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  • 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
  • Introduction to Genomic Variant Interpretation

    6 - 7 April 2020

    Sheffield, United Kingdom

    Introduction to Genomic Variant Interpretation https://tess.elixir-europe.org/events/introduction-to-genomic-variant-interpretation This course covers state-of-the-art and best-practice tools for the analysis of genomes. We describe, and give hands-on experience of, the entire analysis workflow from raw data generated by a sequencing machine to deriving variant calls (e.g. Single Nucleotide Variants) that are ready for downstream analysis, interpretation and prioritisation. We will describe the steps involved to go from sequencing library to a prioritised, clinically-relevant list of DNA variants. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control, variant-calling and annotation. 2020-04-06 08:30:00 UTC 2020-04-07 16:00:00 UTC Bartolome House, Seminar Room EG03, Sheffield, United Kingdom Bartolome House, Seminar Room EG03 Sheffield United Kingdom S3 7ND [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Introduction to identifying and characterising somatic variants

    21 April - 21 May 2020

    Sheffield, United Kingdom

    Introduction to identifying and characterising somatic variants https://tess.elixir-europe.org/events/introduction-to-identifying-and-characterising-somatic-variants-907ec326-e958-4c2e-a935-4780254ae845 This course covers state-of-the-art and best-practice tools for the analysis of genomes. We describe, and give hands-on experience of, the entire analysis workflow from raw data generated by a sequencing machine to deriving variant calls (e.g. Single Nucleotide Variants) that are ready for downstream analysis, interpretation and prioritisation. We will describe the steps involved to go from sequencing library to a prioritised, clinically-relevant list of DNA variants. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control, variant-calling and annotation. 2020-04-21 08:30:00 UTC 2020-05-21 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S1 3JD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • ELIXIR Bioinformatics Industry Forum

    28 April 2020

    London, United Kingdom

    ELIXIR Bioinformatics Industry Forum https://tess.elixir-europe.org/events/elixir-bioinformatics-industry-forum With the ELIXIR Bioinformatics Industry Forum we want to build a community for technical specialists to discuss visionary ideas, bottlenecks and solutions to some of the major challenges in the data driven life science sector. What unites all participants is the drive to move science forward through a collaborative effort.   With these events we will:  Give companies the chance to present technical advances in their field, and to discuss and share feedback on these from ELIXIR members. Provide a forum for knowledge exchange and collaboration in the pre-competitive space. Create networking opportunities with bioinformatics opinion leaders, academic experts in ELIXIR and other industry members. Provide a forum to articulate scientific and technical challenges with experts in the field and potentially develop innovative solutions for e.g. analytics, infrastructure and AI exploitation.   What can attendees expect: Attendees at this event will be immersed in a world of data-driven innovation, with a mix of high-level keynote presentations, roundtable sessions to discuss and interact with other participants, panel discussions addressing hot topics in the data driven life science sector and visionary talks on the latest developments in bioinformatics.    A dedicated session with five minute Flash Talks will give you the chance to introduce your work to a broad audience (see registration form to submit a Flash Talk).    Who should attend: Bioinformaticians, Developers, IT specialists, Data Scientist/Engineers and anyone interested in the data driven life sciences sector   2020-04-28 10:00:00 UTC 2020-04-28 10:00:00 UTC Wellcome Collection, London, United Kingdom Wellcome Collection London United Kingdom NW1 2BE [] [] [] meetings_and_conferences [] []
  • 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
  • RNA-seq Analysis for Beginners

    13 May 2020

    Sheffield, United Kingdom

    RNA-seq Analysis for Beginners https://tess.elixir-europe.org/events/rna-seq-analysis-for-beginners-910fd563-0c77-49c8-9f3a-878af00ba1b9 High-throughput RNA-sequencing is now the standard technique for quantifying transcript abundance in a biological sample of interest. In this course we will describe the processes that take place once you submit a library for RNA sequencing, and what data you should expect to receive from the Bioinformatics Core. We will describe the steps involved to go from sequencing library to a list of genes that show statistically significant differences between your biological conditions of interest. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control and assessing differential expression. We will also showcase some web sites you can use for enrichment and pathways analysis. 2020-05-13 08:30:00 UTC 2020-05-13 16:00:00 UTC Bartolome House, Seminar Room EG03, Sheffield, United Kingdom Bartolome House, Seminar Room EG03 Sheffield United Kingdom S3 7ND [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • CABANA: Data-driven Biology to Address UN Grand Challenges in Latin America Symposium

    14 May 2020

    London, United Kingdom

    Elixir node event
    CABANA: Data-driven Biology to Address UN Grand Challenges in Latin America Symposium https://tess.elixir-europe.org/events/cabana-data-driven-biology-to-address-un-grand-challenges-in-latin-america-symposium The CABANA project is a Global Challenge Research Fund project operating in Latin America. We will be hosting a one-day symposium at the Royal Society on 14th May 2020 entitled "Data-driven biology to address UN grand challenges in Latin America". We will have members of the science and donor community from the UK and Latin America attending. Our speakers will be a mix of academics from the UK and Latin America working with Bioinformatics for the prevention of infectious diseases, food security and the protection of biodiversity. 2020-05-14 09:00:00 UTC 2020-05-14 18:00:00 UTC The Royal Society, London, United Kingdom The Royal Society London United Kingdom SW1Y 5AG [] Marina Pujol [] [] [] [] HDRUK
  • CABANA: Addressing UN Sustainable Goals in Latin America Through Data-driven Biology Symposium

    14 May 2020

    London, United Kingdom

    Elixir node event
    CABANA: Addressing UN Sustainable Goals in Latin America Through Data-driven Biology Symposium https://tess.elixir-europe.org/events/cabana-addressing-un-sustainable-goals-in-latin-america-through-data-driven-biology-symposium The CABANA (www.cabana.online) project is a Global Challenge Research Fund project operating in Latin America. We will be hosting a one-day symposium at the Royal Society on Thursday 14th May 2020 entitled "Addressing UN Sustainable Goals in Latin America through data-driven biology". 2020-05-14 09:00:00 UTC 2020-05-14 18:00:00 UTC The Royal Society, London, United Kingdom The Royal Society London United Kingdom SW1Y 5AG [] Marina Pujol [] [] [] [] HDRUK
  • 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. 31 March 2020 Registration closes, or earlier, if capacity is reached. Deadline for poster submissions, or earlier, if capacity is reached. Submission of posters is re-opened. Priority will be given to those participants that have not previously submitted a poster. 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 Registration The registration to the All Hands meeting is now open with limited capacity. We welcome registrations from participants from ELIXIR Nodes. The registration will close 31 March, or sooner if capacity is reached. Check the Weekly Brief on 24 February for details on how to register or log in to the site and return to this page. You will see the registration link once you are logged in. Code of Conduct The ELIXIR Code of Conduct has been created to ensure that people at ELIXIR events can interact with each other in a respectful and safe environment. It provides ways you can voice your concern if you believe there has been a breach to this Code of Conduct. The ELIXIR Code of Conduct will be in place at this event. Social activities This Google doc lists recommended tourist sites, social activities and things to do in your free time. Note: The All Hands meeting ends on Thursday 11 Jun 2020 at 11:00 CEST. After the end of the meeting, there are two project meetings taking place starting at 11:00 CEST. These are the CONVERGE AGM and the Federated Human Data Strategic Implementation Study meeting. Both of these meetings are restricted to named project partners. 2020-06-08 12:00:00 UTC 2020-06-11 11:00:00 UTC Eye Filmmuseum, Amsterdam, Netherlands Eye Filmmuseum Amsterdam Netherlands 1031 KT [] [] [] meetings_and_conferences [] []
  • RNA-seq Analysis for Beginners

    3 July 2020

    Sheffield, United Kingdom

    RNA-seq Analysis for Beginners https://tess.elixir-europe.org/events/rna-seq-analysis-for-beginners-13c9f173-2fdd-4ea6-9005-58aa798bf289 High-throughput RNA-sequencing is now the standard technique for quantifying transcript abundance in a biological sample of interest. In this course we will describe the processes that take place once you submit a library for RNA sequencing, and what data you should expect to receive from the Bioinformatics Core. We will describe the steps involved to go from sequencing library to a list of genes that show statistically significant differences between your biological conditions of interest. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control and assessing differential expression. We will also showcase some web sites you can use for enrichment and pathways analysis. 2020-07-03 08:30:00 UTC 2020-07-03 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Introduction to RNA-seq analysis in R

    13 - 14 July 2020

    Sheffield, United Kingdom

    Introduction to RNA-seq analysis in R https://tess.elixir-europe.org/events/introduction-to-rna-seq-analysis-in-r-34ffdcbc-a5b7-49ac-afb9-7d338a38ea26 In this workshop, you will be learning how to analyse RNA-seq count data, using R. This will include reading the data into R, quality control and performing differential expression analysis and gene set testing, with a focus on the edgeR analysis workflow. You will learn how to generate common plots for analysis and visualisation of gene expression data, such as boxplots and heatmaps. You will also be learning how alignment and counting of raw RNA-seq data can be performed in R. This workshop is aimed at biologists interested in learning how to perform differential expression analysis of RNA-seq data when reference genomes are available.. 2020-07-13 08:30:00 UTC 2020-07-14 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
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