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  • 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
  • C3DIS 2020

    16 - 20 March 2020

    Melbourne, Australia

    C3DIS 2020 https://tess.elixir-europe.org/events/c3dis-2020 2020-03-16 09:00:00 UTC 2020-03-20 17:00:00 UTC C3DIS Melbourne Convention and Exhibition Centre (MCEC), 1, Convention Centre Place, Melbourne, Australia Melbourne Convention and Exhibition Centre (MCEC), 1, Convention Centre Place Melbourne Australia Bioinformatics [] [] [] [] [] bioinformaticslife sciences
  • Introduction to Regular Expressions

    18 March 2020

    Heidelberg, Germany

    Introduction to Regular Expressions https://tess.elixir-europe.org/events/introduction-to-regular-expressions Educators: Supriya Khedkar, Toby Hodges (HD-HuB) Date: 18/03/2020 09:30 - 16:00 Location: EMBL Heidelberg; Room 202 Contents: Do you often work with lots of data files on the computer, are you often trying to spot particular files or lines of text in them that are important for you? If so, then using regular expressions could save you a lot of time and frustration! Regular expressions (regex/REs) are a language designed to describe patterns of characters that you want to match in a body of text. For example, if you want to extract every Ensembl Gene ID in a GFF file, find tandem repeats in a large set of sequences, or extract every email address in a large document, regular expressions are the perfect tool. Regular expressions are incorporated into a wide range of software and programming languages, and the workshop will include examples of their use on the UNIX command line and in R and Python. Learning goals: This workshop will provide an introduction to REs and cover some of the simple but powerful ways that these can be used to find patterns in large volumes of text data. The workshop will be interactive and driven by examples to demonstrate how you might use regular expressions in your work. Prerequisites: Participants are required to bring their own laptop to the workshop, with a text editor suitable for programming (e.g. Atom, Sublime Text, VSCode, Notepad++) installed. Keywords: UNIX command line, R, Python Tools: UNIX command line, R, Python 2020-03-18 09:00:00 UTC 2020-03-18 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • Research Data Alliance Plenary Meeting

    18 - 20 March 2020

    Melbourne, Australia

    Research Data Alliance Plenary Meeting https://tess.elixir-europe.org/events/research-data-alliance-plenary-meeting 2020-03-18 09:00:00 UTC 2020-03-20 17:00:00 UTC RDA Melbourne Convention and Exhibition Centre (MCEC), 1, Convention Centre Place, Melbourne, Australia Melbourne Convention and Exhibition Centre (MCEC), 1, Convention Centre Place Melbourne Melbourne City Australia Bioinformatics [] [] [] [] [] life sciencesbioinformatics
  • 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
  • Data Management Planning workshop for Life Science Projects

    27 March 2020

    Oslo, Norway

    Data Management Planning workshop for Life Science Projects https://tess.elixir-europe.org/events/data-management-planning-workshop-for-life-science-projects-9baab407-a36b-49bf-aa27-76cf0046cc79 We are pleased to announce the Data Management planning workshop for Life Scientists organised in Oslo by [ELIXIR Norway](https://www.elixir-norway.org/), [Digital Life Norway](https://digitallifenorway.org/) and [UiO Research Data team](https://www.uio.no/english/for-employees/support/research/research-data-management/). The intended audience are researchers (PhD candidates, Post Doctoral Fellows, Researchers, Associate Professors and Professors) who are planning to submit a grant application for a research project. Max. number of participants is 30. In this course we will cover how to generate a data management plan for a Life Science research project, which will meet the requirements of the funding organisations. ## Course content: ##### 0900 - 0915 Introduction ##### 0915 - 0945 Requirements from institutions & funding bodies * UiO * H2020/ERC * Research Council Norway ##### 0945 - 1015 About legal requirements * Health Research Act * Personal Data Act ##### 1015 - 1030 Short break ##### 1030 - 1115 Licensing of data, biological material and software ##### 1115 - 1200 Information on national and local storage infrastructures * NeLS/StoreBioInfo * NIRD * TSD * UiO Computing & Storage resources ##### 1200 - 1230 Lunch ##### 1230 - 1315 Relevant deposition repositories/ data archives * domain specific archives (ELIXIR/EMBL-EBI, NCBI) * NIRD archive * DataverseNO * NSD * generic repositories ##### 1315 - 1330 Short break ##### 1330 - 1600 Hands on training and assistance to generate a data management plan ## Requirements: Bring your own laptop and your research project if you have one. You will get the opportunity to set up a data management plan for your project with help of the [Data Steward Wizard tool](https://elixir-no.ds-wizard.org) using a structured and detailed questionnaire with references to relevant resources. #### [Register](https://skjemaker.app.uib.no/view.php?id=7924299) before 20th of March 2020 2020-03-27 09:00:00 UTC 2020-03-27 16:00:00 UTC ELIXIR-Norway Moltke Moes vei 39, Georg Sverdrups hus, Auditorium 2, https://www.uio.no/om/finn-fram/omrader/blindern/bl27/, Oslo, Norway Moltke Moes vei 39, Georg Sverdrups hus, Auditorium 2, https://www.uio.no/om/finn-fram/omrader/blindern/bl27/ Oslo Norway 0851 Data management University of Oslo Elin Stangeland, Ståle Nygård, Korbinian Bösl Digital Life Norway PhD Students Postdocs and Staff members from the University of CambridgeProfessorsResearchers 30 workshops_and_courses first_come_first_served Data management plandata management
  • Ensembl Browser Workshop, DKFZ, 5 May 2020

    5 May 2020

    Heidelberg, Germany

    Elixir node event
    Ensembl Browser Workshop, DKFZ, 5 May 2020 https://tess.elixir-europe.org/events/ensembl-browser-workshop-dkfz-5-may-2020 Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart. 2020-05-05 09:00:00 UTC 2020-05-05 09:00:00 UTC Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC), Heidelberg, Germany Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) Heidelberg Germany 69120 [] Astrid Gall [] [] [] [] HDRUK
  • Ensembl REST API Workshop, DKFZ, 6 May 2020

    6 May 2020

    Heidelberg, Germany

    Elixir node event
    Ensembl REST API Workshop, DKFZ, 6 May 2020 https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-dkfz-6-may-2020 Work with Ensembl to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments. 2020-05-06 09:00:00 UTC 2020-05-06 09:00:00 UTC Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC), Heidelberg, Germany Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) Heidelberg Germany 69120 [] Astrid Gall [] [] [] [] HDRUK
  • ELIXIR Heads of Nodes Retreat (2020)

    6 - 7 May 2020

    Woking, United Kingdom

    ELIXIR Heads of Nodes Retreat (2020) https://tess.elixir-europe.org/events/elixir-heads-of-nodes-retreat-2020 The ELIXIR Heads of Nodes (HoN) will hold their annual Retreat from 6-7 May 2020 in Woking, UK. A full agenda and documents for this meeting will be made available to meeting participants in due course. Location Set in the Surrey country side, this venue has been chosen as an ideal venue just 30 minutes from central London and 20 minutes from Heathrow and Gatwick Airport. You are encouraged to travel to and from Heathrow Airport. Contacts For all documentation inquiries, please contact: Joana Wingender (joana.wingender@elixir-europe.org) For all logistical inquiries, please contact: Melissa Balzano (melissa.balzano@elixir-europe.org)    2020-05-06 11:00:00 UTC 2020-05-07 15:00:00 UTC The Talbot Inn, Woking, United Kingdom The Talbot Inn Woking United Kingdom GU23 6BB [] [] [] meetings_and_conferences [] []
  • 9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis

    26 - 29 May 2020

    České Budějovice, Czechia

    9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis https://tess.elixir-europe.org/events/7th-repeatexplorer-workshop-on-the-application-of-next-generation-sequencing-to-repetitive-dna-analysis The workshop will focus on theoretical and practical aspects of using next generation sequencing (NGS) data for analyzing repeat composition of plant genomes. Special emphasis will be given to repeat characterization methods implemented in the RepeatExplorer pipeline, including practical training in using the pipeline. The workshop should also serve as a platform for exchange of ideas and latest results with ample time dedicated to open discussions. Participants are encouraged to make short presentations of their research related to the workshop topic and/or bring their own data for practical training. The workshop is organized by the Laboratory of Molecular Cytogenetics of the Biology Centre AS CR. It will take place at the Academy of Sciences / University campus in Ceske Budejovice, Czech Republic. The meeting programme will include theoretical lectures and research reports combined with hands-on training (no programming skills required). Registration if open till 5th May. In case of any questions or comments please contact Jiri Macas. 2020-05-26 09:00:00 UTC 2020-05-29 00:00:00 UTC Institute of Plant Molecular Biology, České Budějovice, Czech Republic Branišovská 1160/31, 31, Branišovská, České Budějovice, Czechia Branišovská 1160/31, 31, Branišovská České Budějovice České Budějovice Czechia [] Jiri Macas ELIXIR: The Czech Republic Node PhD StudentspostdocsResearchers workshops_and_courses first_come_first_served []
  • 9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis

    26 - 29 May 2020

    České Budějovice, Czechia

    9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis https://tess.elixir-europe.org/events/repeatexplorer-workshop The workshop will focus on theoretical and practical aspects of using next generation sequencing (NGS) data for analyzing repeat composition of plant genomes. Special emphasis will be given to repeat characterization methods implemented in the RepeatExplorer pipeline, including practical training in using the pipeline. The workshop should also serve as a platform for exchange of ideas and latest results with ample time dedicated to open discussions. Participants are encouraged to make short presentations of their research related to the workshop topic and/or bring their own data for practical training. The workshop is organized by the Laboratory of Molecular Cytogenetics of the Biology Centre AS CR. It will take place at the Academy of Sciences / University campus in Ceske Budejovice, Czech Republic. The meeting programme will include theoretical lectures and research reports combined with hands-on training (no programming skills required). In case of any questions or comments please contact Jiri Macas. 2020-05-26 09:00:00 UTC 2020-05-29 00:00:00 UTC Institute of Plant Molecular Biology building at the Academy of Sciences and University campus in České Budějovice Branišovská 1160/31, 31, Branišovská, České Budějovice, Czechia Branišovská 1160/31, 31, Branišovská České Budějovice České Budějovice Czechia [] Jiri Macas [] Life Science Researchersbioinformaticians workshops_and_courses first_come_first_served []
  • 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 7 February 2020 Accepted presentations (incl. talks, demonstrations and posters) announced by this date 24 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 [] []
  • NBIS Course Umeå: Python programming with applications to bioinformatics, Umeå

    19 - 24 October 2020

    Glasburen

    Elixir node event
    NBIS Course Umeå: Python programming with applications to bioinformatics, Umeå https://tess.elixir-europe.org/events/nbis-course-umea-python-programming-with-applications-to-bioinformatics-umea-2dee9df0-cf81-4e7d-b14e-1dd65909a0fa #training TBA edu.intro-python@nbis.se or education@nbis.se Course leaders: Nina Norgren and Malin Klang 2020-10-19 09:00:00 UTC 2020-10-24 00:00:00 UTC Glasburen Glasburen [] jessica.lindvall@scilifelab.se [] [] [] [] #trainingtraining
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