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  • DNA Methylation: Design to Discovery 2020

    18 - 19 May 2020

    Saarbrücken, Germany

    DNA Methylation: Design to Discovery 2020 https://tess.elixir-europe.org/events/dna-methylation-design-to-discovery-2020 Educators: Abdulrahman Salhab, Michael Scherer (de.NBI-Epi / HD-HuB) Date: 18 -19th May, 2020 Location: Saarbrücken Contents: This course aims to convey basic knowledge on the bioinformatic processing of DNA methylation data. Following the outline of a standard experiment we discuss qualities of various assays and when they are beneficial. In the first half there will be a slight focus on sequencing data. We will prepare raw sequence reads for alignment, methylation calls and identification of differentially methylated sites or regions. Throughout, we consider how experimental settings interact and influence the results and how quality control can be used to understand generated data and might improve on subsequent experiments. The second half will focus on how to evaluate the data and connect it to public resources to further understanding of the results. Presentations will be interleaved with practical sessions Learning goals: • Understand the bioinformatic processing of DNA methylation • Preparation and description of raw read files • Basic generation of methylation calls and differentially methylated regions • How to evaluate DNA methylation data Prerequisites: The course requires basic computer skills: • installation of programs • office package with focus on spread-sheets • Web-browsing Keywords: DNA methylation Tools: gemBS, RnBeads 2020-05-18 09:00:00 UTC 2020-05-19 17:00:00 UTC de.NBI Saarbrücken, Saarbrücken, Germany Saarbrücken Saarbrücken Germany [] [] [] workshops_and_courses [] []
  • Phylogenetic reconstruction course 2020

    20 May 2020

    Kiel, Germany

    Phylogenetic reconstruction course 2020 https://tess.elixir-europe.org/events/phylogenetic-reconstruction-course-2020 Educators: Tal Dagan (CAU) Date: 20.05.2019, 08:15 - 16:00 Location: Kiel Contents/Learning goals: The evolutionary history of genes or species is best studied and described by phylogenetic trees. The accumulating sequence data enable the reconstruction of phylogenetic trees for many diverse gene and species. A robust phylogeny is helpful in identifying phyletic groups as well as ancestral relations in the data and lateral gene transfer. Notwithstanding phylogenetic reconstruction is sensitive to various biases in the analysis that originate in alignment and phylogenetic reconstruction artifacts. Students in the workshop will learn to reconstruct multiple sequence alignment and phylogenetic trees of focal sequences. This includes a quantification of possible biases in the phylogenetic reconstruction and ways to counteract their influence on the results. In addition, the students will learn how to identify the root of phylogenetic trees and extract ancestral-descendent relations. The workshop is intended to address scientists from undergraduate to postdoc level and does not expect previous experience in phylogenetics. Basic knowledge on how to work with Linux will be advantageous. Prerequisites: None Keywords: Tree phylogeny, gene homology, rooting, robustness Tools: MAFFT, Guidance, PhyML, IQTree, MAD rooting, FigTree. 2020-05-20 09:00:00 UTC 2020-05-20 17:00:00 UTC de.NBI Kiel, Kiel, Germany Kiel Kiel Germany [] [] [] workshops_and_courses [] []

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