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  • ELIXIR Train the Trainer

    15 - 16 October 2019

    London, United Kingdom

    ELIXIR Train the Trainer https://tess.elixir-europe.org/events/elixir-train-the-trainer This 2-day workshop session will help you develop or improve your teaching skills, including designing and evaluating learning materials. Materials available at: https://github.com/TrainTheTrainer/ELIXIR-EXCELERATE-TtT 2019-10-15 09:00:00 UTC 2019-10-16 17:00:00 UTC University of Cambridge / Alan Turing Institute The Alan Turing Institute, 96, Euston Road, London, United Kingdom The Alan Turing Institute, 96, Euston Road London Greater London United Kingdom NW1 2DB Alan Turing Institute gr231@cam.ac.uk [] PhD students workshops_and_courses [] []
  • Software Carpentry Workshop

    16 - 18 October 2019

    Heidelberg, Germany

    Software Carpentry Workshop https://tess.elixir-europe.org/events/software-carpentry-workshop-ab3af408-aa91-49ed-bab2-5db1f2e6d15d Educators: Malvika Sharan, Georg Zeller, Mike Smith, Thomas Schwarzl, Frank Thommen (HD-HuB), Holger Dinkel Date: 16-10-2019 - 18-10-2019 09:00-18:00 Location: ATC Computer Training Lab, EMBL Heidelberg 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 2019-10-16 09:00:00 UTC 2019-10-18 17:00:00 UTC de.NBI / ELIXIR Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • SPHN Data Privacy and IT Security Training

    25 October 2019

    Lausanne, Switzerland

    Elixir node event
    SPHN Data Privacy and IT Security Training https://tess.elixir-europe.org/events/sphn-data-privacy-and-it-security-training-45f9b664-6a6d-4fd1-bcad-c2201297c947 Overview Within the Swiss Personalized Health Network (SPHN) and related national initiatives researchers use patient data (i.e., confidential human data) in their research projects. 2019-10-25 09:00:00 UTC 2019-10-25 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Python data analyses met behulp van Pandas

    1 November 2019

    Leiden, Netherlands

    Elixir node event
    Python data analyses met behulp van Pandas https://tess.elixir-europe.org/events/python-data-analyses-met-behulp-van-pandas Til je data-analyse met Python naar het volgende niveau met de Pandas Library. Analyse met vectoren en matrices via de NumPy library kan bij bepaalde analyses al sneller verlopen dan als je python ‘kaal’ gebruikt. Maar datatypes mixen of kolommen… The post Python data analyses met behulp van Pandas appeared first on Dutch Techcentre for Life Sciences. 2019-11-01 09:00:00 UTC 2019-11-01 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] [] workshops_and_courses [] []
  • Schilderen met data in Python: Bokeh voor bioinformatici

    5 November 2019

    Leiden, Netherlands

    Elixir node event
    Schilderen met data in Python: Bokeh voor bioinformatici https://tess.elixir-europe.org/events/schilderen-met-data-in-python-bokeh-voor-bioinformatici Ontsnap aan de standaardgrafieken van Matplotlib! Leer je data live weer te geven met dynamische, interactieve figuren gemaakt met de Python Bokeh Library. Bokeh geeft je de volledige vrijheid in hoe jouw visualisatie eruit moet komen te zien. Je begint… The post Schilderen met data in Python: Bokeh voor bioinformatici appeared first on Dutch Techcentre for Life Sciences. 2019-11-05 09:00:00 UTC 2019-11-05 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] [] 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
  • 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 [] []
  • Linux voor analisten (basis)

    15 November 2019

    Leiden, Netherlands

    Elixir node event
    Linux voor analisten (basis) https://tess.elixir-europe.org/events/linux-voor-analisten-basis Struikelt Excel regelmatig over de data die jij wilt analyseren? Ben je veel tijd kwijt aan het kopiëren, plakken en bewerken van je data? In welk bestand stond ook weer die ene meting waar je leidinggevende naar vraagt? Als analist… The post Linux voor analisten (basis) appeared first on Dutch Techcentre for Life Sciences. 2019-11-15 09:00:00 UTC 2019-11-15 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] [] workshops_and_courses [] []
  • Data Management Plan

    28 - 29 November 2019

    Lausanne, Switzerland

    Elixir node event
    Data Management Plan https://tess.elixir-europe.org/events/data-management-plan-812edd6d-94f8-445e-9830-257ec0790d90 NEW course date: 28-29 November 2019 Overview Recent studies have shown that worldwide, between 51% and 89% of published life sciences research is not reproducible, with consequent losses estimated at around $100 billions/year in biomedical research 2019-11-28 09:00:00 UTC 2019-11-29 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students 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
  • Advanced R Shiny

    3 December 2019

    Lausanne, Switzerland

    Elixir node event
    Advanced R Shiny https://tess.elixir-europe.org/events/advanced-r-shiny-a89ad51d-0f85-4fbb-9dc3-fc055b677e84 Overview Shiny is the leading R package for developing interactive web apps. These give your clients, users, or students the power and sophistication of R with a friendly, no-code interface custom designed to your purpose. 2019-12-03 09:00:00 UTC 2019-12-03 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • First steps with Git for reproducible research (date to be confirmed)

    5 December 2019

    Lausanne, Switzerland

    Elixir node event
    First steps with Git for reproducible research (date to be confirmed) https://tess.elixir-europe.org/events/first-steps-with-git-for-reproducible-research More information soon 2019-12-05 09:00:00 UTC 2019-12-05 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • 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 [] []
  • High Performance Computing (HPC) in Life Sciences: Vital-IT Infrastructure Training

    12 December 2019

    Lausanne, Switzerland

    Elixir node event
    High Performance Computing (HPC) in Life Sciences: Vital-IT Infrastructure Training https://tess.elixir-europe.org/events/high-performance-computing-hpc-in-life-sciences-vital-it-infrastructure-training-7a057fe4-5717-4c6a-a567-ba2cb95bb755 Overview Several scientific applications require computing and/or storage resources that go beyond the processing power of a single multi-core machine. 2019-12-12 09:00:00 UTC 2019-12-12 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • First steps with Git for reproducible research

    27 February 2020

    Lausanne, Switzerland

    Elixir node event
    First steps with Git for reproducible research https://tess.elixir-europe.org/events/first-steps-with-git-for-reproducible-research-date-to-be-confirmed More information soon 2020-02-27 09:00:00 UTC 2020-02-27 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students 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 [] []
  • Workshop Metagenomics

    1 May 2020

    Leiden, Netherlands

    Elixir node event
    Workshop Metagenomics https://tess.elixir-europe.org/events/workshop-metagenomics-50fa03ae-bc84-447a-92fe-b353cea33030 In deze cursus wordt een algemene achtergrond van metagenomics gegeven. Hands-on data-analyse is een belangrijk onderdeel: tijdens computer practica kan je 16S- en metagenoom datasets analyseren. De workflow van monstervoorbereiding, DNA-isolatie, selectie van platform, read mapping, annotatie en metagenoomassemblage wordt behandeld.… The post Workshop Metagenomics appeared first on Dutch Techcentre for Life Sciences. 2020-05-01 09:00:00 UTC 2020-05-01 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] [] workshops_and_courses [] []
  • ELIXIR Heads of Nodes Retreat (2020)

    6 - 7 May 2020

    Woking, United Kingdom

    ELIXIR Heads of Nodes Retreat (2020) https://tess.elixir-europe.org/events/elixir-heads-of-nodes-retreat-2020 The ELIXIR Heads of Nodes (HoN) will hold their annual Retreat from 6-7 May 2020 in Woking, UK. A full agenda and documents for this meeting will be made available to meeting participants in due course. Location Set in the Surrey country side, this venue has been chosen as an ideal venue just 30 minutes from central London and 20 minutes from Heathrow and Gatwick Airport. You are encouraged to travel to and from Heathrow Airport. Contacts For all documentation inquiries, please contact: Joana Wingender (joana.wingender@elixir-europe.org) For all logistical inquiries, please contact: Melissa Balzano (melissa.balzano@elixir-europe.org)    2020-05-06 11:00:00 UTC 2020-05-07 15:00:00 UTC The Talbot Inn, Woking, United Kingdom The Talbot Inn Woking United Kingdom GU23 6BB [] [] [] [] [] []
  • Analyse Next Generation Sequencing (NGS) data

    8 June 2020

    Leiden, Netherlands

    Elixir node event
    Analyse Next Generation Sequencing (NGS) data https://tess.elixir-europe.org/events/analyse-next-generation-sequencing-ngs-data Deze tweedaagse workshop geeft toepasbare up to date informatie over NGS. Verschillende platforms, de werking van sequencers en nucleïnezuur isolatie komen uitvoerig aan bod. De analyse van NGS data bij DNA en RNA sequencing wordt geïntroduceerd. Verschillende toepassingen zoals genoom… The post Analyse Next Generation Sequencing (NGS) data appeared first on Dutch Techcentre for Life Sciences. 2020-06-08 09:00:00 UTC 2020-06-08 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] [] 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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