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  • Automated Workflow Composition in the Life Sciences

    9 - 13 March 2020

    Leiden, Netherlands

    Automated Workflow Composition in the Life Sciences https://tess.elixir-europe.org/events/automated-workflow-composition-in-the-life-sciences In the age of computational science, researchers in the life sciences – just as in other domains – regularly face the need of composing several individual software tools into pipelines or workflows that perform the specific data analysis processes that they need in their research. For over 20 years now, dedicated scientific workflow management systems have been supporting scientists in this task, and they continue to gain popularity. In fact, recent years have seen significant progress in the functional annotation of bioinformatics software tools, as well as their virtualization, containerization and assembly into workflows for automatically executing the processes. At least since the rise of the Semantic Web in the early 2000s, also the idea of semantics-based automated composition of workflows has been around to simplify the work with scientific workflows further and free life science researchers from having to deal with the technicalities of software composition. This would not only save valuable research time, but also reduce errors, allow benchmarking of data analysis pipelines and enable new scientific findings by discovering workflows that researchers would not have thought of themselves. However, despite its obvious potential and appeal, the need for optimizing data analysis workflows, and despite different research groups working on the topic, automated workflow composition has not yet arrived in the daily practice of life science researchers. The reasons for this are manifold. Some are more practical (for example the lack of automatic composition tools in the commonly used software frameworks), others are of more fundamental nature (such as questions on specification languages, composition algorithms, formal semantics and workflows representations). On one important aspect, namely the semantic annotation of tools on a large scale, the life science community has made significant progress in the last years: The EDAM ontology provides a controlled vocabulary of bioinformatics operations, data types and formats, and the bio.tools registry has become a large collection of bioinformatics tools that are semantically annotated with terms from the EDAM ontology. As demonstrated in a recent Bioinformatics publication (https://academic.oup.com/bioinformatics/article/35/4/656/5060940), this forms a solid basis for performing automated workflow composition in the life sciences domain. Nevertheless, it is still a long way to its use in daily scientific practice. This workshop will bring together researchers and practitioners who have been working on different aspects related to automated workflow composition in the life sciences. These include life science researchers, tool providers, infrastructure developers, ontologists, algorithmics researchers and many more. They do not normally come together as a group at the regular scientific events, so a Lorentz workshop devoted to this topic provides a unique opportunity to join forces and together significantly advance the field. 2020-03-09 09:00:00 UTC 2020-03-13 17:00:00 UTC Jon Ison, Anna-Lena Lamprecht, Magnus Palmblad and Veit Schwämmle Lorentz Center Oort, Leiden, Netherlands Lorentz Center Oort Leiden Netherlands 2333 Omics Workflows Leiden University reinards@lorentzcenter.nl ELIXIRLorentz CenterLUMC software developers, bioinformaticiansbiocurators 50 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
  • 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 [] []
  • 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
  • Basic statistics in R - Ghent

    21 - 28 April 2020

    Ghent, Belgium

    Elixir node event
    Basic statistics in R - Ghent https://tess.elixir-europe.org/events/basic-statistics-in-r-ghent-956bd94b-3c4a-442a-8b32-782efc8ed054 Get an idea of what R and Rstudio is Use R to handle data: creating, reading, reformatting and writing data Use R to create graphics Use basic statistical techniques in R : normality tests, t-tests, wilcoxon tests, chi square tests, correlations, survival analysis... Write and use R scripts 2020-04-21 09:00:00 UTC 2020-04-28 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
  • Workshop Metagenomics

    1 May 2020

    Leiden, Netherlands

    Elixir node event
    Workshop Metagenomics https://tess.elixir-europe.org/events/workshop-metagenomics-50fa03ae-bc84-447a-92fe-b353cea33030 In deze cursus wordt een algemene achtergrond van metagenomics gegeven. Hands-on data-analyse is een belangrijk onderdeel: tijdens computer practica kan je 16S- en metagenoom datasets analyseren. De workflow van monstervoorbereiding, DNA-isolatie, selectie van platform, read mapping, annotatie en metagenoomassemblage wordt behandeld.… The post Workshop Metagenomics appeared first on Dutch Techcentre for Life Sciences. 2020-05-01 09:00:00 UTC 2020-05-01 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] [] workshops_and_courses [] []
  • 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
  • Analyse Next Generation Sequencing (NGS) data

    8 June 2020

    Leiden, Netherlands

    Elixir node event
    Analyse Next Generation Sequencing (NGS) data https://tess.elixir-europe.org/events/analyse-next-generation-sequencing-ngs-data Deze tweedaagse workshop geeft toepasbare up to date informatie over NGS. Verschillende platforms, de werking van sequencers en nucleïnezuur isolatie komen uitvoerig aan bod. De analyse van NGS data bij DNA en RNA sequencing wordt geïntroduceerd. Verschillende toepassingen zoals genoom… The post Analyse Next Generation Sequencing (NGS) data appeared first on Dutch Techcentre for Life Sciences. 2020-06-08 09:00:00 UTC 2020-06-08 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] [] 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 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 [] []
  • Analyzing flow cytometry data using FlowJo

    9 June 2020

    Ghent, Belgium

    Elixir node event
    Analyzing flow cytometry data using FlowJo https://tess.elixir-europe.org/events/analyzing-flow-cytometry-data-using-flowjo-c46f238c-d46d-45cd-ac64-df9421f741b6 Learn researchers how to analyze flow cytometry data in an efficient way using FlowJo v10,the world’s nr.1 analysis software tool for flow cytometry data. This training will make you familiar with all the basic and advanced features of FlowJo v10. In the end you will be able to analyze and visualize your flow data and learn how to get the statistics out of it 2020-06-09 09:00:00 UTC 2020-06-09 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
  • Introduction to Git & GitHub

    19 June 2020

    Ghent, Belgium

    Elixir node event
    Introduction to Git & GitHub https://tess.elixir-europe.org/events/introduction-to-git-github-fb8f30cf-2699-400d-a699-5822a2d9f825 Get you started with Git from zero (note that if you already use Git, this workshop will be too basic for you). We'll work with GitHub (Desktop) and have a look into git on a command-line level.  Introduction, set-up & configurations Working locally: Create a repository, clone, edit, staging commits, commit & push Working with your history & logs Working in a project: Forking, branching & pull requests How to version control your code in Rstudio & Jupyter with GitHub 2020-06-19 09:00:00 UTC 2020-06-19 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
  • Analyzing qPCR data with qbase+

    14 September 2020

    Ghent, Belgium

    Elixir node event
    Analyzing qPCR data with qbase+ https://tess.elixir-europe.org/events/analyzing-qpcr-data-with-qbase This training specifically focuses on the analysis of gene expression data using qbase+. During this training you will: create an experiment in qbase+ import run data customize sample properties select reference genes assess the quality of your qPCR data visualize and export the results 2020-09-14 09:00:00 UTC 2020-09-14 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
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