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  • Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance

    1 January - 31 December 2021

    Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance https://tess.elixir-europe.org/events/bacterial-genomes-disease-outbreaks-and-antimicrobial-resistance-b178602b-e29f-4ac7-afbf-5deafd52f8dd # Overview * **Duration**: There is no longer a live period for this course, and there will be no live monitoring of the forums, but you can still join and complete the course throughout 2021. * Free * Certificate of achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (9 credits), Royal College of Nursing (9 credits)** ** ### Why join the course? The increase in resistance of harmful bacteria to antibiotics is a major global threat to health. Here we explore bacterial genomes and the use of genome sequencing to identify and track these drug resistant bacteria. Join us to discover how genome research is helping scientists and healthcare professionals track disease outbreaks and prevent the rise of antibiotic resistant ‘superbugs’. ### Who is the course for? This course will be of interest to scientists, healthcare professionals, biomedical researchers and bioinformaticians. The course offers all learners an opportunity to learn about genomes, disease, and antimicrobial resistance. You require no previous knowledge of genome science to complete the course. ### What do people say about this course? "_I would definitely point students to this resource. Text, videos, and figures were all very well done._" Pablo Tsukayama, Assistant Professor of Microbiology "_A highlight of the course was the introduction to whole genome sequencing – new information for me._" Christine Laws, Medical Doctor “_Exchanging genetic information quickly throughout the world is clearly going to revolutionise the ability to combat disease._” Prue van der Hoorn, Artist # Programme and start dates ### What topics will you cover? * Diseases caused by bacteria * What bacterial genomes look like * Genome sequencing technology * Mechanisms of transmission and resistance * Genomic epidemiology – tracking the spread of bacterial pathogens * Antimicrobial resistance ### What will you achieve? By the end of the course, you'll be able to... * Explain why some bacteria are pathogenic * Explore the structure of bacterial genomes * Describe the uses of different genome sequencing technologies * Investigate how genome data are used to track the spread of bacterial disease * Discuss the role of genome sequencing in stopping the spread of antimicrobial resistance # Educators ## **Lead Educators** **[Dr Adam Reid][1]** I am a senior staff scientist at the Wellcome Sanger Institute near Cambridge in the United Kingdom. I'm interested in using genomics and bioinformatics to better understand infectious diseases. **[Dr Josie Bryant][2]** I am a Henry Wellcome Postdoctoral Fellow in the University of Cambridge, Department of Medicine. I am working on bacterial genomics and evolution with a focus on within-patient microbial diversity ### Dr Francesca Short I am a scientist at the Wellcome Sanger Institute. I am interested in using functional genomics techniques to understand infections caused by the bacterium _Klebsiella pneumoniae_. ## **Programme Lead Educator** **[Professor Nicholas Thomson][3]** I am a Group Leader at the Wellcome Sanger Institute. I provide scientific oversight for this course. I am interested in bacterial evolution and the spread of infectious disease. ### The course also features interviews with distinguished scientists, including: * **[Mathew Beale][4]** - Wellcome Sanger Institute * **[Daryl Domman][5]** - Wellcome Sanger Institute * **[Gal Horesh][6]** - Wellcome Sanger Institute * **[Catherine Ludden][7]** - London School of Hygiene and Tropical Medicine * **[Tapoka Mkandawire][8]** - Wellcome Sanger Institute * **[Julian Parkhill][9]** - Wellcome Sanger Institute * **Lindsay Pike** - Wellcome Sanger Institute * **[Michael Quail][10]** - Wellcome Sanger Institute * **[Susannah J. Salter][11]** - Wellcome Sanger Institute * **[Estee Torok][12]** - Addenbrooke’s Hospital and University of Cambridge [1]: http://www.sanger.ac.uk/people/directory/reid-adam-james [2]: https://www.infectiousdisease.cam.ac.uk/directory/josie-bryant [3]: http://www.sanger.ac.uk/people/directory/thomson-nicholas-robert [4]: http://www.sanger.ac.uk/people/directory/beale-mathew [5]: http://www.sanger.ac.uk/people/directory/domman-daryl [6]: http://www.sanger.ac.uk/people/directory/horesh-gal [7]: https://www.lshtm.ac.uk/aboutus/people/ludden.catherine [8]: http://www.sanger.ac.uk/people/directory/mkandawire-tapoka-t [9]: http://www.sanger.ac.uk/people/directory/parkhill-julian [10]: http://www.sanger.ac.uk/people/directory/quail-michael-andrew [11]: http://www.sanger.ac.uk/people/directory/salter-susannah-j [12]: https://www.infectiousdisease.cam.ac.uk/directory/et317@medschl.cam.ac.uk # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible # CDP Approval 2021-01-01 09:00:00 UTC 2021-12-31 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesAMRHDRUK
  • 1st de.NBI Summer School 2021 - Analysis and integration of Mass Spectrometry based omics data in Proteomics, Metabolomics and Lipidomics

    27 - 30 September 2021

    1st de.NBI Summer School 2021 - Analysis and integration of Mass Spectrometry based omics data in Proteomics, Metabolomics and Lipidomics https://tess.elixir-europe.org/events/de-nbi-summer-school-2021-proteomics-lipidomics TBA 2021-09-27 09:00:00 UTC 2021-09-30 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • ZIDAS 2021

    27 September - 1 October 2021

    ZIDAS 2021 https://tess.elixir-europe.org/events/zidas-2021 # ZIDAS 2021: switZerland’s Image and Data Analysis School - When: 27th September-1st October 2021 - Where: Online event - **Application deadline: 2021-07-01 (23:59 CET)** - Website: [https://2021.zidas.org](https://2021.zidas.org) ## About the school: This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples. ## Lectures on - Image Formation - Denoising - Segmentation - Reproducibility & Ethics ## Hands-ons with - ImageJ/Fiji Macros - GoogleColab for Python notebooks - ZeroCostDL4Mic - Ilastik ## Further tools and topics - Each day will feature 3 parallel sessions with demos of the awesome tools developed by the BioImage Analysis community such as #QuPath, #CLIJ, #CellProfiler, #TrackMate, #FigureJ, #StarDist and more! - This year will have a strong "work on your own project" component, so you can take advantage of all our great trainers to help you work with your own data! **_Find us at [https://2021.zidas.org](https://2021.zidas.org)_** 2021-09-27 09:00:00 UTC 2021-10-01 17:00:00 UTC ETHZ, EPFL ETH ZurichEPFL Center for Experimental and Clinical Imaging Technologies Zurich (EXCITE Zurich) Life Science ResearchersBiologists workshops_and_courses registration_of_interest image processingbioinformatics
  • International Summer School on Rare Disease Registries and FAIRification of Data

    27 September - 1 October 2021

    International Summer School on Rare Disease Registries and FAIRification of Data https://tess.elixir-europe.org/events/international-summer-school-on-rare-disease-registries-and-fairification-of-data-3f5621f8-73b6-4de3-a069-a30b68e0ca3f The International Summer School on Rare Disease Registries and FAIRification of Data is a part of a series of training activities proposed by the European Joint Programme on Rare Diseases (EJP-RD). EJP-RD is a European Commission funded project with the goal “to create a comprehensive, sustainable ecosystem allowing a virtuous circle between research, care and medical innovation”. For more information about the EJP-RD, see https://www.ejprarediseases.org/ This course is composed of two training modules: – During the first three days module (27-29 September 2021), participants will learn (a) what resources are needed for the establishment/maintenance of a high-quality registry (b) the features of successful strategies to ensure (i) long-time sustainability of the registry, (ii) quality, (iii) legal and ethical issues in compliance with the EU (European Union) General Data Protection Regulation – During the second two days module “FAIRification of data”, (September 30 -October 1, 2021) participants will deepen their knowledge on the single steps of the FAIRification of data and will discover the potential of FAIR registries. In this part a time slot will be allocated to discuss FAIR data management and FAIR project planning. 2021-09-27 14:00:00 UTC 2021-10-01 17:10:00 UTC European Joint Programme on Rare Diseases (EJP-RD), Istituto Superiore di Sanità of Italy Istituto Superiore di Sanità claudio.carta@iss.it [] Cliniciansmedical specialistsregistry curatorsdatabase managershealthcare professionalsrare disease patients representatives 30 workshops_and_courses first_come_first_servedregistration_of_interest Rare DiseasesRegistryethical issues
  • Advanced Python for Biologists 2021

    4 - 15 October 2021

    Advanced Python for Biologists 2021 https://tess.elixir-europe.org/events/advanced-python-for-biologists-2021 This Advanced level workshop is ideal for researchers and technical workers with a background in biology and a basic knowledge of Python, to develop bigger or more complicated programs and increase skills and knowledge about the language, including object-oriented approaches to programming. 2021-10-04 09:00:00 UTC 2021-10-15 17:00:00 UTC Earlham Institute [] training@earlham.ac.uk [] [] [] [] []
  • ELIXIR Fluxomics Training School 2021

    4 - 8 October 2021

    Elixir node event
    ELIXIR Fluxomics Training School 2021 https://tess.elixir-europe.org/events/elixir-fluxomics-training-school-2021 The 1st ELIXIR Fluxomics Training School is organized by ELIXIR-GR (FORTH/ICE-HT) in collaboration with ELIXIR-ES (UB) in the context of the ELIXIR Metabolomics Community-lead Implementation Study “Standardizing the fluxomics workflows”. This 5-day course, will take place in virtual mode on October 4-8 2021 from 9:00 to 17:00 Central European Time (CET) and will provide an introduction to the field of fluxomics and the experimental and computational methods used to estimate and predict metabolic fluxes. The course is addressed mainly to graduate students and junior post-docs, of either experimental or computational background. Learning outcomes include familiarity with the basic concepts, experimental techniques, data deposition standards and computational methods and software tools in fluxomics. The course includes hands-on experience in computational methods and software tools and mini team projects that will help the students apply the taught concepts. The course will involve up to 30 students and the selection will be made based on an application package submitted by designated application deadline. Sponsored by ELIXIR, the course is free of charge for personnel of academic/research/non-profit institutions in ELIXIR Nodes. Registration fees apply for the rest. ECTS credits may be granted to graduate students of European Institutions upon request after approval of the involved Graduate Programs. 2021-10-04 09:00:00 UTC 2021-10-08 17:00:00 UTC ELIXIR-GR (FORTH/ICE-HT) in collaboration with ELIXIR-ES (UB) FORTH/ICE-HT You may contact the organizers of the Fluxomics Training School either by phone at the school secretariat (Mrs Aggeliki KOSMATOU, +30-2610-965266) or preferably by e-mail at fluxomics_school@iceht.forth.gr ELIXIR Mainly graduate students and Junior post-docs, of either experimental or computational background, with basic training in life sciences, or (bio)chemistry, or physics, or mathematics, or engineering 30 workshops_and_courses registration_of_interest FluxomicsC13 Labeling Fluxomics MetabolomicsMetabolic Network Analysis Isotopic labelingGenome-scale Metabolic Modeling Systems biology Metabolic Reaction DatabasesMass Spectrometry - based fluxomicsNMR-based fluxomicsMetabolic flux analysisMetabolismMetabolic pathway
  • 2nd de.NBI Summer School 2021 - Microbial Community Analysis

    4 - 8 October 2021

    2nd de.NBI Summer School 2021 - Microbial Community Analysis https://tess.elixir-europe.org/events/2nd-de-nbi-summer-school-2021-microbial-community-analysis Educators: Dr. Dirk Benndorf (Magdeburg, BiGi), Prof. Dr. Alexander Goesmann (Giessen, BiGi), Dr. Sebastian Jaenicke (Giessen, BiGi), Prof. Dr. Stefan Janssen (JLU Giessen), Sebastian Jünemann (Bielefeld, BiGi), Dr. Nils Kleinbölting (Bielefeld, BiGi), Kay Schallert (Magdeburg, BiGi), Prof. Dr. Alexander Sczyrba (Bielefeld, BiGi), Dr. Daniel Wibberg (Bielefeld, de.NBI Administration office), Dr. Georg Zeller (Heidelberg, HD-HuB), Dr. Robert Heyer (Magdeburg, BiGi), Jakob Wirbel (Heidelberg, HD-Hub), Dr. Alessio Milanese (ETH Zürich) Date: 04. - 08.10.21 Location: Online Content: We are pleased to announce that the de.NBI Summer School 2021 on Microbial Community Data Analysis will take place from October 4th to 8th, 2021. The German Network for Bioinformatics Infrastructure (de.NBI) presents the Summer School on Microbial Community Data Analysis that is organized by the Bielefeld-Gießen (BiGi) Center for Microbial Bioinformatics. The BiGi center is specialized in the field of Omics data analysis for microbes and is well-known for its software platforms such as EMGB, MetaProtServ, or MGX. During the event, we will cover topics such as sequence data preprocessing, amplicon data analysis (metabarcoding), read- and assembly based metagenomics, and metaproteomics. Program: *All times refere to Central European Summer Time (CEST)! The program includes talks, lectures and hands-on trainings that the participants will conduct on their own computers/laptops. Monday, 04.10.2021 10:00-10:30 Welcome note (A. Goesmann) 10:30-11:00 Presentation of the de.NBI network (D. Wibberg) 11:00-12:00 Keynote by M. Ziegler 12:00-13:00 Lunch break 13:00-14:00 Keynote: Sequencing technologies (T. Hain) 14:00-14:15 Break 14:15-16:15 From raw data to feature tables (S. Janssen, S. Jaenicke) 16:15-17:00 Break 17:00-18:00 Keynote: Advancing microbiome research through Qiita (A. Gonzalez) Tuesday, 05.10.2021 10:00-12:00 Assessing biodiversity (alpha/beta) (S. Janssen) 12:00-13:00 Lunch break 13:00-13:30 Statistical testing (S. Janssen) 13:30-13:45 Break 13:45-15:00 Tools for taxonomic classification (S. Jaenicke) 15:00-16:00 MGX (S. Jaenicke) Wednesday, 06.10.2021 10:00-12:00 Metagenome assembly (A. Sczyrba, S. Jünemann, N. Kleinbölting) 12:00-13:00 Lunch break 13:00-14:00 Binning into MAGs (A. Sczyrba, S. Jünemann, N. Kleinbölting) 14:00-14:45 Annotation & evaluation of MAGs (A. Sczyrba, S. Jünemann, N. Kleinbölting) 14:45-15:00 Break 15:00-16:00 Keynote: Critical assessment of metagenome interpretation - CAMI2 (A. McHardy) Thursday, 07.10.2021 10:00-11:00 Keynote: Shinichi Sunagawa 11:00-11:15 Break 11:15-13:00 Taxonomic profiling of shotgun metagenomes (Georg Zeller, Alessio Milanese) 13:00-14:00 Lunch break 14:00-14:30 Taxonomic profiling of shotgun metagenomes (Georg Zeller, Alessio Milanese) 14:30-15:15 Comparative metagenome analysis (Georg Zeller) 15:15-15:30 Break 15:30-17:00 Comparative metagenome analysis (Jakob Wirbel) Friday, 08.10.2021 10:00-11:00 Introduction in analyzing microbial communities by metaproteomics (Dirk Benndorf) 11:00-12:00 Identification of mass spectrometry data using the MetaProteomeAnalyzer (Robert Heyer) 12:00-13:00 Lunch break 13:00-14:00 Taxonomic and functional comparison of human gut samples using the MetaProteomeAnalyzer (Robert Heyer) 14:00-15:00 Biostatistical data evaluation and data visualization (Robert Heyer) 15:00-15:15 Break 15:15-16:00 Keynote: Metaproteomics: where are we now? A community-driven evaluation of experimental and computational techniques (Thilo Muth) Keynote speakers: Dr. Maren Ziegler, Systematics and Biodiversity Lab, Justus Liebig University Giessen, Germany PD Dr. Torsten Hain, Medical Microbiology, Justus Liebig University Giessen, Germany PhD Antonio González Peña, University of California, San Diego, USA Prof. Dr. Alice McHardy, Helmholtz Centre for Infection Research, Braunschweig, Germany Prof. Dr. Shinichi Sunagawa, Department of Biology, ETH Zurich, Switzerland Dr. Thilo Muth, Bundesanstalt für Materialforschung und -prüfung (BAM), Berlin, Germany Prerequisites: Participants need: - Basic knowledge in Linux/CLI - Basic knowledge of executing programs on the command line (shell) - Working knowledge of R Registration: Please fill out the application form to sign up. The number of participants is limited to 20! The application deadline is September 12th. 2021-10-04 09:00:00 UTC 2021-10-08 17:00:00 UTC de.NBI [] [] [] [] [] []
  • 3DAROC21 3C-based data analysis and 3D reconstruction of chromatin folding

    4 - 6 October 2021

    3DAROC21 3C-based data analysis and 3D reconstruction of chromatin folding https://tess.elixir-europe.org/events/3daroc21-3c-based-data-analysis-and-3d-reconstruction-of-chromatin-folding 3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are in close spatial proximity in the cell nucleus. Overall, those interaction matrices have been used to study how the genome folds within the nucleus, which is one of the most fascinating problems in modern biology. The rigorous analysis of those paired-reads using computational tools has been essential to fully exploit the experimental technique, and to study how the genome is folded in space. Currently, there is a clear expansion on the wealth of data on genome structure with the availability of many datasets of Hi-C experiments down to 1Kb resolution (see for example: http://hic.umassmed.edu/welcome/welcome.php or http://www.aidenlab.org/data.html). In this course, participants will learn to use TADbit, a software designed and developed to manage all dimensionalities of the Hi-C data: 1D - Map paired-end sequences to generate Hi-C interaction matrices 2D - Normalize matrices and identify constitutive domains (TADs, compartments) 3D - Generate populations of structures which satisfy the Hi-C interaction matrices 4D - Compare samples at different time points Participants can bring specific biological questions and/or their own 3C-based data to analyze during the course. At the end of the course, participants will be familiar with the TADbit software and will be able to fully analyze Hi-C data. Although the TADbit software is central in this course, alternative software will be discussed for each part of the analysis. 2021-10-04 09:00:00 UTC 2021-10-06 17:00:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência bicourses@igc.gulbenkian.pt Oeiras Valley experimental researchers and bioinformaticians at the graduate and post-graduate levels 20 workshops_and_courses registration_of_interest TADbit
  • EMBO Practical Course - Research to service: Planning and running a bioinformatics core facility

    4 - 8 October 2021

    Elixir node event
    EMBO Practical Course - Research to service: Planning and running a bioinformatics core facility https://tess.elixir-europe.org/events/embo-practical-course-research-to-service-planning-and-running-a-bioinformatics-core-facility-62ea6744-3a2b-4478-886d-69be519d5e25 Computational core facilities play a vital role in enabling molecular life science, and the number of such facilities has grown considerably. There are many relatively inexperienced managers of core facilities, who often have to juggle their own research projects with the development and operation of services. This can be exceptionally challenging, not least because scientific impact tends only to be recognised and rewarded for research. The "EMBO Practical Course | Research to Service: Planning and Running a Bioinformatics Core Facility" is aimed at newly appointed managers of bioinformatics core facilities, especially those with one foot in the research camp, or those managers willing to stabilize and grow their services. The training set will provide an opportunity to learn from experienced core facilities managers on how to build a framework for the future development, resourcing, operation and impact assessment of your core services. By the end of the course, participants will have learned how to: *Identify the strengths and limitations of their core facility and prioritise areas for improvement *Design bioinformatics services and training using a user-centred approach and assuring best practices *Estimate the computing and human resources required to operate their facility effectively *Support users to manage their data, including sensitive data 2021-10-04 12:00:00 UTC 2021-10-08 14:00:00 UTC Barcelona Supercomputing Center (BSC), EMBL-European Bioinformatics Institute (EMBL-EBI), Izmir Biomedicine and Genome Center (IBG), INCLIVA Health Research Institute, Spanish National Bioinformatics Institute (INB/ELIXIR-ES) Bioinformatics INB/ELIXIR-ESBSC BSC Organising Team: embo.bioinfocore@bsc.es [] Core Facility Managers 20 workshops_and_courses registration_of_interest managing skillsdata managementsustainabilityservice designcomputing resourcesstorage needs
  • Train the Trainer (TrT) online course

    4 - 7 October 2021

    Train the Trainer (TrT) online course https://tess.elixir-europe.org/events/train-the-trainer-trt-online-course The ELIXIR Training Platform is pleased to announce a Train the Trainer (TtT) event online, in collaboration with ELIXIR-IL and Weizmann Institute of Science. ELIXIR TtT courses aim to give new instructors tools and tips for providing an enriching learning experience to trainees, irrespective of the topic, and to include best-practice guidance on course and training material development. Course dates: 04-07 October, 2021, 13:30 – 17:00 (IDT) There is no course attendance fee. 2021-10-04 13:30:00 UTC 2021-10-07 17:00:00 UTC Weizmann Institute of Science [] Danny Ben-Avraham dan.ben-avraham@weizmann.ac.il [] [] 20 workshops_and_courses first_come_first_served Train the trainertraining
  • Pathogen research through VEuPathDB resources

    11 - 12 October 2021

    Pathogen research through VEuPathDB resources https://tess.elixir-europe.org/events/pathogen-research-through-veupathdb-resources Educators: Jesús Alvarado Valverde, Renato Alves (HD-HuB) Date: 11. – 12.10.2021 (09:30-12:30 CEST) Location: Online Contents: The aim of the course is to make people familiar with VEuPathDB resources (https://veupathdb.org/veupathdb/app/), a suite of dedicated databases to collect and provide information and tools to assist research on Eukaryotic pathogens, their vectors, and hosts. Pathogens in the suite include Plasmodium, Toxoplasma, Trypanosomes, Leishmania and more. Learning goals: In this course you will learn how to: Explore their different databases Use their genome and protein browsers Retrieve orthologous sequences Create specialised search strategies and experimental data queries Prerequisites: None Keywords: Eukaryitic pathogens; VEuPathDB; Tools: VEuPathDB 2021-10-11 09:30:00 UTC 2021-10-12 12:30:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • Ready for BioData Management? | DMP Double Course

    12 - 13 October 2021

    Ready for BioData Management? | DMP Double Course https://tess.elixir-europe.org/events/ready-for-biodata-management-dmp-double-course Day 1: "Introduction to Data Management Plans" is an introductory course aimed at disseminating Data Management best practices and teaching the basics of making and using Data Management Plans (DMPs) in the context of research activities. It features two introductory lectures, respectively on Research Data Management and DMPs, followed by a hands-on DMP exercise where participants will form groups to fill in a DMP for a mock research project, using Google Spreadsheets. The produced DMPs will then be reviewed and discussed. Day 2: "Advanced Data Management Plans" is a follow-up course aimed at empowering participants to make their own real Data Management Plan according to the Science Europe DMP Template (adopted by FCT) on an online platform. It features three lectures covering advanced concepts in data management, the Science Europe DMP Template, and Data Stewardship Wizard (the DMP creation tool that participants will use), followed by a hands-on session where participants create their DMP, either alone or in pairs, with assistance from the teachers. Participants are encouraged to bring their own research projects to be the object of their DMP. 2021-10-12 10:00:00 UTC 2021-10-13 17:00:00 UTC BioData.pt Data management Instituto Gulbenkian de Ciência, Biodata.pt - Elixir's portuguese node of the european projec BioData.pt / ELIXIR-Portugal: info@biodata.pt [] Life Science ResearchersPhD studentsMaster studentsTechnicians 20 workshops_and_courses first_come_first_served Data management plan
  • DNA Methylation: Design to Discovery 2021

    28 - 29 October 2021

    DNA Methylation: Design to Discovery 2021 https://tess.elixir-europe.org/events/dna-methylation-design-to-discovery-2021 Educators: Abdulrahman Salhab, Epigenetics Department @ Saarland University (de.NBI-Epi / HD-HuB) Date: 28-29 October 2021 Location: Online Contents: This course aims to convey basic knowledge on the bioinformatic processing of DNA methylation data. Following the outline of a standard experiment we discuss qualities of various assays and when they are beneficial. In the first half there will be a slight focus on sequencing data. We will prepare raw sequence reads for alignment, methylation calls and identification of differentially methylated sites or regions. Throughout, we consider how experimental settings interact and influence the results and how quality control can be used to understand generated data and might improve on subsequent experiments. The second half will focus on how to evaluate the data and connect it to public resources to further understanding of the results. Presentations will be interleaved with practical sessions Learning goals: • Understand the bioinformatic processing of DNA methylation • Preparation and description of raw read files • Basic generation of methylation calls and differentially methylated regions • How to evaluate DNA methylation data Prerequisites: The course requires basic skills in: • Linux/bash • R Keywords: DNA methylation Tools: nf-core/methylseq, RnBeads, methylSeekR 2021-10-28 09:00:00 UTC 2021-10-29 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • HPC and NIRD toolkit user course

    2 - 5 November 2021

    Elixir node event
    HPC and NIRD toolkit user course https://tess.elixir-europe.org/events/hpc-and-nird-toolkit-user-course HPC and NIRD toolkit user course November 2021 In November 2021, the Norwegian Research Infrastructure Services NRIS (formerly known as the Metacenter) partners Sigma2, UiB, UiO & UiT are jointly offering a hands-on course for current and future users of national HPC systems (Saga, Fram, Betzy) and the NIRD Toolkit. The course is open to all users and free of charge. For individual sessions we list recommended prerequisites. The participants can choose which session they want to attend and you’re certainly welcome to just attend all sessions you are interested in. On each course day, we will start at 09:00 and conclude at around 13:00. Each “morning” will include presentations and hands-on time on one of the actual HPC systems or the NIRD Toolkit. We recommend that participants use the afternoon on each day to repeat examples from the morning to get more experience on the systems. Practical Information This is an online course via zoom. Participants require access to a computer (not provided by the course organisers) with internet connectivity and pre-installed programs to participate in the video meeting of the course (zoom, might work from a browser), to access the HPC systems (e.g., ssh or Putty), to transfer data to/from an HPC system (e.g., scp or WinSCP) and to access the NIRD Toolkit (web browser). Note Those who do not have an account on one of the HPC machines or NIRD (storage, Toolkit, …) yet need to apply for an account. The application page is available here and documentation for the application procedure is available here. You are applying for an HPC account. For the project, please select “NN9987K: Course Resources as a Service #3” (the Project manager will be filled in automatically), choose Saga under Resources, set the Account start date to 2021-10-26 and the Account end date to one week after the course, that is 2021-11-12. In order to use the NIRD Toolkit during the course you will need either a Feide account or a Feide OpenIDP guest account. You can create a Feide OpenIDP guest account at https://openidp.feide.no/. See your eduPersonPrincipalName (eduPPN) at http://innsyn.feide.no . You can always contact us by sending an email to support@metacenter.no. If you want to receive further information about training events, and other announcements about IT resources and services for researchers, there are a couple of information channels you can subscribe to: users at University of Bergen and affiliated institutes: register to hpcnews@uib.no users of Sigma3 services: subscribe to Sigma2’s newsletter Dates: 2021 November 2, 3, 4 and 5 Time: each day 09:00-13:00 with short breaks Location: Video meeting (zoom), we use HackMD for asking questions (information will be send to registered participants via email). Note, sessions will be recorded and made publicly available after the course! Participants may choose the lectures which they are interested in. Registration The course is free of charge and is organised by the NRIS partners Sigma2, UiB, UiO & UiT. Registration deadline for the course is October 20th. Register your participation here Code of Conduct All participants in our course are expected to show respect and courtesy to others. We follow carpentry code of conduct. If you believe someone is violating the Code of Conduct, we ask that you report it either to Radovan Bast or Dhanya Pushpadas 2021-11-02 08:50:00 UTC 2021-11-05 13:00:00 UTC Sigma2 - NRIS University of BergenUniversity of OsloUniversity of TromsøSigma2 radovan.bast@uit.no Dhanya.Pushpadas@uib.no Sigma2 HPC users workshops_and_courses [] HPCstorage
  • FAIR data (session 2)

    15 - 18 November 2021

    Elixir node event
    FAIR data (session 2) https://tess.elixir-europe.org/events/fair-data The training is four half-days. It is delivered in French. 2021-11-15 09:00:00 UTC 2021-11-18 12:30:00 UTC Institut Français de Bioinformatique (IFB) Open science FAIR data Biology Bioinformatics Data management [] [] BiologistsbioinformaticiansBiomedical researchers health professionals workshops_and_courses [] metadataData management plandata organisationstoragelife science standardslicensing

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