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Target audience: software developers, bioinf...  or Pathologists 

  • ELIXIR-EXCELERATE HPC Train-the-Researcher

    6 - 7 April 2017

    Málaga, Spain

    ELIXIR-EXCELERATE HPC Train-the-Researcher https://tess.elixir-europe.org/events/elixir-excelerate-hpc-train-the-researcher This course to be held 6-7 April 2017 in Malaga, Spain is part of the Train-the-Researcher (TtR) subtask of the ELIXIR-EXCELERATE project. The course is organised as a two-day mini-symposium, and aims at introducing the participants in the complexities of parallel programming with emphasis on genome-scale comparison algorithms. The theoretical aspects of this course cover (a) the parallel programing background, with a quick overview in the architectures and programming models; and (b) the basis for genome-scale sequence comparison algorithms. The practical aspects are organised to master the concepts of data distribution and balancing using a Map-Reduce strategy and internal coding with MPI. Organization Overview This course has been prepared for two days including theoretical and practical parts. The first day will start with a brief introduction to HPC condensed during the morning. A practical introductory part to HPC will complete the first day. The second day will firstly provide the necessary background on the multiple genome comparison application GECKO. Secondly, on the same day, we will motivate the potential HPC techniques to be applied to this application and will let the students organize in groups to start thinking about a parallelization approach and later on implementing it. At the end of the day each group will briefly describe how they have implemented it and will present their results (i.e. speedup). Methods The course is comprised of practical exercises preceded by short lectures. Exercises will be conducted primarily in the C programming language using the MPI library. Target Audience This course is open to bioinformatics users and developers that aim at using HPC resources to extend their activity beyond the limitations of sequential applications on commodity hardware. This course will not suit participants that are looking for entry-level concepts in HPC. 20 participants will be selected by CV and motivation. Gender equality will be an additional aspect to select the participants. As an applicant to this course you need to fill out your personal information, attach your CV and provide a short paragraph to explain why you want to apply for this course. Optionally if you are part of an ELIXIR node you can also attach a letter of endorsement from the node manager. The last application day will be March 3rd, the result of the candidate selection will be notified March 8th. The course registration is free, but by sending this participation you commit to attend the course in case you are selected as it is stated in the conditions/policy document of the registration form. Pre-Requisites This course has a broad technical scope and hence programming skills are required. Experience in the command-line, writing and compiling C code would make the course easier to follow. 2017-04-06 09:00:00 UTC 2017-04-07 17:00:00 UTC Málaga, Málaga, Spain Málaga Málaga Málaga Spain Sequence analysis Computer science [] [] software developers, bioinformaticians workshops_and_courses registration_of_interest []
  • BioData.pt Business Forum: Advanced data management for added value

    6 May 2019

    Oeiras, Portugal

    Elixir node event
    BioData.pt Business Forum: Advanced data management for added value https://tess.elixir-europe.org/events/biodata-pt-business-forum Research and development institutions annually produce zetabytes of biological information, of which only terabytes are used by the bio-industry. There is a large biological information, the big biodata, still to be explored by the bio-industry, which can add value into new products and services. The BioData.pt Business Forum: advanced data management for added value, organized by BioData.pt and PBio, will bring together four national companies related to the health sector, the sea, agriculture and bioindustry, and tell their stories to inspire new ideas and new businesses. There will also be an opportunity to discuss best practices in curation, management and use of biodata, as well as the use of bioinformatics tools essential to its success. 2019-05-06 14:30:00 UTC 2019-05-06 18:00:00 UTC Biodata.pt Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande, Oeiras, Portugal Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande Oeiras Portugal 2780-156 Instituto Gulbenkian de CiênciaBiodata.pt - Elixir's portuguese node of the european projec info@biodata.pt [] Clinical ScientistsbioinformaticiansBiologists, Genomicists, Computer Scientistssoftware developers, bioinformaticiansbiology and bioinformatics sophomore undergraduatesbiocurators Institutions and other external Institutions or individualsIndustry health professionalsplant researchersBiomedical researchers studies human diseases or developmental biology 120 meetings_and_conferences [] Biodata, Bioinformatics, Biodata
  • DNA Methylation Data Analysis Workshop

    2 - 5 November 2020

    Berlin, Germany

    DNA Methylation Data Analysis Workshop https://tess.elixir-europe.org/events/dna-methylation-data-analysis-workshop Advance your epigenetics research with NGS methods. In a nutshell - Learn how bisulfite sequencing works - Understand how bisulfite-treated reads are mapped to a reference genome - Perform basic analyses (call methylated regions, perform basic downstream analyses) - Use shell scripting to create reusable data pipelines - Visualize results (ready-to-publish) The purpose of this workshop is to get a deeper understanding of the use of bisulfite-treated DNA in order to analyze the epigenetic layer of DNA methylation. Advantages and disadvantages of the so-called 'bisulfite sequencing' and its implications on data analyses will be covered. The participants will be trained to understand bisulfite-treated NGS data, to detect potential problems/errors and finally to implement their own pipelines. After this course they will be able to analyze DNA methylation and create ready-to-publish graphics. By the end of this workshop the participants will: - be familiar with the sequencing method of Illumina - understand how bisulfite sequencing works - be aware of the mapping problem of bisulfite-treated data - understand how bisulfite-treated reads are mapped to a reference genome - be familiar with common data formats and standards - know relevant tools for data processing - automate tasks with shell scripting to create reusable data pipelines - perform basic analyses (call methylated regions, perform basic downstream analyses) - plot and visualize results (ready-to-publish) - be able to reuse all analyses 2020-11-02 09:00:00 UTC 2020-11-05 17:00:00 UTC ecSeq Bioinformatics GmbH PC-COLLEGE Berlin, 78, Stresemannstraße, Berlin, Germany PC-COLLEGE Berlin, 78, Stresemannstraße Berlin Germany 10963 Sequencing Sequence analysis Bioinformatics [] ecSeq Bioinformatics GmbH Sternwartenstr. 29 D-04103 Leipzig Germany Email: events@ecSeq.com [] BiologistsBiologists, Genomicists, Computer ScientistsMolecular BiologistsPhD studentspost-docsPathologistsbioinformaticians 25 workshops_and_courses first_come_first_served EpigeneticsDNA MethylationBisulfite-Seq

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