Dear All Check out our new bioinformatics courses happening this autumn. We've just advertised another 'Introduction to RNA-seq data analysis' workshop which will be running again this November in the Chancellors Building, Little France (BioQuarter). There are also some last minute spaces available on this weeks Metagenomics and Metabarcoding course, but you'll have to be quick! ........ Metagenomics and Metabarcoding - 28-30 August 2019<https://genomics.ed.ac.uk/services/metagenomics-metabarcoding> *Last Minute Sign-ups Welcome* <https://genomics.ed.ac.uk/services/introduction-python-biologists-0> This course focuses on the computational methods used to analyse the wealth of data produced by shotgun metagenomics and metabarcoding (Amplicon targeted metagenomics) studies. This course will provide you insights in to DNA metabarcoding analyses, from preprocessing and quality control of the raw data to the construction of OTU/ASV tables, taxon assignment, diversity analysis and differential abundance analysis using QIIME2. Further, you will also learn about methods to generate the reference-based profile to generate microbial community features like taxonomic abundances or functional profile and how to identify the ones characterizing differences between two biological conditions. You will then be introduced to methods used for assembly from metagenomics samples. Attendees will use tools to assemble metagenome assembled genomes (MAGs) from short read and long read data. We will discuss the different approaches and tools available for these assemblies and the benefits and limitations of each options. Tutors: Urmi Trivedi, Bioinformatician, Edinburgh Genomics; Amanda Warr, Research Geneticist, Roslin Institute; Rob Stewart, Bioinformatician, Roslin Institute; Albert Phillimore, Institute of Evolutionary Biology, University of Edinburgh (guest lecturer); Nathan Medd, Training and Outreach Manager, Edinburgh Genomics (demonstrator) Registration fee: £500 (including lunches and refreshments) Where: Peter Wilson Building, The Kings Buildings, Edinburgh Register here<https://www.surveymonkey.co.uk/r/8MKKK96> Network Analysis of High Dimensional Biological Data - 6th September 2019 <https://genomics.ed.ac.uk/services/network-analysis-high-dimensional-biological-data-15th-july-2019> *Following the Edinburgh Genome Science Conference (http://genomescience.co.uk/)* <https://genomics.ed.ac.uk/services/introduction-python-biologists-0><https://genomics.ed.ac.uk/services/introduction-python-biologists-0> This one day practical course is designed to introduce participants to the joys of networks, focusing on their application to biological research and in particular, their use in the analysis of complex data. The course will start by introducing the principles of networks and their use as a generic medium to understand the relationships between entities. It will then introduce participants to a new analysis platform, Graphia, going through the basics of its functionality for network visualisation and navigation, and demonstrating the tool‘s use in the exploration of large networks of protein interaction data and phylogenetic trees. Tutor: Prof Tom Freeman, Roslin Institute & Kajeka Registration fee: £45 (including lunch and refreshments) Where: James Clerk Maxwell Building, The Kings Buildings, Edinburgh. Register here<https://www.surveymonkey.co.uk/r/H7PNDYF> Bioinformatics for Genomics - 9-13 September 2019 <https://genomics.ed.ac.uk/services/bioinformatics-genomics> <https://genomics.ed.ac.uk/services/introduction-python-biologists-0><https://genomics.ed.ac.uk/services/introduction-python-biologists-0> This is a week-long workshop that combines our popular ‘Linux for Genomics’, ‘R for Genomics’, and ‘Introduction to RNA-seq Data Analysis’, taught by Edinburgh Genomics’ Bioinformaticians. By the end of the five days, you will be: comfortable on the Linux command line; able to view, filter and manipulate large text files; able to write pipelines to perform certain bioinformatics tasks; familiar with and able to use the basics of R; confident using several data QC and processing tools; able to generate gene counts and differential expression statistics; and prepared to put it all together with visualization, interpretation, and gene set analysis. Tutors: Urmi Trivedi, Bioinformatician, Edinburgh Genomics; Frances Turner, Bioinformatician, Edinburgh Genomics; Tim Booth, Analyst - Developer, Edinburgh Genomics; Nathan Medd, Training and Outreach Manager, Edinburgh Genomics Registration fee: £750 (including lunches and refreshments) Where: Peter Wilson Building, The Kings Buildings, Edinburgh. Register here<https://www.surveymonkey.co.uk/r/8P6NW8H> <http://genomics.ed.ac.uk/services/bioinformatics-workflows-snakemake> Bioinformatics Workflows with Snakemake - 30 September - 01 October 2019 *NEW*<http://genomics.ed.ac.uk/services/bioinformatics-workflows-snakemake> Are you running data analysis workflows? Want to step up to the next level of organisation and efficiency? Save yourself time, increase replicability, and master your analysis with Snakemake. The Snakemake workflow system provides effective solutions to organise your tasks, document and share your methods, make effective use of compute resources, and handle unexpected errors in processing. Edinburgh Genomics are offering a two-day course that will have you confident in using Snakemake to tackle complex workflow problems and in your day-to-day research. Tutors: Tim Booth, Analyst - Developer, Edinburgh Genomics; Hywel Dunn-Davis, Analyst - Developer, Edinburgh Genomics Registration fee: £400 (including lunches and refreshments) Where: Ashworth Building, The Kings Buildings, Edinburgh. Register here <https://www.surveymonkey.co.uk/r/X8GFP99> Bioinformatics for Genomics - 28 October - 01 November 2019 <https://genomics.ed.ac.uk/services/bioinformatics-genomics-0> <https://genomics.ed.ac.uk/services/bioinformatics-genomics-0> *Little France Campus* <https://genomics.ed.ac.uk/services/introduction-python-biologists-0><https://genomics.ed.ac.uk/services/introduction-python-biologists-0> This is a week-long workshop that combines our popular ‘Linux for Genomics’, ‘R for Genomics’, and ‘Introduction to RNA-seq Data Analysis’, taught by Edinburgh Genomics’ Bioinformaticians. By the end of the five days, you will be: comfortable on the Linux command line; able to view, filter and manipulate large text files; able to write pipelines to perform certain bioinformatics tasks; familiar with and able to use the basics of R; confident using several data QC and processing tools; able to generate gene counts and differential expression statistics; and prepared to put it all together with visualization, interpretation, and gene set analysis. Tutors: Urmi Trivedi, Bioinformatician, Edinburgh Genomics; Frances Turner, Bioinformatician, Edinburgh Genomics; Tim Booth, Analyst - Developer, Edinburgh Genomics; Nathan Medd, Training and Outreach Manager, Edinburgh Genomics Registration fee: £750 (including lunches and refreshments) Where: Chancellors Building, The little France (BioQuarter) Campus, Edinburgh. Register here<https://www.surveymonkey.co.uk/r/PRXMJL2> <http://genomics.ed.ac.uk/services/bioinformatics-workflows-snakemake> Introduction to Linux and Workflows for Biologists, 04 - 08 November 2019 <https://genomics.ed.ac.uk/services/introduction-linux-and-workflows-biologists> This week-long course will introduce the Linux command line environment from scratch and teach students how to make the most of its tools to achieve a high level of productivity when working with biological data. Tutor: Martin Jones (Founder of Python for Biologists) Registration fee: £550 (includes coffee/tea, but no lunch) Where: Ashworth Building, Kings Buildings, University of Edinburgh, Edinburgh, EH9 3FL Register here <https://www.surveymonkey.co.uk/r/VZQY9HZ> Introduction to R for Genomics, 14 - 15 November 2019 <https://genomics.ed.ac.uk/services/r-genomics> The aim of this course is to introduce participants to the statistical computing language 'R' using examples and skills relevant to genomic data science. This two day workshop is taught by experienced Edinburgh Genomics’ bioinformaticians and trainers. By the end of the workshop, you will be comfortable with the basics of the R and R studio environments, learning about the rules of the language and how R works with different data types. We then move on to using functions, including those specific to genomic science. We look at how to handle various genomic data files and where to find relevant tools via online resources. Finally we use mock RNA-seq data to learn how to visualize your data to generate publication ready plots using the package ggplot2. Tutors: Nathan Medd, Training and Outreach Manager, Edinburgh Genomics; Hywel Dunn-Davis, Analyst - Developer, Edinburgh Genomics Registration fee: £400 (includes coffee/tea, but no lunch) Where: Microlabs, The Chancellors Buildings, Little France Campus (BioQuarter), Edinburgh. Register here <https://www.surveymonkey.co.uk/r/83FGGXV> Introduction to RNA-seq Data Analysis 18-20 November 2019 <https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis> *NEW THREE-DAY FORMAT*<https://genomics.ed.ac.uk/services/introduction-rna-seq-data-analysis> <https://genomics.ed.ac.uk/services/introduction-python-biologists-0> RNA sequencing (RNA-seq) is the method of choice for transcriptome profiling. Nevertheless, it is a non-trivial task to transform the vast amount of data obtained with high-throughput sequencers into useful information. Thus, RNA-seq data analysis is still a major bottleneck for most researchers in this field. The ability of correctly interpreting RNA-seq results, as well as knowledge on the intrinsic properties of these data, are essential to avoid incorrect experimental designs and the application of inappropriate analysis methodologies. The aim of this workshop is to familiarise researchers with RNA-seq data and to initiate them in the analysis by providing lectures and practicals on analysis methodologies. In the practicals Illumina-generated sequencing data and various widely used software programs will be used. Tutors: Urmi Trivedi, Bioinformatician, Edinburgh Genomics; Frances Turner, Bioinformatician, Edinburgh Genomics; Nathan Medd, Training and Outreach Manager, Edinburgh Genomics (demonstrator) Registration fee: £500 (including lunches and refreshments) Register here<https://www.surveymonkey.co.uk/r/9PGK7KX> For more courses coming soon please check out our training web-page: https://genomics.ed.ac.uk/services/training Can't see the course you need to progress your skills? Tell us what your training needs are by completing this short survey<https://www.surveymonkey.co.uk/r/7M6QB2D>. Kind Regards Nathan Medd Training and Outreach Manager - Edinburgh Genomics -- ======================================================== Edinburgh Genomics' Privacy Notice can be viewed at: http://genomics.ed.ac.uk/about-us/privacy-notice This email and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. 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