, 4th industrial revolution, computer vision, hybridization issues, optimization-simulation, meta-modeling, high-performance computing, parallel and distributed optimization and learning, surrogate modeling, multi-objective optimization ... Submission papers: We will accept two different types of submissions: - S1: Extended abstracts of work-in-progress and position papers of a maximum of 3 pages - S2: Original research contributions of a maximum of 12 pages Important dates: =============== Paper submission deadline extension Dec 19, 2025 Proceedings: Accepted papers in categories S1 and S2 will be published in the proceedings. A SCOPUS and DBLP indexed Springer book will be published for accepted long papers. Proceedings will be available at the conference. -- *********************************************************************** OLA'2026 10th International Conference on Optimization and Learning (SCOPUS, Springer) April 28-30, 2026, Creta, Greece, https://ola2026.sciencesconf.org *********************************************************************** *********************************************************************** MCDM'2026 28th International Conference on Multiple Criteria Decision Making May 19-24, 2026, Marrakech, Morocco, https://mcdm2026.sciencesconf.org *********************************************************************** Prof. El-ghazali TALBI Polytech'Lille, University Lille - INRIA CRISTAL - CNRS

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Registration open for Git/GitHub, Docker and Apptainer and Nextflow courses Autumn 2025 series
by BeNeLux bioinformaticians forum 16 Sep '25

16 Sep '25

Dear all, The registration for the individual courses of the reproducible data analysis track are open for registration: Version control with Git/GitHub<https://training.vib.be/all-trainings/introduction-git-github-14> – 9 and 10 October 2025 Introduction to High Performance Computing<https://training.vib.be/all-trainings/introduction-high-performance-computi…> – 17 October 2025, PM Containerisation with Docker and Apptainer<https://training.vib.be/all-trainings/introduction-docker-and-apptainer-rep…> – 23 and 24 October 2025 Automated pipelines with Nextflow<https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d…> – 27 and 28 November 2025 We are looking forward to seeing you at one of these courses. Best regards, Alex

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Don’t Miss Out: WiDS Belgium Conference Registration Extended
by BeNeLux bioinformaticians forum 09 Sep '25

09 Sep '25

Dear all, We hope you had a wonderful summer! In case you missed it during the holiday season, we’re excited to share that the registration for the second annual *Women in Data Science (WiDS) Belgium conference* is extended until *September 15th*! This one-day conference will be held on *September 26th, 2025 at the VIB in the city of Ghent* and *all genders are invited to attend* and show support to the cause. The conference is an annual event that aims to inspire and educate data scientists and to support women in the field by providing a platform for learning, sharing, and networking. *No need to be an expert data scientist; just bring your curiosity and a desire to learn! * We’re also offering two mentorship sessions with limited spots available, allocated on a first-come, first-served basis: - *Anastasia Karavdina* — How to Prepare Your Transition into Industry as a Data Professional - *Lynn Verbeke* — Navigating the Biotech Jungle: Real-World Skills for Bioinformaticians Visit our *website <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.women…>* to find out more about WiDS Belgium and the conference. Follow us on *LinkedIn <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.linke…>* or *X <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.c…>* to be up to date when we reveal more details of the agenda. *Know someone who’d be interested? Don’t hesitate to pass this invitation along!* We hope to see you in Ghent in September! Best regards, Women in Data Science Belgium

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Research Software Engineering Day: Promotion for the call for contributions
by BeNeLux bioinformaticians forum 05 Sep '25

05 Sep '25

Dear colleagues, We would like to thank you for your efforts in helping us to promote the upcoming edition of the Research Software Engineering Day, taking place on 4 December 2025. As the submission deadline for contributions (15 September) is approaching, we would like to ask you to shar the call through your communication channels once more, if appropriate. We have attached the promotional materials to this email. Please feel free to use or adapt them as needed. Thank you in advance for helping us spread the word and generate enthusiasm for RSE Day 2025! Rebecca Burke Informationspecialist Research KU Leuven Libraries – Artes and Nexus Mgr. Ladeuzeplein 21 - bus 5591 3000 Leuven Universitylibrary, kantoor 02.39 (Artes) or 02.13 (Nexus-RDM) | ( +32 16 37 74 20 [World] Artes Research website<https://bib.kuleuven.be/english/artes/artesresearch> • The Scholarly Tales blog<https://scholarlytales.hcommons.org/> • artesresearch(a)kuleuven.be<mailto:artesresearch@kuleuven.be> • rdm(a)kuleuven.be<mailto:rdm@kuleuven.be> I do not work on Mondays [Logo_e-mailhandtekening] [cid:image004.png@01DC1E77.0173A590]<https://www.kuleuven.be/rdm/en/training/events/rse-day-2025/research-softwa…> From: Rebecca Burke On Behalf Of RDM Events Sent: woensdag 18 juni 2025 14:15 Subject: Research Software Engineering Day: Promotion for the call for contributions Dear colleagues, On December 4, 2025, KU Leuven will host the next edition of the Research Software Engineer Day (RSE day). The RSE Day event aims to further shape and stimulate the Belgian Research Software Engineering Community (BE-RSE), on the one hand, and to serve as a platform to exchange best practices around research software that can improve scientific research, on the other. This year, there will be a special focus on open source and open hardware initiatives. To shape the program, we are launching a Call for Contributions to encourage research software engineers, researchers, research support staff and others to take part in the event. More information about the event can be found on our website<https://www.kuleuven.be/rdm/en/training/events/rse-day-2025/research-softwa…>. We would greatly appreciate your help in promoting this event and the call for contributions through your channels (newsletters, calendars, info screens, social media, blog). Attached to this email, you will find both a short and a long version of the promotional message, which you are welcome to adapt to suit your platform. If you would prefer us to tailor the message to a specific format, just let us know! We have also developed a few visuals such as an emailbanner, infoscreen and Linkedin/instagramimage. If you are able to include the event in your communications, we would love to hear how and where you plan to do so, so we can keep track of the audiences we’re reaching. Thank you very much in advance! Kind regards, Rebecca Burke Informationspecialist Research KU Leuven Libraries – Artes and Nexus Mgr. Ladeuzeplein 21 - bus 5591 3000 Leuven Universitylibrary, kantoor 02.39 (Artes) or 02.13 (Nexus-RDM) | ( +32 16 37 74 20 [World] Artes Research website<https://bib.kuleuven.be/english/artes/artesresearch> • The Scholarly Tales blog<https://scholarlytales.hcommons.org/> • artesresearch(a)kuleuven.be<mailto:artesresearch@kuleuven.be> • rdm(a)kuleuven.be<mailto:rdm@kuleuven.be> I do not work on Fridayafternoon [Logo_e-mailhandtekening] [cid:image003.png@01DBE042.030EDA50]<https://www.kuleuven.be/rdm/en/training/events/rse-day-2025/research-softwa…>

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BioSB courses - Fall 2025
by BeNeLux bioinformaticians forum 01 Sep '25

01 Sep '25

Dear colleagues, BioSB is thrilled to announce three high‑quality courses scheduled for Fall 2025. Whether you’re looking to sharpen your skills or broaden your expertise, these courses are designed to keep you at the forefront of bioinformatics and systems biology. Check out the details by following the links and see which course fits your interests—or share this with colleagues who might benefit. ✅ ALGORITHMS for GENOMICS 📅 13–17 Oct 2025 – Wageningen From genome assembly and variant analysis to pangenomics. Read more..<https://www.dtls.nl/courses/algorithms-for-genomics-2025/> ✅ SPATIAL OMICS Analysis (co-organized by MGC) 📅 10 – 13 Nov 2025 – Leiden (apply before 12 Sept!) Hands‑on training in spatially resolved transcriptomics (SRT). Read more..<https://www.dtls.nl/courses/spatial-omics-analysis-early-announcement/> ✅ DYNAMIC MODELING in SYSTEMS BIOLOGY (fundamental) 📅 8 – 12 Dec 2025 – Wageningen (early bird discount until 13 Oct) Theory, methods & optimization techniques for systems biology models. Read more..<https://www.dtls.nl/courses/dynamic-modeling-in-systems-biology-2025/> ✨ Don’t miss out on the early bird discounts! ✨ Kind regards, Hartelijke groet, Petra -- Petra Aarnoutse BioSB community manager Office: Health-RI @HI-FIVE✋Beatrixgebouw, Jaarbeursplein 6 , Utrecht Working days: Mon-Thu [cid:f43dde14-6d46-41e0-b184-ff3d20d192f1]

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