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  • Essential Data Analysis Skills for Researchers

    20 - 21 January 2020

    Sheffield, United Kingdom

    Essential Data Analysis Skills for Researchers https://tess.elixir-europe.org/events/essential-data-analysis-skills-for-researchers This workshop is designed to teach basic concepts, skills and tools for working more effectively with data, using a combination of tools with a main focus in R. The workshop is aimed at researchers in the life sciences at all career stages and is designed for learners with little to no prior knowledge of programming, shell scripting, or command line tools 2020-01-20 09:30:00 UTC 2020-01-21 17:00:00 UTC Bartolome House, Seminar Room EG03, Sheffield, United Kingdom Bartolome House, Seminar Room EG03 Sheffield United Kingdom S3 7ND [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Software Carpentry

    21 - 22 January 2020

    Norwich, United Kingdom

    Software Carpentry https://tess.elixir-europe.org/events/software-carpentry-e28d91b4-59e7-47d7-a7f0-54b3d09e0172 Our goal is to help scientists become more productive by teaching them basic computing skills like program design, version control, testing and task automation. In this two-day bootcamp, short tutorials will alternate with hands-on practical exercises. Participants will be encouraged both to help one another, and to apply what they have learned to their own research problems during and between sessions. 2020-01-21 09:00:00 UTC 2020-01-22 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ Earlham Institute training@earlham.ac.uk [] PhD studentspost-docspostgrad workshops_and_courses first_come_first_served SoftwareCarpentrypythonUnix Shell
  • Data Carpentry Workshop 2020

    29 - 31 January 2020

    Heidelberg, Germany

    Data Carpentry Workshop 2020 https://tess.elixir-europe.org/events/educators-toby-hodges-florian-huber-thea-van-rossum-georg-zeller-hd-hub-fotis-e-psomopoulos-date-28-01-2019-30-01-2019-location-atc-computer-training-lab-contents-the-missing-step-between-data-collection-and-research-progress-is-a-lack-of-training-for-researchers-in-crucial-skills-for-effectively-managing-and-analysing-large-amounts-of-data-this-hands-on-workshop-teaches-researchers-the-fundamental-data-skills-they-need-to-conduct-their-work-and-provides-high-quality-domain-specific-training-covering-the-full-lifecycle-of-data-driven-research-the-domain-specific-approach-allows-participants-to-tailor-the-data-content-and-tools-to-reflect-the-specific-data-and-analysis-needs-of-different-areas-data-organisation-and-cleaning-introduction-to-r-data-analysis-and-visualisation-in-r-interacting-with-databases-from-r-data-analysis-with-applications-to-genomics-learning-goals-you-will-learn-how-to-organise-data-and-some-practices-for-more-effective-data-handling-to-effectively-clean-and-format-data-and-automatically-track-any-changes-to-use-r-to-handle-filter-and-summarise-tabular-data-to-use-the-split-apply-combine-concept-for-data-analysis-to-visualise-the-results-of-these-analyses-in-r-using-the-ggplot2-library-to-apply-all-of-the-concepts-in-an-exploratory-analysis-of-a-typical-biological-dataset-prerequisities-the-course-is-aimed-at-graduate-students-and-other-researchers-in-the-life-sciences-who-would-like-to-learn-good-practices-in-data-management-and-analysis-the-course-is-ideally-suited-to-students-without-prior-experience-in-computational-research-but-some-familiarity-with-working-with-tabular-data-on-a-computer-is-welcome-keywords-data-carpentry-r-tools-r Educators: Toby Hodges, Florian Huber, Thea Van Rossum, Georg Zeller, (HD-HuB) Fotis E. Psomopoulos Date: 28/01/2020 - 30/01/2020 Location: ATC Computer Training Lab Contents: The missing step between data collection and research progress is a lack of training for researchers in crucial skills for effectively managing and analysing large amounts of data. This hands on workshop teaches researchers the fundamental data skills they need to conduct their work, and provides high-quality, domain-specific training covering the full lifecycle of data-driven research. The domain-specific approach allows participants to tailor the data, content, and tools to reflect the specific data and analysis needs of different areas: - Data organisation and cleaning - Introduction to R - Data analysis and visualisation in R - Interacting with databases from R - Data analysis with applications to genomics Learning goals: You will learn... - how to organise data and some practices for more effective data handling - to effectively clean and format data and automatically track any changes - to use R to handle, filter, and summarise tabular data - to use the split-apply-combine concept for data analysis - to visualise the results of these analyses in R using the ggplot2 library - to apply all of the concepts in an exploratory analysis of a typical biological dataset Prerequisities: The course is aimed at graduate students and other researchers in the life sciences who would like to learn good practices in data management and analysis. The course is ideally suited to students without prior experience in computational research, but some familiarity with working with tabular data on a computer is welcome. Keywords: Data Carpentry, R Tools: R 2020-01-29 09:00:00 UTC 2020-01-31 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • Introduction to the command line for Bioinformatics

    12 February 2020

    Sheffield, United Kingdom

    Introduction to the command line for Bioinformatics https://tess.elixir-europe.org/events/introduction-to-the-command-line-for-bioinformatics This course offers an introduction to working with Linux. We will describe the Linux environment so that participants can start to utilize command-line tools and feel comfortable using a text-based way of interacting with a computer. We will use a case study of dealing with next-generation sequencing data 2020-02-12 09:30:00 UTC 2020-02-12 17:00:00 UTC Bartolome House, Seminar Room EG03, Sheffield, United Kingdom Bartolome House, Seminar Room EG03 Sheffield United Kingdom S3 7ND [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Introduction to RNA-seq analysis in R

    13 February 2020

    Sheffield, United Kingdom

    Introduction to RNA-seq analysis in R https://tess.elixir-europe.org/events/introduction-to-rna-seq-analysis-in-r-1fad26a6-c2d7-463b-b1fb-ca50cdb508d9 In this workshop, you will be learning how to analyse RNA-seq count data, using R. This will include reading the data into R, quality control and performing differential expression analysis and gene set testing, with a focus on the edgeR analysis workflow. You will learn how to generate common plots for analysis and visualisation of gene expression data, such as boxplots and heatmaps. You will also be learning how alignment and counting of raw RNA-seq data can be performed in R. This workshop is aimed at biologists interested in learning how to perform differential expression analysis of RNA-seq data when reference genomes are available.. 2020-02-13 09:30:00 UTC 2020-02-13 17:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7ND [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Data Carpentry

    3 - 4 March 2020

    Norwich, United Kingdom

    Data Carpentry https://tess.elixir-europe.org/events/data-carpentry-6bde217e-337f-4bea-96f7-e419c62f5fe9 Data Carpentry workshops are for any researcher who has data they want to analyse, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. 2020-03-03 09:00:00 UTC 2020-03-04 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ Earlham Institute training@earlham.ac.uk [] post-docsPhD studentspostgrad workshops_and_courses first_come_first_served Data carpentryCommand lineData analysis
  • De Novo Assembly 2020

    12 March 2020

    Norwich, United Kingdom

    De Novo Assembly 2020 https://tess.elixir-europe.org/events/de-novo-assembly-2020 The course will provide an introduction to de novo assembly, with a hands on introduction followed by in-depth analysis of the key steps in the process. It covers several aspects such as the initial setup of a de novo genome sequencing project, quality control and preprocessing of datasets, generation and evaluation of first pass assemblies and assembly improvement. 2020-03-12 09:00:00 UTC 2020-03-12 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ Earlham Institute training@earlham.ac.uk [] PhD studentspost-docs workshops_and_courses [] De Novode-novo genome assembly
  • Training on the data integration platforms tranSMART & cBioPortal

    26 - 27 March 2020

    Amsterdam, Netherlands

    Elixir node event
    Training on the data integration platforms tranSMART & cBioPortal https://tess.elixir-europe.org/events/training-on-the-data-integration-platforms-transmart-cbioportal The data integration platforms tranSMART and cBioPortal are widely used by researchers and clinicians to integrate, analyse and visualise large amounts of data. In this CORBEL course, data stewards/data managers are offered the opportunity to learn how to upload data to these platforms and how to use the different user interfaces. They will gain insight into these platforms and the possibilities that they offer. 2020-03-26 08:30:00 UTC 2020-03-27 17:00:00 UTC Aristo Amsterdam, Amsterdam, Netherlands Aristo Amsterdam Amsterdam Netherlands 1043 EJ [] Michelle Mendonca [] [] [] [] HDRUK
  • CORBEL workshop: Training on the data integration platforms tranSMART & cBioPortal

    26 - 27 March 2020

    Amsterdam, Netherlands

    Elixir node event
    CORBEL workshop: Training on the data integration platforms tranSMART & cBioPortal https://tess.elixir-europe.org/events/corbel-workshop-training-on-the-data-integration-platforms-transmart-cbioportal The data integration platforms tranSMART and cBioPortal are widely used by researchers and clinicians to integrate, analyse and visualise large amounts of data. In this CORBEL course, data stewards/data managers are offered the opportunity to learn how to upload data to these platforms and how to use the different user interfaces. They will gain insight into these platforms and the possibilities that they offer. 2020-03-26 08:30:00 UTC 2020-03-27 17:00:00 UTC Aristo Amsterdam, Amsterdam, Netherlands Aristo Amsterdam Amsterdam Netherlands 1043 EJ [] Michelle Mendonca [] [] [] [] HDRUK
  • Introduction to Genomic Variant Interpretation

    6 - 7 April 2020

    Sheffield, United Kingdom

    Introduction to Genomic Variant Interpretation https://tess.elixir-europe.org/events/introduction-to-genomic-variant-interpretation This course covers state-of-the-art and best-practice tools for the analysis of genomes. We describe, and give hands-on experience of, the entire analysis workflow from raw data generated by a sequencing machine to deriving variant calls (e.g. Single Nucleotide Variants) that are ready for downstream analysis, interpretation and prioritisation. We will describe the steps involved to go from sequencing library to a prioritised, clinically-relevant list of DNA variants. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control, variant-calling and annotation. 2020-04-06 08:30:00 UTC 2020-04-07 16:00:00 UTC Bartolome House, Seminar Room EG03, Sheffield, United Kingdom Bartolome House, Seminar Room EG03 Sheffield United Kingdom S3 7ND [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Single-Cell RNAseq Training Course 2020

    20 - 25 April 2020

    Norwich, United Kingdom

    Single-Cell RNAseq Training Course 2020 https://tess.elixir-europe.org/events/single-cell-rnaseq-training-course-2020-1444ff72-59f8-4c26-bc86-813bc4ee8efd The course will provide an introduction to Single-Cell Genomics for bench-based researchers with no required prior experience of computational data analysis. It covers several aspects such as the experimental design, cell sorting and processing for production of high-quality samples for sequencing, generation of sequencing data, assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variations at the single-cell level. Options when applying are: Single-Cell RNAseq Course (Mon-Fri: lab and bioinformatics @800) Single-Cell RNAseq Bioinformatics only (Weds-Fri @£300) 2020-04-20 09:00:00 UTC 2020-04-25 00:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ [] training @ earlham . ac . uk [] PhD studentspost-docsBench biologists workshops_and_courses registration_of_interest []
  • Introduction to identifying and characterising somatic variants

    21 April - 21 May 2020

    Sheffield, United Kingdom

    Introduction to identifying and characterising somatic variants https://tess.elixir-europe.org/events/introduction-to-identifying-and-characterising-somatic-variants-907ec326-e958-4c2e-a935-4780254ae845 This course covers state-of-the-art and best-practice tools for the analysis of genomes. We describe, and give hands-on experience of, the entire analysis workflow from raw data generated by a sequencing machine to deriving variant calls (e.g. Single Nucleotide Variants) that are ready for downstream analysis, interpretation and prioritisation. We will describe the steps involved to go from sequencing library to a prioritised, clinically-relevant list of DNA variants. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control, variant-calling and annotation. 2020-04-21 08:30:00 UTC 2020-05-21 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S1 3JD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • ELIXIR Bioinformatics Industry Forum

    28 April 2020

    London, United Kingdom

    ELIXIR Bioinformatics Industry Forum https://tess.elixir-europe.org/events/elixir-bioinformatics-industry-forum 2020-04-28 10:00:00 UTC 2020-04-28 10:00:00 UTC Wellcome Collection, London, United Kingdom Wellcome Collection London United Kingdom NW1 2BE [] [] [] [] [] []
  • Genome Annotation Workshop 2020

    13 May 2020

    Norwich, United Kingdom

    Genome Annotation Workshop 2020 https://tess.elixir-europe.org/events/genome-annotation-workshop-2020 With the fast-moving pace of sequencing technology and the plethora of options available to you, it can be difficult to know which is the optimal platform for your biological question and therefore how to design your experiment for maximum return from your samples. Once you’ve got the data, how do you know if what you’ve got is good enough quality? We’ll take you through the latest developments in sequencing technology, identify common challenges in producing good RNA for sequencing, help you to understand what you can expect from your data and what you can do with it. 2020-05-13 09:00:00 UTC 2020-05-13 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ Earlham Institute training@earlham.ac.uk [] Advanced PhD studentspost-docs [] first_come_first_served genome annotationNext Generation Sequencing technologies
  • RNA-seq Analysis for Beginners

    3 July 2020

    Sheffield, United Kingdom

    RNA-seq Analysis for Beginners https://tess.elixir-europe.org/events/rna-seq-analysis-for-beginners-13c9f173-2fdd-4ea6-9005-58aa798bf289 High-throughput RNA-sequencing is now the standard technique for quantifying transcript abundance in a biological sample of interest. In this course we will describe the processes that take place once you submit a library for RNA sequencing, and what data you should expect to receive from the Bioinformatics Core. We will describe the steps involved to go from sequencing library to a list of genes that show statistically significant differences between your biological conditions of interest. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control and assessing differential expression. We will also showcase some web sites you can use for enrichment and pathways analysis. 2020-07-03 08:30:00 UTC 2020-07-03 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Introduction to RNA-seq analysis in R

    13 - 14 July 2020

    Sheffield, United Kingdom

    Introduction to RNA-seq analysis in R https://tess.elixir-europe.org/events/introduction-to-rna-seq-analysis-in-r-34ffdcbc-a5b7-49ac-afb9-7d338a38ea26 In this workshop, you will be learning how to analyse RNA-seq count data, using R. This will include reading the data into R, quality control and performing differential expression analysis and gene set testing, with a focus on the edgeR analysis workflow. You will learn how to generate common plots for analysis and visualisation of gene expression data, such as boxplots and heatmaps. You will also be learning how alignment and counting of raw RNA-seq data can be performed in R. This workshop is aimed at biologists interested in learning how to perform differential expression analysis of RNA-seq data when reference genomes are available.. 2020-07-13 08:30:00 UTC 2020-07-14 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
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