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  • 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
  • Plant Phenotyping

    12 November 2019

    Oeiras, Portugal

    Plant Phenotyping https://tess.elixir-europe.org/events/plant-phenotyping Plant phenotyping research has gone through a data revolution with the automation of plant phenotyping platforms, making it critical to adopt good data management practices in order the exploit the torrent of data to its full potential. Concretely, data should be published in a Findable, Accessible, Interoperable and Reusable (FAIR) way in order to enable the integration of data from disparate sources and the discovery of new knowledge. Yet, this is one of the more challenging domains to standardize, as it is extremely heterogeneous in terms of experimental settings and types of data. The ELIXIR infrastructure, with prominent contributions from BioData.pt (the Portuguese ELIXIR node) has been tackling this challenge at the European and international level, by developing standards and services to enable the management of plant phenotype-genotype data and its publication in accordance with the FAIR principles. In this workshop, we will be presenting the outcomes of this work from the ELIXIR plant sciences community, featuring a keynote from one of its key members, Dr. Anne-Françoise Adam-Blondon (ELIXIR-France), a detailed tutorial about the design and usage of the MIAPPE (Minimum Information About Plant Phenotyping Experiments), a hands-on data annotation and publication session, and a demonstration of ELIXIR’s Plant Data Search service. 2019-11-12 14:00:00 UTC 2019-11-12 19:00:00 UTC ITQB Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal Instituto de Tecnologia Química e Biológica António Xavier Oeiras Lisbon Portugal 2775-412 Oeiras ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de LisboaBiodata.pt - Elixir's portuguese node of the european projec [] Life Science ResearchersBiologists, Genomicists, Computer Scientistsplant researchers workshops_and_courses [] Plant PhenotypingGenotypingdata managementbioinformatics
  • Practical Statistics for the Life Sciences

    20 - 24 January 2020

    Oeiras, Portugal

    Elixir node event
    Practical Statistics for the Life Sciences https://tess.elixir-europe.org/events/practical-statistics-for-the-life-sciences This intermediate level course is one of our Foundations courses. It covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. The course positions applied statistics, starting from important aspects of experimental design and data exploration. We then move into statistical modeling and data analysis. We will focus on the link between linear regression and analysis of variance. Together, these methods contribute to the study of General Linear Models. The course also introduces the basics of non-parametric testing, and addresses categorical data analysis and logistic regression. The concepts and methods are exclusively introduced via case-studies in the life sciences. For every study we elaborate on a concrete research question and then provide a study design, which is followed by data exploration. Next, we will focus on how to model the data and elaborate on the link between model parameters and the subject matter research question. 2020-01-20 09:30:00 UTC 2020-01-24 18:00:00 UTC The Gulbenkian Training Programme in Bioinformatics, Biodata.pt - Elixir's portuguese node of the european project 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 Ciência bicourses@igc.gulbenkian.pt [] Life Science Researchers 20 workshops_and_courses registration_of_interest Statistics

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