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

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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Postdoctoral Opportunity in Protein Function Prediction at Sorbonne Université
by BeNeLux bioinformaticians forum 10 Oct '24

10 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, Here is the announcement for a postdoctoral opening in Computational Biology at Sorbonne Université (Paris) in the group of Prof. Alessandra Carbone. *"I am seeking a motivated postdoctoral researcher to join my team, Analytical Genomics, at the Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université - CNRS. This position will focus on developing innovative computational methods for the functional classification of the vast array of Carbohydrate-Active Enzymes (CAZymes).* *Our goal is to predict functions for proteins that are not yet classified in CAZy (http://www.cazy.org/ <http://www.cazy.org/>), the leading international resource for glycobiology, which has provided high-quality annotations for nearly 30 years. CAZy manually classifies enzymes that assemble, break down, or bind polysaccharides, covering six major catalytic mechanisms—primarily hydrolases, lyases, and transferases—across nearly 500 enzyme families with well-conserved catalytic mechanisms and substrate-specific functions. Many crystallographic structures are available for these enzyme classes.* *The postdoctoral researcher will develop algorithmic and AI-based approaches, leveraging protein sequences from genomes and metagenomes, as well as protein structures and structural models, to advance our understanding of enzyme functionality and evolution. Working within an interdisciplinary team that includes biochemists, structural biologists, and CAZy curators—who are experts in glycobiology—the successful candidate will contribute to creating a groundbreaking collection of functional data linked to millions of protein sequences involved in carbohydrate enzymatic activities. This work aims to enhance our fundamental understanding of enzyme functions and open new avenues for biotechnological innovation.* *Background of the candidate:The ideal candidate should have a background in computer science, physics, or mathematics.* *Where:The LCQB (http://www.lcqb.upmc.fr <http://www.lcqb.upmc.fr/>) is located in the heart of Paris (5th district) and is part of the Institut de Biologie Paris-Seine at Sorbonne Université - CNRS. The department is dedicated to interdisciplinary research and fosters a collaborative environment for geneticists, molecular biologists, synthetic biologists, physicists, mathematicians, and computer scientists. We benefit from a highly dynamic academic community both on campus and throughout the Paris area.* *When:The tentative start date is January 1st, 2025.* *Contact:Interested candidates should send a CV and a motivation letter to alessandra.carbone(a)lip6.fr "* Best, Fabrizio Pucci, Université Libre de Bruxelles

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Job opportunities in data management, secure process environments and AI models evaluation/validation
by BeNeLux bioinformaticians forum 07 Oct '24

07 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. -------------------------------------- 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 BBC list, The Technical Coordination Node and Computational Node of the Spanish National Bioinformatics Institute (INB/ELIXIR-ES <https://inb-elixir.es/>) based at the Barcelona Supercomputing Center (BSC <https://www.bsc.es>) in Barcelona, Spain, has *three exciting positions to contribute in research data management, secure process environments and AI models evaluation/validation*. Research Data Managers, Biomedical data stewardship and FAIR data management <https://www.bsc.es/join-us/job-opportunities/60624lsinbre2> (RE2) - Closing Date: Wednesday, 16 October, 2024 Research Engineer Securing Processing Environments for Analysing Sensitive Data <https://www.bsc.es/join-us/job-opportunities/51724lsinbre3> (RE3) - AI4S - Closing Date: Tuesday, 15 October, 2024 Research Engineer AI Models Evaluation and Validation @ OpenEBench <https://www.bsc.es/join-us/job-opportunities/51624lsinbre3> (RE3) - AI4S - Closing Date: Tuesday, 15 October, 2024 Should you be interested in any of the vacancies, please submit your application as soon as possible as applications are regularly reviewed and potential candidates are contacted for interviews. We would also be grateful if you could share these positions as you see fit. Warm regards, -- -- Eva Alloza Training coordinator, communication and support officer Spanish National Bioinformatics Institute (INB/ELIXIR-ES) coordination node mail:eva.alloza@bsc.es web:http://inb-elixir.es Barcelona Supercomputing Center (BSC-CNS) Pl. Eusebi Güell, 1-3. E-08034 Barcelona, Spain

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Upcoming Courses @ Edinburgh Genomics
by BeNeLux bioinformaticians forum 07 Oct '24

07 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. -------------------------------------- Secure Your Spot in Our October Courses – A Few Places Remaining! Ready to enhance your skills this October? Register now to reserve your spot in one of our upcoming courses. Whether you're looking to master workflow automation, dive into variant analysis, or get hands-on with RNA sequencing, we’ve got the perfect course for you. Please feel free to share with colleagues and anyone in your network who might be interested. ________________________________ Snakemake Online Course | 14-17th October Boost Your Data Analysis with Snakemake Learn how to streamline complex workflows with Snakemake, the open-source tool for automating, scaling, and documenting your analyses. Key Topics: * Task organization and error handling * Running workflows on local servers or cloud * Conda integration and workflow optimization No Python needed—just basic Linux skills! Register Now<https://genomics.ed.ac.uk/event/snakemake/> to automate your data analysis. ________________________________ Variant Analysis Online Course | 22-25th October Discover Short Variants with GATK Get hands-on experience with short variant discovery (germline & somatic) from short-read data. Learn to: * Process, align reads, and handle BAM files * Call, filter, and annotate variants using GATK Ideal for researchers looking to refine their variant analysis skills. Register Here<https://genomics.ed.ac.uk/event/variant-analysis/> to enhance your expertise. ________________________________ Illumina RNA Library Prep Lab Course | 23-24th October Hands-On RNA Library Prep Master RNA-Seq library preparation in this practical, 2-day lab course. Bring your own RNA samples and work with expert instructors using Illumina kits. What You’ll Learn: * RNA-Seq technology fundamentals * Preparing libraries from RNA samples * Sequencing demonstration and expert guidance from Illumina representatives Seats are limited—Register Now<https://genomics.ed.ac.uk/event/illumina-rna-library-preparation-lab-course/> to gain hands-on experience. BONUS: Complete your learning with our RNAseq Data Analysis Online Course (25-28th November). Take your RNA libraries from bench to publication. Register Here: RNA-seq Data Analysis Course<https://genomics.ed.ac.uk/event/rna-seq-data-analysis/> ________________________________ For a full list of this years courses visit https://genomics.ed.ac.uk/service/training/ We hope to see you in October! 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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Postdoc position (18-24 months) in the data science institute, Hasselt University
by BeNeLux bioinformaticians forum 07 Oct '24

07 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. -------------------------------------- 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, Can you please forward the email below to members of your email list. It is related to a new postdoc passion in my institute. Thanks and best regards, ziv. ########################################### Dear All, Please see below an announcement for a new postdoc position in UHasselt. Best regards, ziv *The data science institute in Hasselt University announces a position for a (m/f/x):* *Postdoc researcher in Bioinformatics/Biostatistics (18-24 months): Integrated analysis of High Dimensional omics data.* *General information about the project * The postdoc research project will be conducted in a close collaboration between the data science institute (DSI, https://www.uhasselt.be/en/instituten-en/dsi <https://rssb.us1.list-manage.com/track/click?u=38957383d167dce9fd9fab623&id…>) in Hasselt University and a global pharmaceutical company and will be focused on integrated data analysis for immune profiling purposes applied to vaccinology. Data analysis tools and software products that will be developed in this project would be available as R or Python packages with full documentation. *Project description* The research project consists of two main tasks: *Task 1 - Unsupervised analysis:* To identify methods for single omics and multi-omics clustering (gene expression, single cell omics data ,individual TCR sequences, surface proteins) that can better approximate antigen-specificity. *Task 2 - Supervised analysis:* Based on the results obtained in part 1, we will define which of the identified features may be predictive of antigen specificity and cross-reactivity. *Data analysis methodology*: cluster analysis & biclustering (for both single and multi-omics setting) , classification and prediction. *Profile and diploma* As a postdoc researcher you will join the dynamic bioinformatics team in the data science institute (DSI) in UHasselt (Belgium) and will collaborate with scientists from both academia and industry. The research work related to both tasks will be conducted in a close collaboration between DSI and a large pharmaceutical company. A successful candidate should have · PhD in bioinformatics/ statistical bioinformatics/biostatistics (with experience of high dimensional data). · You are acquainted with statistical methodologies and had exposure to computer programming in R/Python. · You published (or submitted) manuscripts in the area of bioinformatics/biostatistics. · You are interested in developing new methodology from both theoretical and applied aspects. · You are interested in developing software to the pipeline for data analysis and implement this software within a company environment. · You are willing to closely collaborate with biologists/biostatistians/bioinformations from academia and the pharmaceutical industry. · You have a strong interest in working on both vaccine and drug development problems. · You can work independently and within a team. · You have excellent communication skills. · You enjoy working in a multidisciplinary and multicultural environment. · You speak and write English fluently. *Offer* The appointment takes effect from January/February 2025 for a period of 18-24 months, depending on the candidate experience. *Further information* Prof. dr. Ziv Shkedy, +32 11-26 82 40, ziv.shkedy(a)uhasselt.be <christel.faes(a)uhasselt.be> *Application* Applicants must send their application to , ziv.shkedy(a)uhasselt.be <christel.faes(a)uhasselt.be> *Please add a copy of your PhD diploma and CV (including publication list) to your application.* Deadline for the Application 08, December, 2024

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ELIXIR Single-Cell Omics community course: Spatial Omics Data Analysis, 21-24 January 2025, Lausanne
by BeNeLux bioinformaticians forum 04 Oct '24

04 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. -------------------------------------- We are pleased to announce that the following ELIXIR Single-Cell Omics community course on: Spatial Omics Data Analysis<https://www.sib.swiss/training/course/20250121_SPODA> which will ONLY be in person, in Lausanne (Switzerland) on 21-24 January 2025, is now open for applications. This course delves into the cutting-edge field of Spatial Omics, focusing on Spatially-Resolved Transcriptomics (SRT) technology which provides unprecedented insights into the spatial organization of gene expression within tissues. The rapid and recent advances in SRT technology are transforming our understanding of biological systems, and this course is designed to equip researchers with the tools to harness the power of SRT, adding significant value to biological knowledge and opening new avenues for scientific discovery. In this 3-day course, through lectures and practical sessions, participants will explore both imaging-based and sequencing-based SRT technologies, learning to navigate the entire workflow of SRT data analysis. Further detailed information, prerequisites and application form are available here<https://www.sib.swiss/training/course/20250121_SPODA>. Should you have any questions, please don’t hesitate to contact us at training(a)sib.swiss<mailto:training@sib.swiss>. Please help us spread the new as much as possible by forwarding this announcement to your own channels/networks. Thanks a lot! Best wishes, Diana Marek, for the course organizers [SIB logo] Diana Marek Training Manager & Computational Biologist SIB | Swiss Institute of Bioinformatics Quartier Sorge - Bâtiment Amphipôle - CH 1015 Lausanne - Switzerland t +41 21 692 40 77 Diana.Marek(a)sib.swiss<mailto:Diana.Marek@sib.swiss> - www.sib.swiss<http://www.sib.swiss/> Not working on Wednesdays

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Last Chance! Early Registration & Type E Abstract Deadline for BNAIC 2024
by BeNeLux bioinformaticians forum 02 Oct '24

02 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, Just a quick reminder: the early bird registration deadline for BNAIC 2024 is coming up on 10 October! Register now to secure the discounted rate. Don’t forget, Type E abstract submissions are also due on the same day. Check here: https://bnaic2024.sites.uu.nl/ We look forward to seeing you there! Best regards, Sanne Abeln & Ayoub Bagheri General Chairs BNAIC/BeNeLearn 2024<https://bnaic2024.sites.uu.nl/> BNAIC/BeNeLearn 2024 Organizing Committee Email: bnaic2024(a)uu.nl<mailto:bnaic2024@uu.nl> Website: https://bnaic2024.sites.uu.nl/ Twitter: https://x.com/BNAIC2024 LinkedIn: https://www.linkedin.com/company/bnaic2024/ [A black and yellow logo Description automatically generated] Joint International Scientific Conferences On AI and Machine Learning BNAIC/BeNeLearn 2024 Jaarbeursplein 6, 3521 AL Utrecht. November 18th, 19th and 20th, 2024

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