December 2024 - BBClist - maillist.psb.ugent.be

'Constraint-based Modeling' - BioSB course 10 feb - Early Bird Discount!
by BeNeLux bioinformaticians forum 02 Jan '25

02 Jan '25

************************************ CHECK THIS OUT: UPCOMING BioSB course: CONSTRAINT-BASED MODELING 10 - 14 Febr 2025 - Wageningen ************************************ We have found a great team of (international) teachers willing to share their insights. International guest speakers: * Almut Heinken https://www.aiche.org/community/bio/almut-heinken * Chris Henry https://www.anl.gov/profile/christopher-s-henry Don't miss out and take advantage of the Early Bird discount - Valid until 16 December! For more information and registration, please follow this link: Constraint-based Modeling<https://www.dtls.nl/courses/constraint-based-modeling-introduction-and-adva…> Happy holidays! Petra Aarnoutse, BioSB community manager [cid:part1.AkII6PEx.kVWjfiPb@health-RI.nl]

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PhD position on explainable AI in pediatric cancer
by BeNeLux bioinformaticians forum 20 Dec '24

20 Dec '24

Dear all, We currently have an opening for a PhD position to work on developing explainable AI models that help us understand which genes and pathways drive tumor type predictions in pediatric cancer. Interested and want to work in a highly dynamic, international environment within the largest pediatric cancer research hospital in Europe, then plesase apply! https://werkenbijprinsesmaximacentrum.nl/en/vacancy/phd-student-explainable… -- Patrick Kemmeren, PhD Principal Investigator & head Big Data Core Princess Máxima Center Associate Professor UMC Utrecht T +31 (0)88 972 90 00 | M +31 (0)6 53 11 25 53 [signature_3833532013] [signature_2266230909] Princess Máxima Center for Pediatric Oncology Heidelberglaan 25 | 3584 CS Utrecht | T +31 (0)88 972 90 00 | > Website<https://research.prinsesmaximacentrum.nl/en/research-groups/kemmeren-group>

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Artificial Intelligence and Machine Learning in Life Sciences: from foundations to applications, 19-23 May 2025, Aussois (FR)
by BeNeLux bioinformaticians forum 19 Dec '24

19 Dec '24

Dear colleagues, We are delighted to announce that the course Artificial Intelligence and Machine Learning in Life Sciences: from foundations to applications <https://moodle.france-bioinformatique.fr/course/view.php?id=34> which will take place in Aussois, France on May 19-23 2025 is now open for applications. Artificial intelligence (AI) has permeated our lives, transforming how we live and work. Over the past few years, a rapid and disruptive acceleration of progress in AI has occurred, driven by significant advances in widespread data availability, computing power and machine learning. Remarkable strides were made in particular in the development of foundation models - AI models trained on extensive volumes of unlabelled data. Moreover, given the large amounts of omics data that are being generated and made accessible to researchers due to the drop in the cost of high-throughput technologies, analysing these complex high-volume data is not trivial, and the use of classical statistics can not explore their full potential. As such, Machine Learning (ML) and Artificial Intelligence (AI) have been recognized as key opportunity areas, as evidenced by a number of ongoing activities and efforts throughout the community. However, beyond the technological advances, it is equally important that the individual researchers acquire the necessary knowledge and skills to fully take advantage of Machine Learning. Being aware of the challenges, opportunities and constraints that ML applications entail, is a critical aspect in ensuring high quality research in life sciences. Recognizing this need, this week-long training will bring together experts from four ELIXIR Nodes and deliver a hands-on, high-intensity course available for members from all ELIXIR Nodes. Learners will be guided across the various steps in Machine Learning, from the foundational concepts, through the deep learning and generative AI techniques, closely complemented by insights into the existing reporting (DOME Recommendations) and regulatory frameworks (EU AI Act). This 4-day school will involve around 10 trainers/helpers from across 4 different ELIXIR nodes and 30 participants from across all ELIXIR nodes. Further detailed information, prerequisites and application form are available here <https://moodle.france-bioinformatique.fr/course/view.php?id=34>. Should you have any questions, please don't hesitate to contact us at contact-formation(a)groupes.france-bioinformatique.fr <mailto:contact-formation@groupes.france-bioinformatique.fr> Kind regards, Olivier Sand ELIXIR-FR Training Coordinator CNRS UAR3601 IFB-core/ UAR2014-US41 PLBS

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4-year postdoc rhizosphere bioinformatics
by BeNeLux bioinformaticians forum 18 Dec '24

18 Dec '24

Dear colleagues, We have an amazing opportunity for a postdoc to study metabolic interactions in the rhizosphere: https://www.uu.nl/en/organisation/working-at-utrecht-university/jobs/bioinf… This is a 4y position shared between our labs, in the context of the MICROP consortium: https://www.microp.org/ Please forward this to interested candidates, and please consider reposting our social media posts: LinkedIn: https://www.linkedin.com/feed/update/urn:li:activity:7270106228121358336/ BlueSky: https://bsky.app/profile/bedutilh.bsky.social/post/3lcik3c4evc2v All the best for end of the year and the holidays! Marnix Medema and Bas Dutilh -- Prof. Dr. Bas E. Dutilh <http://tbb.bio.uu.nl/dutilh> Viral Ecology and Omics Group <https://www.veo.uni-jena.de/> | Metagenomics Group Microverse Cluster <https://microverse-cluster.de/en/> | Theoretical Biology and Bioinformatics <https://tbb.bio.uu.nl/> European Virus Bioinformatics Centre <http://evbc.uni-jena.de/> | Utrecht Bioinformatics Center <https://ubc.uu.nl/> Friedrich Schiller University Jena <https://www.uni-jena.de/en/> | Utrecht University <https://www.uu.nl/>

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Reproducible data analysis trajectory as microcredential: joint offering of VIB & Ghent University
by BeNeLux bioinformaticians forum 18 Dec '24

18 Dec '24

Dear all, Are you ready to ensure the reproducibility of your work and make your research future-ready? Join us for “𝘙𝘦𝘱𝘳𝘰𝘥𝘶𝘤𝘪𝘣𝘭𝘦 𝘋𝘢𝘵𝘢 𝘈𝘯𝘢𝘭𝘺𝘴𝘪𝘴: 𝘈𝘯 𝘌𝘴𝘴𝘦𝘯𝘵𝘪𝘢𝘭 𝘊𝘢𝘱𝘢𝘣𝘪𝘭𝘪𝘵𝘺 𝘪𝘯 𝘔𝘰𝘥𝘦𝘳𝘯 𝘚𝘤𝘪𝘦𝘯𝘤𝘦,” a 9-day microcredential course offered by VIB & Ghent University<https://www.linkedin.com/company/ghent-university/> from February to May 2025. 𝗪𝗵𝘆 𝗶𝘀 𝗥𝗲𝗽𝗿𝗼𝗱𝘂𝗰𝗶𝗯𝗶𝗹𝗶𝘁𝘆 𝗖𝗿𝘂𝗰𝗶𝗮𝗹? Reproducibility lies at the heart of scientific discovery. As analyses become more complex and interdisciplinary, ensuring reliable and replicable results is vital. This course provides the tools and techniques you need to meet these challenges, promoting transparency and robustness in your research. 𝗪𝗵𝗮𝘁 𝗪𝗶𝗹𝗹 𝗬𝗼𝘂 𝗟𝗲𝗮𝗿𝗻? During this hands-on course, you'll gain expertise in: - Version Control with Git and GitHub: Simplify collaboration and manage your code. - Containerization: Master Docker and Apptainer for diverse computational environments. - High-Performance Computing (HPC): Learn concepts and practical use. - NextFlow Pipelines: Build and optimize reproducible workflows for local and supercomputer environments. - Best Practices for Reproducibility: Ensure your work is impactful and reliable. 𝗖𝗼𝘂𝗿𝘀𝗲 𝗗𝗲𝘁𝗮𝗶𝗹𝘀 • Micro-credits: Earn 3 ECTS from Ghent University. • Format: Hands-on projects and oral evaluation. • Location: Ghent, Technologiepark - FSVM II. • Pre-Requisites: Basic shell command knowledge and scripting experience (preparation resources available). • Register here: https://training.vib.be/all-trainings/reproducible-data-analysis Best regards, Alex

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postdoc position available
by BeNeLux bioinformaticians forum 17 Dec '24

17 Dec '24

Dear colleagues, I have a two-year postdoc opening to work on an exciting AI for drug discovery project based at Imperial College in collaboration with the University of Cambridge. Further information at https://imperial.ac.uk/jobs/search-jobs/description/index.php?jobId=21928<https://t.co/ALtuTz5j4T> The deadline is 19/12/2024, but I will consider candidates beyond this until the position is filled. Best regards Pedro Dr. Pedro J. Ballester | Royal Society Wolfson Fellow & Senior Lecturer Imperial College | Department of Bioengineering Group website | https://ballestergroup.github.io/<https://ballestergroup.github.io/> College website | https://www.imperial.ac.uk/people/p.ballester/research.html <https://www.imperial.ac.uk/people/p.ballester/research.html> Networking profiles | https://www.linkedin.com/in/pedroballester/ https://x.com/pjballester <https://x.com/pjballester> Address | Sir Michael Uren Hub, White City campus, 86 Wood Lane, London - W12 0BZ, UK

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PhD position in bio- and cheminformatics
by BeNeLux bioinformaticians forum 15 Dec '24

15 Dec '24

Dear all, Wageningen Bioinformatics is looking for a PhD student in machine learning for bio- and cheminformatics. Are you looking for a PhD position at the intersection of biology, chemistry, and computer science? Are you interested in developing new machine learning methodologies in proximity to and collaboration with experimentalists? If yes, this fully funded PhD position might be an excellent match for you. Please find more information and an application link (deadline 5th January, 2025) here: https://www.wur.nl/en/education-programmes/phd-programme/graduate-schools/w… Daniel Probst & Dick de Ridder Bioinformatics Group, Wageningen University [cid:6d6bb479-cc02-472c-a697-cfc4f9cf82c0]<https://outlook.office.com/bookwithme/user/e1bf24157a0b4dfba8c0e0e3c99fcab4…> Book time to meet with me<https://outlook.office.com/bookwithme/user/e1bf24157a0b4dfba8c0e0e3c99fcab4…>

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ESSAI 2025 CALL FOR COURSE PROPOSALS - extended deadline
by BeNeLux bioinformaticians forum 12 Dec '24

12 Dec '24

(apologies for multiple postings) ESSAI 2025 CALL FOR COURSE PROPOSALS - extended deadline The 3rd European Summer School on Artificial Intelligence - ESSAI 2025 June 30 to July 4, 2025 Bratislava, Slovakia https://essai2025.eu/ <https://essai2025.eu/> IMPORTANT DATES: January 8, 2025 (AoE): Full course proposal submission January 31, 2025: Notification of acceptance or rejection ESSAI SUMMER SCHOOLS ESSAI 2025 is the third edition of the annual summer school on AI held under the auspices of the European Association for Artificial Intelligence (EurAI). ESSAI 2025 will provide an interdisciplinary setting in which courses are offered in all areas of Artificial Intelligence and also from wider scientific, historical, and philosophical perspectives. ESSAI is a central meeting place for students and young researchers in Artificial Intelligence to discuss current research and share knowledge. The first edition of ESSAI was held in Ljubljana, Slovenia, and the second one in Athens, Greece. Both editions were very successful and received excellent feedback from the student and lecturer participants. We look forward to a third edition of ESSAI, which we believe will be very successful as well. TOPICS AND FORMAT OF COURSES ESSAI aims to cover subdisciplines of AI and the interactions between them. Proposals for courses at ESSAI 2024 are invited in all areas of Artificial Intelligence, including but not limited to the following: * Autonomous Agents and Multi-agent Systems (MAS) * Causality and Causal Learning (CL) * Ethical, Legal and Social Aspects of AI (ELS) * Foundation Models (FM) * Knowledge Representation and Reasoning (KR) * Learning Theory (LT) * Natural Language Processing (NLP) * Neuro-Symbolic Learning and Reasoning (NSLR) * Planning & Strategic Reasoning (PLAN) * Reinforcement Learning (RL) * Robotics (ROB) * Safe, Explainable and Trustworthy AI (SET) * Search & Optimization (SO) * Supervised and Unsupervised Learning (ML) * Vision (VIS) * Human-In-The-Loop AI (HLAI) * AI for Social Good (A4SG) * Quantum Machine Learning (QML) Each course will consist of five 90-minute lectures offered daily (Monday-Friday) in the week the school takes place. COURSE CATEGORIES Each proposal should fall under one of the following two categories. *Introductory Courses* Introductory courses are intended to introduce a research area of AI to students, young researchers, and other non-specialists and to foster a sound understanding of its basic methods and techniques. Such courses should enable researchers from related disciplines to develop some comfort and competence in the topic considered. Introductory courses in a cross-disciplinary area may presuppose general knowledge of the related disciplines. *Advanced Courses* Advanced courses are targeted primarily to graduate students who wish to acquire a level of comfort and understanding of current research in an area of AI. While introductory courses will typically focus on one subarea of AI only, advanced courses are encouraged to present a broader perspective on AI, and they should be of interest beyond a single specific area. COURSE PROPOSAL GUIDELINES To be considered, course proposals should closely adhere to the following guidelines. Courses must be presented by lecturers who submitted the proposal. For courses with more than two lecturers, the role of each lecturer should be clearly explained and justified in the proposal. Course proposals should explicitly state the intended course category. Proposals for introductory courses should indicate the intended level, for example, as it relates to standard textbooks and monographs in the area. Proposals for advanced courses should specify the prerequisites in detail. Submitted proposals should include all of the following: a. Contact information for each proposer: Name, affiliation, address, email, web page b. General proposal information: Title, category c. Information about the course content: * Abstract of up to 150 words * Motivation and description (up to two pages) * Tentative outline * Expected level and prerequisites * Appropriate references (e.g., textbooks, monographs, proceedings, surveys) * Whether the course will appeal to students outside of the main area of the course. d. Information about the proposer(s): * Short CVs of the proposer(s) * Evidence that the proposer(s) are excellent lecturers with relevant teaching experience, particularly in delivering intensive interdisciplinary courses. The course proposals will be reviewed by a Program Committee covering all the research areas presented above. PARTICIPATION To keep registration fees to a minimum, all ESSAI's instructional and organizational work is performed completely voluntarily. However, the registration fees of organizers and instructors will be waived. In addition and where appropriate and possible, ESSAI will seek to partially reimburse travel and accommodation expenses associated with delivering a course. If lecturers can cover their travel and accommodation expenses from other sources, this is greatly appreciated. SUBMISSION INFORMATION By January 8, 2025 (AoE): Proposer(s) should upload a PDF with the full course proposal as detailed above. By January 31, 2025, Proposer(s) will be notified whether their proposal has been accepted or not. SUBMISSION PORTAL Please submit your proposals as a single PDF file to https://cmt3.research.microsoft.com/User/Login?ReturnUrl=%2FESSAI2025 <https://cmt3.research.microsoft.com/User/Login?ReturnUrl=%2FESSAI2025> ESSAI 2025 ORGANIZERS General Chair Vida Groznik University of Ljubljana Program Chairs Manolis Koubarakis National and Kapodistrian University of Athens Fabrizio Silvestri Sapienza University of Rome Local Chair Peter Drotár Technical University of Kosice ESSAI Steering Committee Members Giuseppe De Giacomo (Chair, EurAI Board representative) University of Oxford Brian Logan University of Aberdeen & Utrecht University Magdalena Ortiz Technical University of Vienna

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PhD position in the ULB Machine Learning group
by BeNeLux bioinformaticians forum 08 Dec '24

08 Dec '24

Dear all We are looking for a new phd student. Can you please share this information in your professional and social networks? This is the vacancy call; https://euraxess.ec.europa.eu/jobs/297798 Thank you Bien cordialement | Vriendelijke groet | Kind regards Tom ________________________________________________________________________________ prof. Tom Lenaerts co-head of the Machine Learning Group <http://mlg.ulb.ac.be/> Affiliated researcher at the AI lab <http://ai.vub.ac.be/> of the Vrije Universiteit Brussel and the Center for Human-Compatible AI <https://humancompatible.ai/>, UC Berkeley Département d’Informatique Université Libre de Bruxelles (ULB) Boulevard du Triomphe CP212 1050 Brussels. Belgium. Phone: +32 2 650 60 04 Fax: +32 2 650 56 09 Email: Tom.Lenaerts(a)ulb.be <mailto:Tom.Lenaerts@ulb.be> Linkedin <https://www.linkedin.com/in/tom-lenaerts-5606061/>

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Postdoc position in molecular artificial intelligence @ University of Antwerp
by BeNeLux bioinformaticians forum 02 Dec '24

02 Dec '24

Dear colleagues, We have an exciting position for a postdoctoral researcher in molecular artificial intelligence available at the University of Antwerp. You will collaborate with world-leading pharmaceutical companies to develop artificial intelligence solutions to analyze billion-scale mass spectrometry-based metabolomics data. The application deadline for this position is December 18, 2024. We especially encourage candidates with a PhD in quantitative sciences and a strong interest in applying their data science skills to relevant life science challenges to apply. For more detailed information and to apply, please visit our website: https://www.uantwerpen.be/en/jobs/vacancies/academic-staff/?q=3715&descr=Po… We strongly encourage passionate individuals with a keen interest in artificial intelligence and bioinformatics to apply for these positions. The University of Antwerp offers a vibrant research environment, state-of-the-art facilities, and a supportive community of scholars dedicated to pushing the boundaries of knowledge. Please feel free to share this information with anyone who may be interested or qualified. We appreciate your assistance in helping us spread the word and attract exceptional candidates to join our team. Sincerely, Wout Bittremieux Assistant Professor University of Antwerp

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