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Final registration for Research Software Engineering Day and Coding for AI courses on 22nd of November
by BeNeLux bioinformaticians forum 14 Nov '24

14 Nov '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- Dear all, The final registration deadline for Research Software Engineers Day is approaching on 22nd of November. This event will take place on 6 December in Brussels at Hoek 38. Check out our final agenda here: https://www.vibconferences.be/events/research-software-engineers-day If you're a research software developer, make sure not to miss this opportunity! Workshops preceding RSEng24 Preceding the Research Software Engineers Day, a hands-on workshop will occur on 5 December. These workshops dive into the world of AI. You can choose to learn how to best use genAI for coding or how to use local LLMs to run your analysis in the HPC. Tickets to the workshops be purchased separately or in addition to a ticket for the RSE day. Find out more below: Workshop: Getting the Most Out of AI Coding Assistants https://www.vibconferences.be/workshop-getting-the-most-out-of-ai-coding-as… Workshop: Using Large Language Models locally https://www.vibconferences.be/workshop-using-large-language-models-locally Best regards, Alex On behalf of the Organising Committee

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Postdoc Spatial and single cell seed transcriptomics Wageningen University
by BeNeLux bioinformaticians forum 07 Nov '24

07 Nov '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- We are looking for a postdoc with an interest in spatial and single cell transcriptomics who would like to contribute to investigating gene expression and translational profiles in germinating seeds. https://www.wur.nl/en/vacancy/postdoc-spatial-and-single-cell-seed-transcri… Best regards, Harm Nijveen Bioinformatics group Wageningen University https://www.wur.nl/en/research-results/chair-groups/plant-sciences/bioinfor…

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ESSAI 2025 CALL FOR COURSE PROPOSALS
by BeNeLux bioinformaticians forum 07 Nov '24

07 Nov '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- (apologies for multiple postings) ESSAI 2025 CALL FOR COURSE PROPOSALS 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: December 8, 2024: Course preliminary details (mandatory) December 15, 2024: Full course proposal submission January 26, 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 December 8, 2024: Proposers must submit on Microsoft CMT the name(s) of the lecturers(s), the course title, the ESSAI area targeted, the course level, and a short abstract. By December 15, 2024: The submission must be completed by uploading a PDF with the full course proposal as detailed above. By January 24, 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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2025 Course Registration Now Open – Including New Genome Assembly & Annotation Course!
by BeNeLux bioinformaticians forum 07 Nov '24

07 Nov '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- We are thrilled to announce that registration for our first wave of 2025 courses is now open! Among them is our exciting new course, Genome Assembly and Annotation. Find the details for this course and others below – simply click on the course dates for more information. We’re also working on more highly requested courses, including hands-on lab-based sessions, so stay tuned! In the meantime, check out some photos from our recent lab course: [lab_photos.png] PREREQUISITE COURSES If you're new to bioinformatics or need to brush up on the basics, we recommend starting with these foundational courses in R and Linux. These skills are essential for many of our advanced courses and for everyday bioinformatics work. * R for Biologists (Online): 20-22 Nov 2024 (Few places left!)<https://genomics.ed.ac.uk/event/r-for-biologists-3/> 15-17 Jan 2025<https://genomics.ed.ac.uk/event/r-for-biologists-2025/> Learn the essentials of working with data in R, from basic syntax to creating complex graphs with ggplot2. * Introduction to Linux for Genomics (Online): 29-30 Jan 2025<https://genomics.ed.ac.uk/event/introduction-to-linux-for-genomics-3/> 3-4 Mar 2025<https://genomics.ed.ac.uk/event/introduction-to-linux-for-genomics-4/> Master the Linux command line, a crucial tool for handling bioinformatics data, with hands-on guidance in navigating files, writing shell scripts, and managing processes. CODING COURSES For those looking to broaden their programming skills, we offer an Introduction to Python course, perfect for tackling bioinformatics tasks with this powerful, flexible language. * Introduction to Python for Biologists (In person): 20-24 Jan 2025<https://genomics.ed.ac.uk/event/introduction-to-python-for-biologists-2/> Gain hands-on experience with Python, learning how to manipulate text, handle files, write functions, and solve common bioinformatics challenges. LAB COURSES Our lab courses provide a rare opportunity to get practical, in-person experience with cutting-edge technology and techniques. * DNA Library Preparation for Short Read Sequencing 6 Feb 2025 (In person)<https://genomics.ed.ac.uk/event/dna-library-preparation-for-short-read-sequ…> Learn about every step of the DNA library prep process, and take a guided tour of the Edinburgh Genomics lab. TRANSCRIPTOMICS COURSES Explore cutting-edge technologies in RNA sequencing with our in-depth analysis workshops, designed for researchers who want to delve into transcriptomics. * RNA-Seq Data Analysis 17-20 Feb 2025 (In person)<https://genomics.ed.ac.uk/event/rna-seq-data-analysis-3/> From experimental design to biological interpretation, this course covers the full scope of RNA-Seq data analysis. * Single Cell RNA-Seq Data Analysis 24-26 Feb 2025 (In person)<https://genomics.ed.ac.uk/event/single-cell-rna-seq-data-analysis/> Learn how to tackle the added complexity of single cell RNA-Seq data, with strategies to gain deeper insights into gene expression at the single-cell level. BIOINFORMATICS COURSES Our bioinformatics courses cover a wide range of skills, with more new offerings being added all the time. * Genome Assembly and Annotation 10-12 Feb 2025 (Online)<https://genomics.ed.ac.uk/event/genome-assembly-and-annotation/> A brand-new course! Learn how to assemble genomes using long read sequencing data and perform comprehensive genome annotation. * Variant Analysis 17-20 Mar 2025 (Online)<https://genomics.ed.ac.uk/event/variant-analysis-2/> Understand how to analyze genomic variants, including quality control, variant discovery, annotation, and interpretation. * Introduction to Long Read Bioinformatics 28 Apr-1 May 2025 (Online)<https://genomics.ed.ac.uk/event/introduction-to-long-read-bioinformatics-3/> Explore the world of long read sequencing, with hands-on sessions on data preprocessing, genome assembly, and structural variant detection. * Metabarcoding and Metagenomics 6-9 May 2025 (Online)<https://genomics.ed.ac.uk/event/metabarcoding-and-metagenomics/> Learn how to analyze metagenomic data and create annotated metagenomes using both short and long read sequencing data. Don’t miss your chance to join these expert-led courses! We look forward to helping you take your skills to the next level. 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. ======================================================== 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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2 positions in medical AI
by BeNeLux bioinformaticians forum 06 Nov '24

06 Nov '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- Dear all, The TumorScope project (https://tumorscope.be/) has two medical AI related positions available: * AI-driven radiogenomic analysis for spatial glioma subtyping * AI-driven radiopathomics for molecular glioma subtyping TumorScope is a joint VUB/UZ Brussels project that aims to build a digital health platform for cancer research, leveraging the unique expertise of an interdisciplinary consortium, to develop AI-driven methods that combine real-world molecular, demographic, clinical and radiomics image data. We focus on cancer as it is a complex disease, with understanding and treatment requiring such multimodal data. Furthermore, we leverage the in-hospital creation of the digital health platform with investigations of the legal and ethical challenges surrounding its development, relating to storage and access of data as well as the use of AI methods for diagnosis. The insights from this research are fed back to the hospital level and connected to practical solutions to enable and stimulate innovative AI-based solutions aimed at improving patient outcomes. If you are interested in these positions, please have a look at the detailed descriptions here: https://tumorscope.be/positions/ Best regards, Wim --------------------------------------------------------------------------------------- Prof. Dr. Wim Vranken Tel: +32 (0)2 6291952<tel:+3226291952> (VUB) VUB - Building E, 5th Floor, E5.02, Pleinlaan 2 1050 Brussels, Belgium Structural Biology Brussels/Artificial Intelligence/Chemistry/Biomedical sciences Associate professor - http://bio2byte.be/ ULB-VUB - Interuniversity Institute of Bioinformatics in Brussels (IB)2 Member and former director - http://ibsquare.be/ ELIXIR - Bringing together life science resources across Europe Co-lead of ELIXIR IDP community, member of ELIXIR-Belgium management board ---------------------------------------------------------------------------------------

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[Save the date] - Disease Maps Community Meeting 2025 in Leuven, Belgium
by BeNeLux bioinformaticians forum 03 Nov '24

03 Nov '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- Dear all, We are happy to announce the upcoming Disease Maps Community Meeting (DMCM2025<https://disease-maps.io/DMCM2025/>), which will be held at KU Leuven in Leuven, Belgium. Event Details: When: April 15-17, 2025 - Block your calendars! Where: KU Leuven<https://www.google.com/maps?ll=50.880655,4.67296&z=14&t=m&hl=en&gl=BE&mapcl…>, Leuven, Belgium Website: disease-maps.io/DMCM2025/<http://disease-maps.io/DMCM2025/> (Please note that the usual domain has changed) Abstract submission deadline: January 31, 2025 via the EasyChair form<https://easychair.org/cfp/DMCM2025> Registration deadline: March 21, 2025 via registration form<https://docs.google.com/forms/d/e/1FAIpQLSfh_A46auLUuvgQpvapHWcG6oAZDtAPhnJ…> We are pleased to inform you that both registration and abstract submission are now open. Please visit the website for more details and submission guidelines. This is the place for our community to share recent developments, exchange ideas, and strengthen collaborations in systems medicine topics, including tool development, standards, curation, network biology, dynamic modelling, and much more on human diseases. We are planning an intensive program with four keynote talks, oral presentation sessions, roundtables, poster sessions, and workshops! Please don't hesitate to reach out with any suggestions or comments regarding the meeting. We look forward to welcoming you to the historic city of Leuven in April 2025! Best regards, on behalf of the organizing committee, Luiz Ladeira ______________________________________ Luiz C. M. Ladeira, PhD Postdoctoral Researcher GIGA Molecular & Computational Biology - Biomechanics Research Unit GIGA Institute, University of Liège Avenue de l'Hôpital, 11, B34 +5 4000 Liège - Belgium

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vacancy postdoc position in machine learning and bioinformatics (3+3 years)
by BeNeLux bioinformaticians forum 24 Oct '24

24 Oct '24

Dear all, At the Department of Data Analysis and Mathematical Modelling of Ghent University we have a vacancy for a postdoctoral researcher in the area of machine learning and bioinformatics. Candidates with a background in uncertainty quantification for ML are especially welcome to apply. More info can be found on the Ugent website: https://jobs.ugent.be/job/Ghent-Post-doctoral-assistant-department-Data-Ana… Kind regards, Willem Waegeman

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Bioschemas for annotation of data - survey for a BioHackathon project
by BeNeLux bioinformaticians forum 24 Oct '24

24 Oct '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- Hi all, I’ll share a survey from a BioHackathon project about annotation of data with Bioschemas (structured data based on schema.org types and profiles). Have you used Bioschemas to markup your data, tools, training materials or other web content? Was it cumbersome, tedious, a joyous experience, or did you fail to get started? Please share your experiences and help us to run the BioHackathon Project 10 ‘Bioschemas for Mortals’ by completing this survey<https://bit.ly/bh2410s> before 1 November. Every response really helps our analysis and takes less than 10 minutes. Your contribution will directly feed into our work as we reimagine, reframe and supplement the existing Bioschemas guidance available. Bioschemas for Mortals pre-event survey<https://bit.ly/bh2410s> We are asking people to describe their familiarity with markup and schemas and how you use them. The responses to this survey will inform the 'Bioschemas for Mortals' project at ELIXIR BioHackathon Europe 2024. Personal details will be treated with confidence by the project organisers. We will not store your email address after the project ends. Complete this form from the perspective of your main role/function, the way you most often use markup. Thanks a lot. Best regards, Alex

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BioSB course: 'Integrated Modeling and Optimization' - 9-13 Dec 2024
by BeNeLux bioinformaticians forum 21 Oct '24

21 Oct '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- Dear colleagues, BioSB is pleased to announce the next course in our course program: INTEGRATED MODELING AND OPTIMIZATION 9 - 13 December 2024, Wageningen (early bird discount until 14 October). About the course: In validating models one always meet with the need to fit models to data. So, the parameters that are present in any realistic model have to be chosen based on comparison of model predictions with data. In this matching process optimization techniques are indispensable. That’s why a considerable part of this course is spent on getting you acquainted with the optimization techniques that are nowadays available and widely used. Numerical optimization also is the basis for so-called flux balance analysis (FBA), commonly used to study large metabolic networks. This type of models and their analysis and simulation is also introduced in the course. Target audience: The course is aimed at PhD students with a background in bioinformatics, systems biology, computer science or a related field, and life sciences. Participants from the private sector are also welcome. A working knowledge of mathematics, especially differential equations, is recommendable, but we will distribute preparation material to be studied by students missing the required background. Furthermore, at the start we offer a math refresher to help those participants who are not (yet) involved in modelling on a daily basis. For more information and for registration, please check our website: Integrated Modeling and Optimization (2024) - Fundamental course - Dutch Techcentre for Life Sciences (dtls.nl)<https://www.dtls.nl/courses/integrated-modeling-and-optimization-2024-funda…> Best regards, Petra -- Petra Aarnoutse BioSB community manager [cid:part1.rYcoYCzS.zi4hvKsP@health-RI.nl]

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💻Just 8 days to submit an abstract for the Research Software Engineers Day - 6th of December, Brussels
by BeNeLux bioinformaticians forum 20 Oct '24

20 Oct '24

Warning! This email originated from outside of PSB. Do not click links or open attachments unless you recognize the sender and know the content is safe. -------------------------------------- Dear all, The abstract deadline for Research Software Engineers Day is approaching fast, make sure not to miss it and submit your abstract before 25 October midnight CET. This event will take place on 6 December in the historical city of Brussels, Belgium and is organized by VIB, a non-profit research institute in life sciences. In addition to the invited speakers we look forward to hearing about your research at this event. You can submit your abstract for the selected talks, flash talks and the BoF sessions (informal discussion based on a shared interest and without any fixed agenda). Submit your abstract here: https://www.vibconferences.be/events/research-software-engineers-day If you're a software engineer and want to show what you're working on, make sure not to miss this opportunity! Workshops preceding RSEng24 Preceding the Research Software Engineers Day, a hands-on workshop will occur on 5 December. These workshops dive into the world of AI. You can choose to learn how to best use genAI for coding or how to use local LLMs to run your analysis in the HPC. Tickets to the workshops be purchased separately or in addition to a ticket for the RSE day. Find out more below: Workshop: Getting the Most Out of AI Coding Assistants https://www.vibconferences.be/workshop-getting-the-most-out-of-ai-coding-as… Workshop: Using Large Language Models locally https://www.vibconferences.be/workshop-using-large-language-models-locally Best regards, Alex On behalf of the Organising Committee

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