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  • Data Carpentry Workshop 2020

    29 - 31 January 2020

    Heidelberg, Germany

    Data Carpentry Workshop 2020 https://tess.elixir-europe.org/events/educators-toby-hodges-florian-huber-thea-van-rossum-georg-zeller-hd-hub-fotis-e-psomopoulos-date-28-01-2019-30-01-2019-location-atc-computer-training-lab-contents-the-missing-step-between-data-collection-and-research-progress-is-a-lack-of-training-for-researchers-in-crucial-skills-for-effectively-managing-and-analysing-large-amounts-of-data-this-hands-on-workshop-teaches-researchers-the-fundamental-data-skills-they-need-to-conduct-their-work-and-provides-high-quality-domain-specific-training-covering-the-full-lifecycle-of-data-driven-research-the-domain-specific-approach-allows-participants-to-tailor-the-data-content-and-tools-to-reflect-the-specific-data-and-analysis-needs-of-different-areas-data-organisation-and-cleaning-introduction-to-r-data-analysis-and-visualisation-in-r-interacting-with-databases-from-r-data-analysis-with-applications-to-genomics-learning-goals-you-will-learn-how-to-organise-data-and-some-practices-for-more-effective-data-handling-to-effectively-clean-and-format-data-and-automatically-track-any-changes-to-use-r-to-handle-filter-and-summarise-tabular-data-to-use-the-split-apply-combine-concept-for-data-analysis-to-visualise-the-results-of-these-analyses-in-r-using-the-ggplot2-library-to-apply-all-of-the-concepts-in-an-exploratory-analysis-of-a-typical-biological-dataset-prerequisities-the-course-is-aimed-at-graduate-students-and-other-researchers-in-the-life-sciences-who-would-like-to-learn-good-practices-in-data-management-and-analysis-the-course-is-ideally-suited-to-students-without-prior-experience-in-computational-research-but-some-familiarity-with-working-with-tabular-data-on-a-computer-is-welcome-keywords-data-carpentry-r-tools-r Educators: Toby Hodges, Florian Huber, Thea Van Rossum, Georg Zeller, (HD-HuB) Fotis E. Psomopoulos Date: 28/01/2020 - 30/01/2020 Location: ATC Computer Training Lab Contents: The missing step between data collection and research progress is a lack of training for researchers in crucial skills for effectively managing and analysing large amounts of data. This hands on workshop teaches researchers the fundamental data skills they need to conduct their work, and provides high-quality, domain-specific training covering the full lifecycle of data-driven research. The domain-specific approach allows participants to tailor the data, content, and tools to reflect the specific data and analysis needs of different areas: - Data organisation and cleaning - Introduction to R - Data analysis and visualisation in R - Interacting with databases from R - Data analysis with applications to genomics Learning goals: You will learn... - how to organise data and some practices for more effective data handling - to effectively clean and format data and automatically track any changes - to use R to handle, filter, and summarise tabular data - to use the split-apply-combine concept for data analysis - to visualise the results of these analyses in R using the ggplot2 library - to apply all of the concepts in an exploratory analysis of a typical biological dataset Prerequisities: The course is aimed at graduate students and other researchers in the life sciences who would like to learn good practices in data management and analysis. The course is ideally suited to students without prior experience in computational research, but some familiarity with working with tabular data on a computer is welcome. Keywords: Data Carpentry, R Tools: R 2020-01-29 09:00:00 UTC 2020-01-31 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • Introduction to high-performance computing (sciCORE cluster)

    12 February 2020

    Basel, Switzerland

    Elixir node event
    Introduction to high-performance computing (sciCORE cluster) https://tess.elixir-europe.org/events/introduction-to-high-performance-computing-scicore-cluster-b7687fe3-7d5d-47c4-aab1-cca8be55e5d0 Overview This full-day course has a practical focus, where participants will learn how to use the Linux command line and interact with the sciCORE cluster. All new users of sciCORE are strongly encouraged to follow this course. 2020-02-12 09:00:00 UTC 2020-02-12 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • CABANA Workshop: Analysis of Crop Genomics Data

    16 - 20 March 2020

    Bogota, Colombia

    Elixir node event
    CABANA Workshop: Analysis of Crop Genomics Data https://tess.elixir-europe.org/events/cabana-workshop-analysis-of-crop-genomics-data-0d1c7271-613b-4672-bac5-19f641f9be70 This course will introduce crop biologists to methods and approaches for analysing crop genomics data. 2020-03-16 08:30:00 UTC 2020-03-20 12:30:00 UTC Universidad de los Andes - UniAndes, Bogota, Colombia Universidad de los Andes - UniAndes Bogota Colombia 111711 [] Marco Cristancho [] [] [] [] HDRUK
  • 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
  • First steps with R in Life Sciences

    16 - 17 April 2020

    Basel, Switzerland

    Elixir node event
    First steps with R in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-r-in-life-sciences-52ebf63a-a4fb-4898-8b44-212e3eced3c5 --> Overview R is a complete, flexible and open source system for statistical analysis and graphics, which has become a tool of choice for biologists and biomedical scientists who need to analyse and visualise large amounts of data. 2020-04-16 09:00:00 UTC 2020-04-17 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • First Steps with Python in Life Sciences

    18 - 20 May 2020

    Basel, Switzerland

    Elixir node event
    First Steps with Python in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-python-in-life-sciences-d45a8059-cedd-4e69-bcac-8da973f4496d Overview Python is an open-source and general-purpose scripting language which runs on all major operating systems. 2020-05-18 09:00:00 UTC 2020-05-20 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • First Steps with Python in Life Sciences

    18 - 20 May 2020

    Basel, Switzerland

    Elixir node event
    First Steps with Python in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-python-in-life-sciences-402cdbc1-5a65-4f48-8581-994a44441dc5 Overview Python is an open-source and general-purpose scripting language which runs on all major operating systems. 2020-05-18 09:00:00 UTC 2020-05-20 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Advanced topics in single-cell transcriptomics

    27 - 29 May 2020

    Basel, Switzerland

    Elixir node event
    Advanced topics in single-cell transcriptomics https://tess.elixir-europe.org/events/advanced-topics-in-single-cell-transcriptomics More information soon 2020-05-27 09:00:00 UTC 2020-05-29 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • 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 [] []
  • First steps in Python, and more!

    9 - 11 June 2020

    Basel, Switzerland

    Elixir node event
    First steps in Python, and more! https://tess.elixir-europe.org/events/first-steps-in-python-and-more Overview Python is an open-source and general-purpose scripting language which runs on all major operating systems. 2020-06-09 09:00:00 UTC 2020-06-11 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Protein Bioinformatics: Sequence-Structure-Function - Dates to be confirmed

    18 - 20 November 2020

    Basel, Switzerland

    Elixir node event
    Protein Bioinformatics: Sequence-Structure-Function - Dates to be confirmed https://tess.elixir-europe.org/events/protein-bioinformatics-sequence-structure-function-dates-to-be-confirmed Overview Sequence-structure-function relationships of proteins are central to a comprehensive understanding of cellular biology. However, many proteins lack direct and detailed information regarding structure, function, and complex formation. 2020-11-18 09:00:00 UTC 2020-11-20 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
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