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  • Entry Level Bioinformatics

    30 March - 3 April 2020

    Oeiras, Portugal

    Elixir node event
    Entry Level Bioinformatics https://tess.elixir-europe.org/events/entry-level-bioinformatics This is an entry level course in three parts, aimed at those with a reasonable biological background but no significant experience with bioinformatics. The course content is designed to show how, by going through guided exercises, a researcher in the bio-medical area can access sequence data and steer his/her analysis to efficiently extract results, checking how credible they are and reason about using them confidently, in a reproducible way. This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, using open source bioinformatics tools. Thirdly, the course will cover the broad theme of analytical automation, and how it enhances the capacity of researchers by widening the scope of their experiments, comparing results in a large scale and summarising the findings in simple but very reproducible ways. 2020-03-30 09:30:00 UTC 2020-04-03 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 [] Researchers at any level, wishing to investigate how they might begin to exploit the ever expanding abundance of computing and data resources. 20 workshops_and_courses first_come_first_served introduction to bioinformaticsNGSAutomationScripting
  • 3C-based data analysis and 3D reconstruction of chromatin folding

    20 - 23 April 2020

    Oeiras, Portugal

    3C-based data analysis and 3D reconstruction of chromatin folding https://tess.elixir-europe.org/events/3c-based-data-analysis-and-3d-reconstruction-of-chromatin-folding 3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are in close spatial proximity in the cell nucleus. Overall, those interaction matrices have been used to study how the genome folds within the nucleus, which is one of the most fascinating problems in modern biology. The rigorous analysis of those paired-reads using computational tools has been essential to fully exploit the experimental technique, and to study how the genome is folded in space. Currently, there is a clear expansion on the wealth of data on genome structure with the availability of many datasets of Hi-C experiments down to 1Kb resolution (see for example: http://hic.umassmed.edu/welcome/welcome.php ; http://promoter.bx.psu.edu/hi-c/view.php or http://www.aidenlab.org/data.html). In this course, participants will learn to use **TADbit**, a software designed and developed to manage all dimensionalities of the Hi-C data: * 1D - Map paired-end sequences to generate Hi-C interaction matrices * 2D - Normalize matrices and identify constitutive domains (TADs, compartments) * 3D - Generate populations of structures which satisfy the Hi-C interaction matrices * 4D - Compare samples at different time points Participants can bring specific biological questions and/or their own 3C-based data to analyze during the course. At the end of the course, participants will be familiar with the TADbit software and will be able to fully analyze Hi-C data. Although the TADbit software is central in this course, alternative software will be discussed for each part of the analysis. 2020-04-20 09:30:00 UTC 2020-04-23 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 [] The course design is oriented towards experimental researchers and bioinformaticians at the graduate and post-graduate levels. The last edition of this course was attended by people with different backgrounds and interested in the genome organization. It is likely that the participants to this course aim at getting involved in generating Hi-C data for chromosome structure determination or that they just want to be able to correctly interpret and analyse publicly available data. 20 workshops_and_courses first_come_first_served Hi-Cdata
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