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Snakemake Online Course @ Edinburgh Genomics
by BeNeLux bioinformaticians forum 12 Sep '24

12 Sep '24

> Snakemake Online Course > 14-17 October > https://genomics.ed.ac.uk/event/snakemake/ --------------------------------------------------------------------------------------------------------------------------- Boost Your Data Analysis with Snakemake! Join our course on Snakemake, the powerful open-source workflow management system that simplifies and scales your data analysis. Why Snakemake? * 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. What You’ll Learn: * Running commands with Snakemake * Placeholders, wildcards, and chaining rules * Workflow optimization and Conda integration * Building and maintaining robust workflows Who Should Attend? If you’re familiar with the Linux BASH command line, you’re ready! No Python required. Register Now to streamline your data analysis with Snakemake: https://genomics.ed.ac.uk/event/snakemake/ Please also share this with anyone in your network that may be interested! Any questions, feel free to contact us. 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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Registration Now Open for BNAIC/BeNeLearn 2024 Conference
by BeNeLux bioinformaticians forum 12 Sep '24

12 Sep '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 are excited to announce that registration for the BNAIC/BeNeLearn 2024 conference is now open! The conference will take place from November 18-20, 2024, in Utrecht, the Netherlands, bringing together researchers and professionals in Artificial Intelligence and Machine Learning from Belgium, the Netherlands, Luxembourg, and beyond. Conference website: https://bnaic2024.sites.uu.nl/ Registration link: https://bnaic2024.sites.uu.nl/registration/ BNAIC/BeNeLearn 2024 will be an in-person event, and registration is mandatory for participation. We invite everyone with an interest in AI and ML, from seasoned researchers to students, to join us for three days of inspiring talks, discussions, and networking. Conference Fees: Category Early Registration (until Oct. 8) Late Registration (after Oct. 8) PI session / faculty meeting* €45 €55 Regular €350 €450 PhD candidate €230 €300 Master / Bachelor student €150 €200 Dinner €10 €20 * This will be an interactive session on the BeNeLux funding landscape. Open to full professors, associate professors, assistant professors, group leaders and attendees from industry.. To register, simply complete the online registration form, and you will be redirected to the payment page to finalize your registration. For more information on the conference program and key dates, please visit the conference website<https://bnaic2024.sites.uu.nl/>. We look forward to welcoming you to Utrecht for what promises to be a stimulating and engaging event. Best regards, 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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REGISTRATION OPEN : HADACA Data Challenge : Multimodal data integration to quantify tumor heterogeneity in cancer // 2-6 Dec. 2024
by BeNeLux bioinformaticians forum 11 Sep '24

11 Sep '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 are delighted to announce that registration is now open for the 3rd edition of the ‘HADACA data challenge: Multimodal data integration to quantify tumor heterogeneity in cancer’. The event will be held from December 2 to 6, 2024, in Aussois (French Alps). This scientific competition will focus on quantifying tumor heterogeneity using supervised deconvolution approaches on bulk multiomics data (transcriptome and DNA methylation). Particular emphasis will be placed on the integration of multi-modal reference data (single cell-RNAseq, RNAseq, and DNAm of pure cell-type profiles). We are excited to welcome three distinguished guest speakers: Andrea Rau, Etienne Becht, and Fatima Al-Shahrour, who will provide insights into multimodal data integration, deconvolution, and computational oncology. Registration for the challenge will open on September 3, 2024, and close on October 4, 2024. To ensure the quality of the discussions and workshop, we are limiting registration to 40 participants. Selection will be based on participants' profiles, expertise, and motivation. We invite students, researchers, engineers, professors, clinicians, and professionals from the private sector to participate. We seek expertise in Biology, Computer Science, Statistics, Bioinformatics, or Medical Sciences For more details on the registration process, please click here <https://hadaca3.sciencesconf.org/?lang=en>. We look forward to your participation! Best regards, Magali Richard, on behalf of the HADACA scientific committee

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Vacancy for PhD student in genome-scale metabolic modeling and machine learning
by BeNeLux bioinformaticians forum 03 Sep '24

03 Sep '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 have a PhD vacancy in our group! At the Maastricht Centre for Systems Biology (MaCSBio), we focus on connecting the dots between different types of biological data. In this PhD role, hybrid approaches combining genome-scale metabolic modeling and machine learning will be developed and applied, to enhance metabotyping and provide deeper insights into human metabolism. For more information and to apply: https://www.academictransfer.com/nl/344851/phd-position-in-systems-biology-… Please forward to anyone who may be interested! Kind regards, Michiel Adriaens [macsbio-logo] [UM-logo] Dr. ir. Michiel E. Adriaens, PhD Assistant Professor Maastricht Centre for Systems Biology - MaCSBio Paul-Henri Spaaklaan 1, 6229 EN Maastricht, The Netherlands T +31433881123 E michiel.adriaens(a)maastrichtuniversity.nl<mailto:michiel.adriaens@maastrichtuniversity.nl>

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Vacancy for postdoc in Bioinformatics & nutrigenomics at Maastricht University - deadline 1/9/2024
by BeNeLux bioinformaticians forum 30 Aug '24

30 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, I was made aware of this mailing list by a colleague at Maastricht University. If you know a good candidate or are interested yourself in a postdoc position in Bioinformatics & nutrigenomics at Maastricht University, please apply quick via this link https://vacancies.maastrichtuniversity.nl/job/Maastricht-Post-doctoral-posi… Best regards Sabine Sabine Langie Assistant Professor Department of Pharmacology & Toxicology Past-president of the European Environmental Mutagenesis and Genomics Society (EEMGS) President of the International Association of Environmental Mutagenesis and Genomic Societies (IAEMGS) (2022-2026) s.langie(a)maastrichtuniversity.nl<mailto:r.godschalk@maastrichtuniversity.nl> www.maastrichtuniversity.nl<http://www.maastrichtuniversity.nl/> Universiteitssingel 50, room G4.208, 6229 ER, Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 (0)433881336 [cid:image001.jpg@01DAFAC7.38DFD500] [signature_3359269286]

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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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