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Introduction to Linux for Genomics Online Course
by BeNeLux bioinformaticians forum 14 Aug '24

14 Aug '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. -------------------------------------- Please see details below of a course which may be of interest, and feel free to share with anyone else that may benefit from this: > Introduction to Linux for Genomics Online Course @ Edinburgh Genomics > 23-24 September > https://genomics.ed.ac.uk/event/introduction-to-linux-for-genomics/ Dive into the world of bioinformatics with our Intro to Linux for Genomics course! Whether you're new to Linux or looking to enhance your bioinformatics skills, this course will equip you with the essential tools to navigate and analyze genomic data efficiently. Learn to harness the command line, write shell scripts, and manage large datasets and processes —all tailored for genomics research. Course objectives: * - Learn how to navigate through the file system * - Use basic commands to manage files on the system * - Set permissions for files * - Download remote files and learn how to zip/unzip them * - Construct more complex commands using pipes and redirects * - Learn pattern matching to manipulate file content * - Write your very first shell scripts * - Manage processes running on the system * - Familiarise yourself with some genomics tools run from the command line Many thanks, 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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VIB course: Strategic use of generative AI
by BeNeLux bioinformaticians forum 12 Aug '24

12 Aug '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. -------------------------------------- [cid:image004.png@01DAEBD4.D382A6C0] Over the last few months, the rapid establishment of generative AI (gen AI) and Large Language Models (LLM) has opened new frontiers in a variety of domains. This hands-on class aims to provide you the necessary skills to effectively use this cutting-edge technology in an interdisciplinary way! The course is available in two formats ½ day or full day. You can join us for half day, and learn all the GENERAL uses of gen AI including good practices, ethics, and ownership. This session is aimed to admin, support and anyone that want to use it for work and beyond. When joining us for the full day you can extend your knowledge about the specific uses FOR RESEARCH. This part is aimed for scientific personnel. You have two chances to join us: In Leuven on 30 September Click for registration<https://vibbio.tech/4ckko7f>, before 20 September In Gent on 18 October Click for registration<https://vibbio.tech/3WWkxco>, before 4 October We also have a waiting list that will be use in case of cancelation and to send invitations when new sessions are scheduled. You will have the guidance of your VIB/ELIXIR trainers and plenty of opportunities to ask questions and discuss. [Bruna] [cid:image001.jpg@01DAEC9E.EDBB3D70] Bruna Piereck Alexander Botzki VIB Training & Conferences ELIXIR Belgium Technologiepark-Zwijnaarde 75, 9052 Ghent - Belgium https://technologytraining.sites.vib.be<https://technologytraining.sites.vib.be/> | https://www.elixir-belgium.org/training [Graphical user interface Description automatically generated]<https://vib.be/en/technology> [cid:image009.png@01DAEBD4.D382A6C0]<https://www.elixir-belgium.org/training>

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VIB training opportunities! Increase reproducibility, research impact and learn some programming magic!
by BeNeLux bioinformaticians forum 24 Jul '24

24 Jul '24

Dear colleagues, In this vast world there are always new things to learn, and why would you do it by yourself if you can join us in a fun and productive adventure?!? Check it out how we are planning to make your life easier and more efficient with the upcoming courses. [cid:image007.png@01DADDBE.42099560] I invite you to find your way to learn some magic! The course of introduction to Python programming will take you to a new world of possibilities. With our trainers it will be an easy and fun journey with plenty of opportunities to interact, practice and solve problems. Click here to register: Gentle hands-on introduction to Python programming - in person<https://training.vib.be/all-trainings/gentle-hands-introduction-python-prog…> Gentle hands-on introduction to Python programming - Online<https://training.vib.be/all-trainings/gentle-hands-introduction-python-prog…> We'll be meeting 4 times (morning - in person) and we are available flexible times for questions and support 03 & 16 of September and 01 & 15 of October. [Do I Need Data Management? - The Business Case - GSC] Make your project long living and increase the impact of your publication! For this all you need is to understand how Research Data Management works and how you can apply in your work. Learn more about metadata, DM plan and GDPR requirements all in one go. Click here to register: 3 half days - Research Data Management: your ally on the way to your publication<https://training.vib.be/all-trainings/research-data-management-your-ally-wa…> 01, 08 and 22 October [Image preview] Improve your versioning control and research reproducibility while working in collaboration or in your own projects! You have two opportunities to join us! Check what fits you best! Click here to register: 05/Sep and 06/Sep - registration to: Introduction to Git & GitHub<https://training.vib.be/all-trainings/introduction-git-github-11> 06/Nov and 07/Nov - registration to: Introduction to Git & GitHub<https://training.vib.be/all-trainings/introduction-git-github-12> [Meme between developer and product manager who are sporting super ironic and sarcastic grins. Developer says: "It works on my computer." Product manager says: "Yes, but we are NOT going to give your computer to the customer."] Go away of the "works on my machine" kind of problem! Learn about using Containers locally and in the Super computer (HPC) to increase reproducibility, avoid version problems, and on top it might increase the impact of your publication. Advance yet another level in the reproducibility goal by applying this in a NextFlow pipeline! Click here to register: 14/Out and 15/Out - registration to: Docker and Apptainer (Singularity) for reproducible and automated analysis<https://training.vib.be/all-trainings/docker-and-apptainer-singularity-repr…> 21/Nov and 22/Nov - registration to: NextFlow for reproducible and automated analysis<https://training.vib.be/all-trainings/nextflow-reproducible-and-automated-d…> See more offers at VIB<https://www.linkedin.com/company/vib/> training website!! Bruna Piereck Bioinformatics Training Expert VIB Technology Training ELIXIR Belgium Technologiepark-Zwijnaarde 75, 9052 Ghent - Belgium https://technologytraining.sites.vib.be<https://technologytraining.sites.vib.be/> | https://www.elixir-belgium.org/training [Graphical user interface Description automatically generated]<https://vib.be/en/technology> [cid:image003.png@01DADDB2.D9226C80]<https://www.elixir-belgium.org/training>

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BNAIC/BeNeLearn 2024 Call for papers deadline
by BeNeLux bioinformaticians forum 23 Jul '24

23 Jul '24

Dear Colleagues, We are pleased to announce the call for papers for the upcoming BNAIC/BeNeLearn 2024 conference, the premier AI and ML event for Belgium, the Netherlands, and Luxembourg. This year's combined 36th BNAIC and 33rd BeNeLearn conference will be held from November 18-20, 2024, at Utrecht, the Netherlands. Conference website: https://bnaic2024.sites.uu.nl/ We invite researchers to submit their unpublished original research in all areas of Artificial Intelligence and Machine Learning. We especially encourage submissions on interdisciplinary topics. High-quality research already published in international AI-related conferences or journals is also welcome for presentation and will be published as extended abstracts. Submission Categories: 1. Type A: Regular Papers – Original research, position, and review papers (up to 14 pages). 2. Type B: Encore Abstracts – Abstracts of recently published work (up to 2 pages). 3. Type C: Demonstration Abstracts – Proposals for demos with a short video (up to 2 pages). 4. Type D: Student Oral and Poster Abstracts – Research by Bachelor and Master students (up to 2 pages). 5. Type E: Late Breaking Poster Abstracts – Ongoing research (up to 2 pages). Important Dates: * Abstract Submission (Type A): August 23, 2024 * Paper Submission (All Types except Type E): August 30, 2024 * Bachelor/Master Thesis Fellowship Application: August 30, 2024 * Late Breaking Poster Submission (Type E): October 8, 2024 * Author Notifications: October 4, 2024 * Camera Ready Submission: October 25, 2024 Accepted contributions will be included in the non-archival conference pre-proceedings. Selected Type A papers will be invited to submit to the post-proceedings in the Springer CCIS series. For more details on submission guidelines and topics of interest, please visit the conference website at BNAIC/BeNeLearn 2024.<https://bnaic2024.sites.uu.nl/call-for-papers-2/> We look forward to your contributions and to welcoming you to Utrecht for an inspiring conference. Best regards, BNAIC/BeNeLearn 2024 Organizing Committee

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PhD position in computational pangenomics
by BeNeLux bioinformaticians forum 22 Jul '24

22 Jul '24

Dear all, The Wageningen Bioinformatics is looking for a PhD student in computational pangenomics. If you're interested in developing efficient algorithms to construct and mine large-scale pangenomes, then this PhD vacancy may be of interest to you! Please find more information and an application link (deadline April 15, 2024) here: https://www.wur.nl/nl/vacature/phd-student-computational-pangenomics-2.htm Sandra Smit & Dick de Ridder Bioinformatics Group, Wageningen University

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PhD position
by BeNeLux bioinformaticians forum 11 Jul '24

11 Jul '24

Dear all, Tomas Pluskal, a collaborator in the ModBioTerp project, has a PhD position available in Prague: https://pluskal.group.uochb.cz/en/open-positions/293/modeling-the-mechanism… Best regards, Aalt-Jan van Dijk Biosystems Data Analysis, Swammerdam Institute, University of Amsterdam

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PhD position in Brussels on AI for Cancer Evolution
by BeNeLux bioinformaticians forum 10 Jul '24

10 Jul '24

Dear all, The Computational Biology and Bioinformatics group of the Université Libre de Bruxelles (Profs Fabrizio Pucci and Marianne Rooman https://3bio.polytech.ulb.be/en/bioinfo) is seeking candidates for a PhD position funded by a Televie grant in collaboration with the IRIBHM group of Prof. Maxime Tarabichi (https://iribhm.org/maxime-tarabichi/) Research project: Fundamental open questions in cancer research include how and which somatic mutations confer an evolutionary advantage to cancer cell clones. Their understanding would contribute to precision immunotherapies and the prediction of tumor evolution. Our project « Leveraging artificial intelligence for improving prediction of cancer cell fitness and clonal evolution » aims to advance the identification of key somatic mutations in cancer initiation and progression and to understand the mechanisms underlying clonal expansion with the help of artificial intelligence techniques. The project will be carried out within a multidisciplinary and enthusiastic bioinformatics team. Offer: We are offering you a PhD position for 4 years, to come and work in our two laboratories with strong expertise in the field of bioinformatics, artificial intelligence and computational genomics. The starting date is October 2024. Required: - Master's degree in sciences (Bioinformatics, Physics, Chemistry, Informatics, Biology) or (Bio)Engineering. - Good programming skills. Desirable: - Experience in artificial intelligence techniques and/or bioinformatics. - Knowledge of computational genomics Contact: Please submit: (1) a cover letter detailing your background and interest in the position, (2) a full CV and (3) one reference (with email address and phone number), to Prof. Fabrizio Pucci (fabrizio.pucci(a)ulb.be<mailto:marianne.rooman@ulb.be>) Fabrizio

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PhD position at Wageningen University
by BeNeLux bioinformaticians forum 10 Jul '24

10 Jul '24

Dear all, We have an open PhD position at Wageningen University that combines bioinformatics and modelling to study spatiotemporal diversity of phages: https://www.wur.nl/en/vacancy/phd-position-in-spatiotemporal-diversity-of-p… Best regards, Anne -- Dr. Anne Kupczok Assistant Professor Bioinformatics, Department of Plant Sciences, Wageningen University http://www.wur.nl/en/Expertise-Services/Chair-groups/Plant-Sciences/Bioinfo…

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PhD position
by BeNeLux bioinformaticians forum 09 Jul '24

09 Jul '24

Dear all, We have a PhD position available on using a combination of machine learning and mechanistic modelling: https://vacatures.uva.nl/UvA/job/PhD-Candidate-in-Integrated-Modeling-for-P… Best regards, Aalt-Jan van Dijk Biosystems Data Analysis, Swammerdam Institute, University of Amsterdam

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Post-doc Researcher in Spatial Gene Expression in Muscular Dystrophy
by BeNeLux bioinformaticians forum 09 Jul '24

09 Jul '24

Dear all, We have a postdoc position at the Leiden University Medical Center to study the effect of gene therapy in the context of muscular dystrophies using spatial transciptomics. This is a joint position between the Neuromuscular Disorders Biomarker group of Dr. Pietro Spitali and my group (Computational genomics group) at the Department of Human Genetics. You can find more information and apply here: https://www.lumc.nl/en/about-lumc/werken-bij/vacancies/d.24.es.dj.86-post-d… Feel free to forward this message and to reach out if you are interested. Cheers, Ahmed Ahmed Mahfouz, PhD | Associate Professor, Department of Human Genetics Leiden University Medical Center | Dept. of Human Genetics | P.O. Box 9600, 2300 RC Leiden | Postal zone S4-P Room R-04-022 | Phone +31 71 52 69513 https://www.mahfouzlab.org/

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