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  • Computing Skills for Reproducible Research: Software Carpentry Course 2020

    19 - 23 October 2020

    Computing Skills for Reproducible Research: Software Carpentry Course 2020 Educators: Renato Alves (HD-HuB) Date: 19-10-2020 - 23-10-2020 09:00-18:00 Location: Online Contents: Computation is an integral part of today's research as data has grown too large or too complex to be analysed by hand. An ever-growing fraction of science is performed computationally and many wet-lab biologists spend part of their time on the computer. Many scientists struggle with this aspect of research as they have not been properly trained in the necessary set of skills. The result is that too much time is spent using inefficient tools when progress could be faster. This course provides training in several key tools, with a focus on good development practices that encourage efficient and reproducible research computing. Topics covered include: Introduction to Python scripting Introduction to the Unix shell and usage of cluster resources Version control with Git and Github Analysis pipeline management Scientific Python & working with biological data Literate programming with Jupyter notebooks Learning goals: This course aims to teach software writing skills and best practices to researchers in biology who wish to analyse data, and to introduce a toolset that can help them in their work. The goal is to enable them to be more productive and to make their science better and more reproducible. Prerequisites: This is a course for researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will be familiar with some command line/programmatic computer usage, will want to become more confident using these tools efficiently and reproducibly. A target student will have written a for loop in some language before, but will not know what git is (or at least not be very comfortable using git). Keywords: Programming; Command Line; Version Control; Bioinformatics; Data Analysis; Cluster Computing Tools: Python; Bash; Unix/Linux; Git; GitHub; SnakeMake; Biopython; Pandas; Numpy; SciPy; Matplotlib 2020-10-19 09:00:00 UTC 2020-10-23 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • DNA Methylation Data Analysis Workshop

    2 - 5 November 2020

    Berlin, Germany

    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: [] BiologistsBiologists, Genomicists, Computer ScientistsMolecular BiologistsPhD studentspost-docsPathologistsbioinformaticians 25 workshops_and_courses first_come_first_served EpigeneticsDNA MethylationBisulfite-Seq

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