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  • NBIS Course: Single cell RNA sequencing analysis course

    27 - 31 January 2020

    Solna, Sweden

    Elixir node event
    NBIS Course: Single cell RNA sequencing analysis course https://tess.elixir-europe.org/events/nbis-course-single-cell-rna-sequencing-analysis-course #training #url: https://nbisweden.github.io/workshop-scRNAseq/ Single cell RNA sequencing analysis course Links:  Course: https://nbisweden.github.io/workshop-scRNAseq/ Registration form: https://forms.gle/6VFVTFep6iYk7wLr9 The first 3 days of the course will cover the basic steps in single cell RNAseq (scRNAseq) processing and data analysis. Topics covered will include: An overview of the current scRNAseq technologies Basic overview of pipelines for processing raw reads into expression values Quality control of scRNAseq data Dimensionality reduction and clustering techniques Data normalization Differential gene expression for scRNAseq data Trajectory analysis Comparison of different analysis pipelines such as Seurat, Scran and Scanpy On the fourth day we offer a “Bring your own data” day where you can analyse your data using the tools that you have discovered during the course, with TAs present to help you run the analyses and discuss your results. If you do not have your own data you can still select a public dataset of interest and analyse during that day. Application deadline -- December 16 Acceptance notification — December 20 contact: education@nbis.se 2020-01-27 09:00:00 UTC 2020-01-31 00:00:00 UTC Solna, Sweden Solna Sweden [] Åsa Björklund - asa.bjorklund@scilifelab.se [] [] [] [] #trainingtraining
  • Multiple Biofluid and Tissue Types, From Sample Preparation to Analysis Strategies for Metabolomics

    10 - 12 February 2020

    Birmingham, United Kingdom

    Elixir node event
    Multiple Biofluid and Tissue Types, From Sample Preparation to Analysis Strategies for Metabolomics https://tess.elixir-europe.org/events/multiple-biofluid-and-tissue-types-from-sample-preparation-to-analysis-strategies-for-metabolomics-793294d9-6efa-46db-a619-72bc81d31ac8 This 3-day course provides a theoretical overview and hands-on training to apply multiple sample preparation and UPLC-MS methods to characterise the metabolomes of complex biological samples using the mass spec... 2020-02-10 09:00:00 UTC 2020-02-12 15:30:00 UTC School of Biosciences - University of Birmingham, Birmingham, United Kingdom School of Biosciences - University of Birmingham Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Training on the data integration platforms tranSMART & cBioPortal

    26 - 27 March 2020

    Amsterdam, Netherlands

    Elixir node event
    Training on the data integration platforms tranSMART & cBioPortal https://tess.elixir-europe.org/events/training-on-the-data-integration-platforms-transmart-cbioportal The data integration platforms tranSMART and cBioPortal are widely used by researchers and clinicians to integrate, analyse and visualise large amounts of data. In this CORBEL course, data stewards/data managers are offered the opportunity to learn how to upload data to these platforms and how to use the different user interfaces. They will gain insight into these platforms and the possibilities that they offer. 2020-03-26 08:30:00 UTC 2020-03-27 17:00:00 UTC Aristo Amsterdam, Amsterdam, Netherlands Aristo Amsterdam Amsterdam Netherlands 1043 EJ [] Michelle Mendonca [] [] [] [] HDRUK
  • CORBEL workshop: Training on the data integration platforms tranSMART & cBioPortal

    26 - 27 March 2020

    Amsterdam, Netherlands

    Elixir node event
    CORBEL workshop: Training on the data integration platforms tranSMART & cBioPortal https://tess.elixir-europe.org/events/corbel-workshop-training-on-the-data-integration-platforms-transmart-cbioportal The data integration platforms tranSMART and cBioPortal are widely used by researchers and clinicians to integrate, analyse and visualise large amounts of data. In this CORBEL course, data stewards/data managers are offered the opportunity to learn how to upload data to these platforms and how to use the different user interfaces. They will gain insight into these platforms and the possibilities that they offer. 2020-03-26 08:30:00 UTC 2020-03-27 17:00:00 UTC Aristo Amsterdam, Amsterdam, Netherlands Aristo Amsterdam Amsterdam Netherlands 1043 EJ [] Michelle Mendonca [] [] [] [] HDRUK
  • Metabolomics with the Q Exactive

    30 March - 1 April 2020

    Birmingham, United Kingdom

    Elixir node event
    Metabolomics with the Q Exactive https://tess.elixir-europe.org/events/metabolomics-with-the-q-exactive-eba04310-9a59-4f5b-9a52-ee37d888cc0c This 3-day course introduces you to using the Q Exactive mass spectrometer in your metabolomics investigations. The course is led by experts in the field of metabolomics and includes lectures, laboratory sessions... 2020-03-30 09:00:00 UTC 2020-04-01 15:45:00 UTC School of Biosciences - University of Birmingham, Birmingham, United Kingdom School of Biosciences - University of Birmingham Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Metabolite Identification with the Q Exactive and LTQ Orbitrap Elite

    2 - 3 April 2020

    Birmingham, United Kingdom

    Elixir node event
    Metabolite Identification with the Q Exactive and LTQ Orbitrap Elite https://tess.elixir-europe.org/events/metabolite-identification-with-the-q-exactive-and-ltq-orbitrap-elite-87815650-e41c-4df1-a050-61ef00722504 This 2-day course provides a hands-on approach to teach attendees about the latest techniques and tools available to perform metabolite identification in non-targeted metabolomics studies. The course is led by experts... 2020-04-02 09:00:00 UTC 2020-04-03 17:30:00 UTC School of Biosciences - University of Birmingham, Birmingham, United Kingdom School of Biosciences - University of Birmingham Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Introduction to Metabolomics for the Microbiologist

    27 - 29 April 2020

    Birmingham, United Kingdom

    Elixir node event
    Introduction to Metabolomics for the Microbiologist https://tess.elixir-europe.org/events/introduction-to-metabolomics-for-the-microbiologist-a6738e97-af92-47b2-bbfe-ba5592458700 This three-day course introduces how untargeted metabolomics can be applied to study microbial systems in academic and industrial research. The course provides an overview of the metabolomics pipeline, experimental... 2020-04-27 09:15:00 UTC 2020-04-29 16:00:00 UTC School of Biosciences - University of Birmingham, Birmingham, United Kingdom School of Biosciences - University of Birmingham Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • ELIXIR All Hands 2020

    8 - 11 June 2020

    Amsterdam, Netherlands

    ELIXIR All Hands 2020 https://tess.elixir-europe.org/events/elixir-all-hands-2020 The ELIXIR All Hands 2020 will be held in the Eye Filmmuseum, Amsterdam. Timeline 21 October - 15 November 2019 Call for workshops and Call for presentations December 2019 Selection of presentations and workshops 24 January 2019 Accepted presentations (incl. talks, demonstrations and posters) announced by this date February 2020 Registration opens for 300 delegates on a first come, first served basis Accommodation For 2020 All Hands meeting, ELIXIR will not have a block reservation for accommodation, but each participant will need to book their own accommodation. The venue is located in central Amsterdam with plenty of options, but keep in mind that June is a busy month in the city and therefore it is recommended to reserve accommodation early. Walking distance hotels from venue Eye Film Museum: Sir Adam Hotel Park Plaza Victoria Ibis Styles Hotel Ibis Amsterdam Central Station Multatuli Hotel Call for workshops is now closed The abstracts received by the deadline of 15 November are being evaluated by the All Hands Programme Committee, considering the overlap with other potential topics of the All Hands meeting, relevance to the ELIXIR Programme, and the potentially interesting outcomes of relevance to ELIXIR.  Call for presentations is now closed ELIXIR All Hands attendees are strongly encouraged to give some form of presentation at the meeting. There are four types of presentation this year: Short talk in plenary Demonstration talk in plenary Mini-symposia talk Poster Review of submissions The abstracts received via EasyChair by the deadline of 15 November are being evaluated by the All Hands Programme Committee. The review criteria for each presentation category are described below. The accepted presentations (incl. talks, demonstrations and posters) will be announced by 24 January 2019. Types of Presentation 1. Short talk in Plenary As in 2019, we plan to run a Plenary session giving attendees the option to give a short talk, focussed on recent developments in an ongoing or recently finished ELIXIR Commissioned Service project (e.g. Implementation Study). Presentations will be selected by the ELIXIR All Hands Programme Committee based on scientific relevance and interest. If not selected for a short talk, the abstract will be considered for a poster. The short talks will run in the morning of Wednesday 10 June. 2. Demonstration talk in Plenary As in 2019, we plan to run a Plenary session giving attendees the option to give a demonstration of an interesting service, tool, or capability. Abstracts for Demonstration talks will be selected by the Programme Committee based on benefits to overall ELIXIR infrastructure and interest. If not selected for a demonstrator, the abstract will be considered for a poster. The Demonstrator session will run in the afternoon of Tuesday 9 June. 3. Mini-symposia talk New for the ELIXIR All Hands meeting, in 2020 we will be running six mini-symposia. These will be in cinema style rooms, and will last for either 1.5 or 3 hours. Presentations will be selected by the mini-symposia organisers (see below, i.e. not the All Hands Programme Committee). Talks in a mini-symposium may be of varying length, duration to be determined by the organisers of the mini-symposium and successful submitters may be asked to shorten or lengthen their presentation. Unsuccessful submissions may be asked to bring a poster. All mini-symposia will run in the morning of Tuesday 9 June. Symposia topic Leads Duration Session description (short) Federated Human Data Thomas Keane (EBI) Ilkka Lappalainen (FI) Jordi Rambla (ES) Gary Saunders (Hub) 3 hours Our vision for ELIXIR Federated Human Data is to create a federated ecosystem of interoperable services that enables population scale genomic and biomolecular data to be accessible across international borders accelerating research and improving the health of individuals resident across Europe. In this session we would like to discuss the delivery of FAIR compliant metadata standards, interfaces, and implementations to support the federated ELIXIR network of human data resources. The overall goal is to provide secure, standardized, documented and interoperable services under the framework of the European Genome-phenome Archive (EGA). Plants Kristina Gruden (Sl) John Hancock (Hub) Astrid Junker (DE) Cyril Pommier (FR) 3 hours The Plant Sciences Community aims to establish a technical infrastructure and associated social practices to allow plant genotype-phenotype analysis through integration of multiomics datasets, based on the widest available public datasets. We invite presentations that are aligned with this vision and that showcase the progress made over the past few years. Impact & Innovation Corinne Martin (Hub) Kathi Lauer (Hub) Erin Haskell (Hub) 1.5 hours Come and share your stories of impact! In this mini-symposium, we aim to showcase examples of where ELIXIR has had an impact, i.e. where ELIXIR enabled/supported/funded a change for the better, which might not have happened otherwise. Perhaps your ELIXIR resource has been used to change a patient’s life? Or to increase someone’s employability? Or to generate employment in an SME? Maybe ELIXIR funded a piece of work that significantly improved research efficiency and/or data availability to new users? The audience will vote for the best (non-technical!) presentation, both in terms of contents and delivery, with exciting prizes to be won and the opportunity to be featured on the ELIXIR website. We welcome entries from all career stages, from individuals as well as teams. Proteins Norman Davey (UK) Zsuzsanna Dosztanyi (HU) Silvio Tosatto (IT) 3D-Bioinfo reps Susanna Repo (Hub) 1.5 hours This session brings together ELIXIR Communities focussed on 3D protein structures (3Dbioinfo) and Intrinsically Disordered Proteins (IDP). We invite presentations that showcase ELIXIR progress in both these Communities, and in particular where it can be shown there may be opportunities to align and cooperate. FAIRification for Knowledge Management Sirarat Sarntivijai (Hub) Erik Hjerde (NO) 1.5 hours In this session, we will focus on the importance of FAIR knowledge management driven by both high-level policies, and operational implementations. What are the incentives for FAIR-enough implementations? What are the success stories and lessons learnt in the practice of standards and guidelines recommendations provided to the industry/regulatory stakeholders (e.g., EMA, FDA, EFPIA), international scientific communities (e.g., HCA, GA4GH, EC-FAIRsFAIR, FAIRplus), and the ELIXIR Communities use-case interactions. Biodiversity Wilfried Haerty (UK)          Jerry Lanfear (Hub) Amandine Nunes-Jorge (DE) 1.5 hours As huge data from the large Biodiversity sequencing projects (Tree of Life, Barcode of Life, i5K, etc.) are being generated, life scientists are faced with similarly huge informatics challenges. Thus, we invite talks that illustrate how ELIXIR could provide services that would support these scientists in accessing and making sense of the ever increasing volume of biodiversity-related data. 4. Poster As in previous years, we will have poster presentations at the ELIXIR All Hands meeting. Abstracts for poster presentation will be selected by the ELIXIR All Hands Programme Committee: Preference will be given to posters where the topic is not covered by oral presentation(s) elsewhere at the meeting. Preference will be given to posters that focus on topics related to Platform, Community, Commissioned Service, or Node Service activities. The poster session will run in the early evening of Tuesday 9 June. 2020-06-08 12:00:00 UTC 2020-06-11 10:30:00 UTC Eye Filmmuseum, Amsterdam, Netherlands Eye Filmmuseum Amsterdam Netherlands 1031 KT [] [] [] meetings_and_conferences [] []
  • Multiple Biofluid and Tissue Types, From Sample Preparation to Analysis Strategies for Metabolomics

    23 - 25 September 2020

    Birmingham, United Kingdom

    Elixir node event
    Multiple Biofluid and Tissue Types, From Sample Preparation to Analysis Strategies for Metabolomics https://tess.elixir-europe.org/events/multiple-biofluid-and-tissue-types-from-sample-preparation-to-analysis-strategies-for-metabolomics-7d1a21e4-32f0-4e9a-a67c-32d2932fa6f5 This 3-day course provides a theoretical overview and hands-on training to apply multiple sample preparation and UPLC-MS methods to characterise the metabolomes of complex biological samples using the mass spec... 2020-09-23 09:00:00 UTC 2020-09-25 15:30:00 UTC School of Biosciences - University of Birmingham, Birmingham, United Kingdom School of Biosciences - University of Birmingham Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Introduction to Metabolomics for the Microbiologist

    7 - 9 October 2020

    Birmingham, United Kingdom

    Elixir node event
    Introduction to Metabolomics for the Microbiologist https://tess.elixir-europe.org/events/introduction-to-metabolomics-for-the-microbiologist-5b05fb3a-a745-44e2-80ec-b515cec15eee This three-day course introduces how untargeted metabolomics can be applied to study microbial systems in academic and industrial research. The course provides an overview of the metabolomics pipeline, experimental... 2020-10-07 09:15:00 UTC 2020-10-09 16:00:00 UTC School of Biosciences - University of Birmingham, Birmingham, United Kingdom School of Biosciences - University of Birmingham Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Metabolomics with the Q Exactive

    2 - 4 November 2020

    Birmingham, United Kingdom

    Elixir node event
    Metabolomics with the Q Exactive https://tess.elixir-europe.org/events/metabolomics-with-the-q-exactive-920cedd9-d06b-4970-9619-562b1e06ae2f This 3-day course introduces you to using the Q Exactive mass spectrometer in your metabolomics investigations. The course is led by experts in the field of metabolomics and includes lectures, laboratory sessions... 2020-11-02 09:00:00 UTC 2020-11-04 15:45:00 UTC School of Biosciences - University of Birmingham, Birmingham, United Kingdom School of Biosciences - University of Birmingham Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Metabolite Identification with the Q Exactive and LTQ Orbitrap Elite

    5 - 6 November 2020

    Birmingham, United Kingdom

    Elixir node event
    Metabolite Identification with the Q Exactive and LTQ Orbitrap Elite https://tess.elixir-europe.org/events/metabolite-identification-with-the-q-exactive-and-ltq-orbitrap-elite-46935e8e-1043-4de4-8494-74207989c510 This 2-day course provides a hands-on approach to teach attendees about the latest techniques and tools available to perform metabolite identification in non-targeted metabolomics studies. The course is led by experts... 2020-11-05 09:00:00 UTC 2020-11-06 17:30:00 UTC School of Biosciences - University of Birmingham, Birmingham, United Kingdom School of Biosciences - University of Birmingham Birmingham United Kingdom B15 2TT [] [] [] [] [] []
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