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  • Final OpenRiskNet Workshop

    23 - 24 October 2019

    Amsterdam, Netherlands

    Final OpenRiskNet Workshop https://tess.elixir-europe.org/events/final-openrisknet-workshop The workshop is addressing all OpenRiskNet stakeholders (scientific, industrial and regulatory communities) that are invited to participate in this interactive event. This will ensure that all relevant and target groups that need to be aware of the project achievements have access to this information and are enabled to give feedback, and also be trained on the provided solutions. 2019-10-23 09:00:00 UTC 2019-10-24 17:00:00 UTC OpenRiskNet O|2 Human Life Sciences building, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands, Amsterdam, Netherlands O|2 Human Life Sciences building, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands Amsterdam Netherlands 1081 Vrije Universiteit Amsterdam [] [] workshops_and_courses [] e-infrastructuresrisk assessment
  • Data Carpentry Workshop 2020

    23 October 2019

    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: 28/01/2019 - 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 2019-10-23 09:00:00 UTC 2019-10-23 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • Machine Learning in R

    6 - 7 November 2019

    Heidelberg, Germany

    Machine Learning in R https://tess.elixir-europe.org/events/machine-learning-in-r Date Nov 6 - Nov 7 2019 Location EMBL Heidelberg Tutors and helpers - Dr. Malvika Sharan - Prof Bernd Bischl - Martin Binder - Giuseppe Casalicchio Affiliation: Ludwig-Maximilians-University Munich Course Information This two-day course, on the implementation of Machine Learning in R, using mlr package will be delivered as practical sessions on programming and data analysis. The main goal of mlr is to provide a unified interface for machine learning tasks as classification, regression, cluster analysis and survival analysis in R. Sessions will be driven by many practical exercises and case studies. Before this workshop, participants are expected to review the official material introducing the principle of Machine Learning (see the prerequisite). Course Content This 2-day course will cover hands-on sessions using `mlr` and other relevant packages. Daily schedule - 09:30-12:30 3h morning, 90 min Theory + 90 min Practical - 12:30-13:30 1h Lunchbreak - 13:30-16:30 3h afternoon, 90 min Theory + 90 min Practical - 16:30-17:00 Time for general questions Day 1 Introduction to the concepts and Practical with mlr - Performance Evaluation and Resampling (Metrics, CV, ROC) - Introduction to Boosting Day 2 Introduction to the concepts and Practical with mlr - Tuning and Nested Cross-Validation - Regularization and Feature Selection Prerequisite The course is aimed at advanced R programmers, preferably with some knowledge of statistics and data modeling (See prerequisite materials from Day-1, 2, & 4). In this course, our learners will learn more about machine learning and its application and implementation through the hands-on sessions and use cases. Optional: Discussion-Based Session On The Principle of Machine Learning Anna Kreshuk (EMBL Group Leader) will lead a one-day discussion-based session on 14 October 2019 to address your questions on the prerequisite materials on the principle of Machine Learning. This will also allow you to connect with other participants of this workshop informally, and discuss the materials in smaller groups. Please register for this workshop separately: https://bio-it.embl.de/events/machine-learning-discussion-workshop-2019/. Registration Please register on this page: https://bio-it.embl.de/events/machine-learning-in-r-2019/ Please note that the maximum capacity of this course is 40 participants and registration is required to secure a place. If you have any questions, please contact Malvika Sharan. In your registration, please mention your EMBL group name, or institute's name (e.g. DKFZ, Uni-HD) if you are registering as an external participant. Costs 60,00 EUR Keywords: Machine Learning, R 2019-11-06 09:00:00 UTC 2019-11-07 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • Nanopore day, Heidelberg

    7 November 2019

    Heidelberg, Germany

    Elixir node event
    Nanopore day, Heidelberg https://tess.elixir-europe.org/events/nanopore-day-heidelberg Hear about the latest tech updates for Oxford Nanopore as well as hearing from local users about their latest work using nanopore technology. There is no delegate fee for this event. Your place at this event will be confirmed via email from events@nanoporetech.com. Completion of this form does not constitute confirmation. Spaces are limited and will be allocated on a first-come, first-served basis. 2019-11-07 09:00:00 UTC 2019-11-07 17:00:00 UTC Oxford Nanopore Technology EMBL Heidelberg, 1, Meyerhofstraße, Heidelberg, Germany EMBL Heidelberg, 1, Meyerhofstraße Heidelberg Karlsruhe Germany [] [] [] meetings_and_conferences first_come_first_served Long read sequencing
  • de.NBI & ELIXIR - Train the Trainer Workshop to Learn Teaching Techniques

    11 - 12 November 2019

    Heidelberg, Germany

    de.NBI & ELIXIR - Train the Trainer Workshop to Learn Teaching Techniques https://tess.elixir-europe.org/events/de-nbi-elixir-train-the-trainer-workshop-to-learn-teaching-techniques de.NBI & ELIXIR - Train the Trainer Workshop to Learn Teaching Techniques Heidelberg Educators: Malvika Sharan, Toby Hodges (HD-HuB), Elisabeth Zielonka Date: 11-11-2019 - 12-11-2019 09:30-17:00 Location: EMBL Heidelberg Room 202 Contents: The course is aimed at everyone who is interested in becoming a better teacher. The workshop is a mix of lectures and hands-on lessons where you practise giving a short lesson using approaches learned and implement some of the teaching techniques which we will discuss. This is training for teaching, not technical training; you do not need any particular technical background, and we will not be teaching that. This workshop is based on the constantly revised and updated curriculum. We will offer two parallel tracks (The Carpentries Track and ELIXIR Track), and you will be asked to choose one track that you would like to attend during this event. The Carpentries Track to become Software Carpentry, Data Carpentry and Library Carpentry instructors, run workshops and contribute to the Carpentry training materials. ELIXIR Track is a non-programming module which will prepare you to organise or teach at the bioinformatics or wet-biology workshops. The Carpentries Track This module is aimed at those who want to become Software Carpentry and Data Carpentry instructors, run workshops and contribute to the Carpentry training materials. You don't currently have to be an instructor or a teacher to attend this workshop, but you do need to be willing and committed to becoming one and to improving your teaching techniques. Software Carpentry and Data Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on two-day workshop covers the basics of educational psychology and instructional design and looks at how to use these ideas in both intensive workshops and regular classes. Please note that after this course is over, you will be asked to do three short follow-up exercises online in order to finish qualifying as an instructor: the details are available athttps://carpentries.github.io/instructor-training/checkout/. If you have any questions about the workshop, the reading material, or anything else, please get in touch. ELIXIR (non-programming) Track ELIXIR unites Europe’s leading life science organisations in managing and safeguarding the increasing volume of data being generated by publicly funded research. It coordinates, integrates and sustains bioinformatics resources across its member states and enables users in academia and industry to access services that are vital for their research. In this module the trainer will deliver the ELIXIR curriculum aimed at the instructors interested in teaching workshops on the topics related to bioinformatics or wet-biology. 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: When possible, participants should bring a laptop that can be connected to the Internet to follow teaching materials and developing a shared note. A device for recording audio and video (mobile phones and laptops are OK) will also be useful as throughout the two days, we are going to record one another teaching in pairs or threes. It does not have to be high-quality, but it should be good enough that you can understand what someone is saying. All participants are required to abide by The Carpentries' Code of Conduct. Keywords: Train the Trainer, 2019-11-11 09:00:00 UTC 2019-11-12 17:00:00 UTC de.NBI / ELIXIR Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • Assembly of long-read sequencing (2 days)

    12 - 13 November 2019

    Brisbane, Australia

    Assembly of long-read sequencing (2 days) https://tess.elixir-europe.org/events/assembly-of-long-read-sequencing-2-days-a1383ac8-7ceb-429e-9360-61be939cbcdb 2019-11-12 09:00:00 UTC 2019-11-13 17:00:00 UTC QFAB Brisbane, Australia Brisbane Australia Bioinformatics [] [] [] [] [] bioinformatics RNA-SeqGalaxy
  • Introduction to RNA-seq analysis in R

    13 - 14 November 2019

    Sheffield, United Kingdom

    Introduction to RNA-seq analysis in R https://tess.elixir-europe.org/events/introduction-to-rna-seq-analysis-in-r-c391c2df-0a11-417b-8bad-2d8951fe2a30 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.. 2019-11-13 09:30:00 UTC 2019-11-14 17:00:00 UTC Pam Liversidge Building, Design Studio 1, D06, Sheffield, United Kingdom Pam Liversidge Building, Design Studio 1, D06 Sheffield United Kingdom S1 3JD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • CABANA Workshop: Analysis of Crop Genomics Data

    2 - 6 December 2019

    Bogota, Colombia

    Elixir node event
    CABANA Workshop: Analysis of Crop Genomics Data https://tess.elixir-europe.org/events/cabana-workshop-analysis-of-crop-genomics-data This course will introduce crop biologists to methods and approaches for analysing crop genomics data. 2019-12-02 08:30:00 UTC 2019-12-06 12:45:00 UTC Universidad de los Andes - UniAndes, Bogota, Colombia Universidad de los Andes - UniAndes Bogota Colombia 111711 [] Marco Cristancho [] [] [] [] HDRUK
  • RNA-Seq using R (2 days - Knowledge of R required)

    3 - 4 December 2019

    Brisbane, Australia

    RNA-Seq using R (2 days - Knowledge of R required) https://tess.elixir-europe.org/events/analysis-of-ngs-data-workshops-advanced-393853d7-8b13-4f51-b774-afb159f5d818 2019-12-03 09:00:00 UTC 2019-12-04 17:00:00 UTC QFAB Translational Research Institute, 37, Kent Street, Brisbane, Australia Translational Research Institute, 37, Kent Street Brisbane Brisbane City Australia Bioinformatics [] [] [] [] [] bioinformaticsGalaxy RNA-Seq
  • RNA-seq Analysis for Beginners

    9 December 2019

    Sheffield, United Kingdom

    RNA-seq Analysis for Beginners https://tess.elixir-europe.org/events/rna-seq-analysis-for-beginners-710ef2db-c711-4b12-9216-5226cb8b6dc7 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. 2019-12-09 09:30:00 UTC 2019-12-09 17:00:00 UTC Pam Liversidge Building, Design Studio 1, D06, Sheffield, United Kingdom Pam Liversidge Building, Design Studio 1, D06 Sheffield United Kingdom S1 3JD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • 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 [] []
  • 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 [] []
  • 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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