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RNAseq and Single Cell Analysis Online Courses @ Edinburgh Genomics
by BeNeLux bioinformaticians forum 26 Aug '24

26 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. -------------------------------------- Do you have a project planned that involves RNAseq or single cell analysis? Or looking to gain skills in exciting new areas of genomics? Our upcoming courses are a great way to dive in, and gain new skills and hands on experience! Whether you have prior experience in data science and looking to try something new, or are taking your first steps into more complex data analysis, our series of courses will help you to gain all the skills you need to effectively undertake projects and analyse data. RNA-seq Data Analysis > 17 - 20 September https://genomics.ed.ac.uk/event/rna-seq-data-analysis-2/ > 25 - 28 November https://genomics.ed.ac.uk/event/rna-seq-data-analysis/ From planning an RNA-Seq experiment to drawing biological conclusions from your data, our expert taught workshop will guide you through every step of data analysis. Learn to avoid common pitfalls and fully exploit this powerful technology to delve into the transcriptome of any organism with our upcoming expert taught online RNA-Seq analysis workshops. Single Cell RNA-Seq Data Analysis > 12 - 13 September https://genomics.ed.ac.uk/event/single-cell-rna-seq-data-analysis-2/ Take your RNA-Seq analysis to the next level with single cell RNA-Seq. This technology allows insights with an unpredicted level of detail, but that brings a new level of complexity to the data analysis. Learn how to plan your experiment, deal with some of the many pitfalls when analysing your data, and effectively gain exciting new biological insights with our upcoming expert taught online scRNA-Seq analysis workshop. Attending these courses, and undertaking RNA-Seq data analysis in general, requires a good working knowledge of both Linux and R. If you feel you’re currently struggling in these areas, you can attend our upcoming courses in these to prepare: R for Biologists > 9 - 11 September https://genomics.ed.ac.uk/event/r-for-biologists/ > 20 - 22 November https://genomics.ed.ac.uk/event/r-for-biologists-3/ Join our online workshop to learn R, the powerful statistical computing language, tailored to biological data science, Whether you’re handling data, performing analysis, or creating stunning visualisations, this course has you covered! You’ll also practice making graphs and publication ready figures using mock RNA-Seq data. What you’ll learn: * Get comfortable with R and RStudio * Work with vectors and complex data structures * Load, clean, and explore data * Create beautiful graphs with ggplot2 * Apply your skills to your own datasets Introduction to Linux for Genomics > 23 - 24 September https://genomics.ed.ac.uk/event/introduction-to-linux-for-genomics/ > 29 - 30 January https://genomics.ed.ac.uk/event/introduction-to-linux-for-genomics-3/ 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 analyse genomic data efficiently. Learn to harness the command line, write shell scripts, and manage large datasets and processes - al tailored for genomics research. What you’ll learn: * Learn how to navigate through the file system * Use basic commands to manage and set permissions for files * Download remote files and learn to zip/unzip them * Construct more complex commands using pipes and redirects * Learn pattern matching to manipulate file content * Write your vert first shell scripts * Manage processes running on the system * Familiarise yourself with some genomics tools run from the command line If you have any questions, feel free to reach out. We hope to see you on one of our courses soon! 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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BNAIC 2024 deadline extension: paper submission deadline September 4th, abstract (for type A) August 30th, Bachelor/Master Thesis Fellowship application September 4th
by BeNeLux bioinformaticians forum 23 Aug '24

23 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. -------------------------------------- Dear Colleagues, We have extended the deadline for the paper and type A abstract submissions and for the Bachelor/Master Thesis Fellowship application for the BNAIC/BeNeLearn 2024 conference, the premier AI and ML event for Belgium, the Netherlands, and Luxembourg. The conference will take place from November 18-20, 2024, in Utrecht, the Netherlands. Key Submission Deadlines: * Abstract Submission (Type A): August 30, 2024 * Paper Submission (All Types except Type E): September 4, 2024 * Bachelor/Master Thesis Fellowship Application: September 4 2024 * Late Breaking Poster Submission (Type E): October 8, 2024 We invite submissions in the following categories: * Type A: Regular Papers – Original research, position, and review papers (up to 14 pages). * Type B: Encore Abstracts – Abstracts of recently published work (up to 2 pages). * Type C: Demonstration Abstracts – Proposals for demos with a short video (up to 2 pages). * Type D: Student Oral and Poster Abstracts – Research by Bachelor and Master students (up to 2 pages). * Type E: Late Breaking Poster Abstracts – Ongoing research (up to 2 pages). For more detailed information on submission guidelines and topics of interest, please visit the conference website: BNAIC/BeNeLearn 2024<https://bnaic2024.sites.uu.nl/>. We look forward to receiving your contributions and to seeing you in Utrecht for an inspiring and innovative conference. Best regards, BNAIC/BeNeLearn 2024 Organizing Committee

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Meet the Jury seminar 3 September 11AM - Leuven - Advanced Machine Learning in Drug Discovery
by BeNeLux bioinformaticians forum 20 Aug '24

20 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. -------------------------------------- Dear all, On behalf of Martijn Oldenhof and Yves Moreau, I’d like to share the announcement of this seminar of Igor Tetko on Advanced Machine Learning in Drug Discovery. It’ll take place on the 3rd of September between 11-12h - Elektrotechnisch Instituut (335-01), ELEC 01.62, Kasteelpark Arenberg 10 , 3001 Heverlee. More information: https://set.kuleuven.be/phd/seminars/tetko Abstract: Modern Machine Learning (ML) based on deep neural networks (DNNs), which form the basis of Artificial Intelligence (AI), is gaining popularity in the field of drug discovery. These methods can digest large amounts of information and provide reliable predictions for new molecules. Notably, such methods need not rely anymore on descriptors, but can learn their internal representations based on text or molecular graphs. They can also incorporate non-traditional information, such as images produced by high content screening, to better utilize results of in vitro measurements. Emerging solutions include the use of meta- and transfer-learning approaches, which enable the pre-training of models on a large corpus of chemical data of different modalities, and then efficiently applies the models to small datasets. The estimation of the accuracy of such predictions, which allows for the discrimination between reliable vs non-reliable predictions, is another important direction of the development of these methods. Being considered for a long time as black boxes, DNNs can become interpretable via eXplainable AI (XAI) methods. These developments open new perspectives for the use of ML in chemistry. Best regards, Alex

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Online and In Person Coding Courses @ Edinburgh Genomics
by BeNeLux bioinformaticians forum 20 Aug '24

20 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. -------------------------------------- Edinburgh Genomics have a number of exciting coding courses coming up ranging from beginner to more advanced, so whether you’re just starting out on your coding journey or looking to sharpen your skills, we think these courses will be of interest to you! Please do also share these with anyone in your network that you think may benefit from these courses. Introduction to Python for Biologists (IN PERSON) > 20-24 January 2025: https://genomics.ed.ac.uk/event/introduction-to-python-for-biologists-2/ > The Kings Buildings, University of Edinburgh, EH9 3FL, Scotland Our introductory course is perfect for those with a biological background and no programming experience. Python is a versatile, readable language ideal for bioinformatics, from simple scripts to complex projects. Start coding useful programs after just a few sessions and work on your own data with expert guidance. What you’ll learn: * Basic programming concepts with hands-on coding practice * Text manipulation, file handling, and working with lists and loops * Writing functions and using regular expressions * Practical problem-solving for bioinformatics tasks R for Biologists (online) > 9-11 September 2024: https://genomics.ed.ac.uk/event/r-for-biologists/ > 20-22 November 2024: https://genomics.ed.ac.uk/event/r-for-biologists-3/ Join our online workshop to learn R, the powerful statistical computing language, tailored for biological data science. Whether you’re handling data, performing analysis, or creating stunning visualisations, this course has you covered. Taught by experienced Edinburgh Genomics trainers, you’ll leave with the tools you need to excel in R and produce publication ready results. What you’ll learn: * Get comfortable with R and RStudio * Load, clean and explore data * Work with vectors and complex data structures * Create beautiful graphs with ggplot2 * Apply your skills to your own datasets Linux for Genomics (online) > 23-24 September 2024: https://genomics.ed.ac.uk/event/introduction-to-linux-for-genomics/ > 29-10 January 2025: https://genomics.ed.ac.uk/event/introduction-to-linux-for-genomics-3/ 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 bioinformatic skills, this course will equip you with the essential tools to navigate and analyse genomic data efficiently. Learn to harness the command line, write shell scripts and manage large datasets and processes - all tailored for genomics research. What you’ll learn: * Learn how to navigate through the file system * Use basic commands to manage files and set permissions * Download remote files and learn to zip/unzip them * Manage processes * Learn pattern matching to manipulate file content * Construct more complex commands using pipes and redirects * Write your very first shell scripts * Familiarise yourself with some genomic tools run from the command line Snakemake (online) > 14-16 October 2024: https://genomics.ed.ac.uk/event/snakemake/ Join our course on Snakemake, the powerful open-source workflow management system that simplifies and scales your data analysis. Organize Tasks: Break down complex analyses. Scale Seamlessly: Run workflows from local servers to the cloud without modification. Error Handling: Automate error management. Reproducibility: Document and share methods easily. If you’re familiar with the command line, you’re ready! No prior python experience required! If you’re new to coding we recommend our Linux for Genomics course first. What you’ll learn: * Running commands with Snakemake * Placeholders, wildcards and chaining rules * Workflow optimisation and condo integration * Building and maintaining robust workflows If you have any questions please feel free to get in touch! We hope to see you at one of our courses soon! 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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Reminder: BNAIC/BeNeLearn 2024 Call for Papers Deadline Approaching
by BeNeLux bioinformaticians forum 19 Aug '24

19 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. -------------------------------------- Dear Colleagues, This is a friendly reminder about the upcoming submission deadlines for the BNAIC/BeNeLearn 2024 conference, the premier AI and ML event for Belgium, the Netherlands, and Luxembourg. The conference will take place from November 18-20, 2024, in Utrecht, the Netherlands. Key Submission Deadlines: * 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 We invite submissions in the following categories: * Type A: Regular Papers – Original research, position, and review papers (up to 14 pages). * Type B: Encore Abstracts – Abstracts of recently published work (up to 2 pages). * Type C: Demonstration Abstracts – Proposals for demos with a short video (up to 2 pages). * Type D: Student Oral and Poster Abstracts – Research by Bachelor and Master students (up to 2 pages). * Type E: Late Breaking Poster Abstracts – Ongoing research (up to 2 pages). For more detailed information on submission guidelines and topics of interest, please visit the conference website: BNAIC/BeNeLearn 2024<https://bnaic2024.sites.uu.nl/>. We look forward to receiving your contributions and to seeing you in Utrecht for an inspiring and innovative conference. Best regards, BNAIC/BeNeLearn 2024 Organizing Committee

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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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