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  • Introduction to Next Generation Sequencing

    23 - 27 September 2019

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Next Generation Sequencing https://tess.elixir-europe.org/events/introduction-to-next-generation-sequencing-95cd61bd-167b-4139-830b-73243fb13341 This course will provide an introduction to the technology, data analysis, tools and resources for next generation sequencing (NGS) data. 2019-09-23 09:00:00 UTC 2019-09-27 16:30:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] EMBL-EBI Training Team [] [] [] [] []
  • Metabolomics: Understanding Metabolism in the 21st Century

    23 September - 18 October 2019

    Edgbaston, United Kingdom

    Elixir node event
    Metabolomics: Understanding Metabolism in the 21st Century https://tess.elixir-europe.org/events/metabolomics-understanding-metabolism-in-the-21st-century-8c9cebe4-268d-4e19-9073-3a9d99e51df5 This online course explores metabolomics, an emerging field that aims to measure the complement of metabolites (the metabolome) in living organisms. The metabolome represents the downstream effect of an organism's... 2019-09-23 09:00:00 UTC 2019-10-18 23:59:00 UTC Online, Edgbaston, United Kingdom Online Edgbaston United Kingdom B15 2TT [] [] [] [] [] []
  • Next Generation Sequencing Bioinformatics

    23 - 26 September 2019

    Cambridge, United Kingdom

    Elixir node event
    Next Generation Sequencing Bioinformatics https://tess.elixir-europe.org/events/next-generation-sequencing-bioinformatics-8e7d122d-e273-4475-8064-9c366ac6a70f This course will provide an introduction to the technology, analysis workflows, tools and resources for next generation sequencing data analysis. 2019-09-23 09:00:00 UTC 2019-09-26 16:30:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Rebecca Nicholl [] [] [] [] HDRUK
  • Autumn School in Data Science: Machine learning applications for life sciences

    23 - 26 September 2019

    Cambridge, United Kingdom

    Elixir node event
    Autumn School in Data Science: Machine learning applications for life sciences https://tess.elixir-europe.org/events/summer-school-in-biomedical-data-science-best-practices-for-single-cell-analysis-and-machine-learning-applications THIS EVENT IS NOW FULLY BOOKED! This Autumn School aims to familiarise biomedical students and researchers with principles of Data Science. Focusing on utilising machine learning algorithms to handle biomedical data, it will cover: effects of experimental design, data readiness, pipeline implementations, machine learning in Python, and related statistics, as well as Gaussian Process models. Providing practical experience in the implementation of machine learning methods relevant to biomedical applications, including Gaussian processes, we will illustrate best practices that should be adopted in order to enable reproducibility in any data science application. This event is sponsored by [Cambridge Big Data](https://www.bigdata.cam.ac.uk/). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3050610&amp;course-title=Autumn%20School%20in%20Data%20Science).'' 2019-09-23 10:30:00 UTC 2019-09-26 14:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Machine learning Bioinformatics University of Cambridge Bioinformatics Training [] Students and researchers from life-sciences or biomedical backgroundswho haveor will shortly havethe need to apply the techniques presented during the course to biomedical data.The course is open to Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals<span style="color:#FF0000">Please note that all participants attending this course will be charged a registration fee. <span style="color:#0000FF"> Non-members of the University of Cambridge to pay £350. </span style> <span style="color:#0000FF">All Members of the University of Cambridge to pay £175. </span style> <span style="color:#FF0000">A booking will only be approved and confirmed once the fee has been paid in full.</span style> workshops_and_courses [] HDRUK
  • de.NBI - CeBiTec Nanopore Best Practice Workshop 2019

    25 - 27 September 2019

    Bielefeld, Germany

    de.NBI - CeBiTec Nanopore Best Practice Workshop 2019 https://tess.elixir-europe.org/events/de-nbi-cebitec-nanopore-best-practice-workshop-2019 de.NBI - CeBiTec Nanopore Best Practice Workshop 2019 Bielefeld Educators: Stefan Albaum, Sebastian Jünemann, Nils Kleinbölting, Alexander Sczyrba (BiGi), Daniel Wibberg (CAU), Björn Usadel (GCBN), Christian Rückert, Jörn Kalinowski (CeBiTec) Date: 25 - 27 September 2019 Location: Bielefeld University, Universitätsstraße 25, 33615 Bielefeld Content: Aim of this workshop is to familiarise the participants with the Nanopore sequencing technology, its applications and the "Best Practice" bioinformatics workflow. The Nanopore technology have greatly facilitated the assembly of prokaryotic and eukaryotic genomes. Therefore, the workshop is focused on the establishment of finalized genome sequences. This workshop will be composed of different talks including introductions to the Nanopore sequencing technology and working in the de.NBI cloud as well as different hands-on sessions. During the talks, the advantages and pitfalls of Nanopore sequencing will be discussed. The hands-on sessions will illustrate the typical workflow from the Nanopore sequencing to the final assembled genome. Learning goals: This workshop aims to teach basic skills and best practices to researchers working with Nanopore data. The final goal is to enable them to use the resulting reads for a de novo assembly. Prerequisites: This workshop is intended for PhD students and postdocs with molecular biology background in genomics. Good understanding of command line tools is a plus, but not required. Tool: Canu, Pilon, Albacore, Porechop, Metricor, Poretools Keywords: Nanopore sequencing, genome assembly, genomics 2019-09-25 09:00:00 UTC 2019-09-27 17:00:00 UTC de.NBI / CeBiTec Bielefeld, Bielefeld, Germany Bielefeld Bielefeld Detmold Germany [] [] [] [] [] []
  • First Steps with UNIX in Life Sciences

    25 September 2019

    Lausanne, Switzerland

    Elixir node event
    First Steps with UNIX in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-unix-in-life-sciences-4430cc52-cd66-4a18-89c1-dc7e7fbe1bc1 Overview With a constant evolution of technologies, life scientists (such as laboratory biologists) are faced with an increasing need for bioinformatics skills to deal with high-throughput data storage, retrieval and analysis. 2019-09-25 09:00:00 UTC 2019-09-25 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Introduction to working with UNIX and bash

    30 September 2019

    Cambridge, United Kingdom

    Elixir node event
    Introduction to working with UNIX and bash https://tess.elixir-europe.org/events/introduction-to-working-with-unix-and-bash Using the Linux operating system and the bash command line interface, we will demonstrate the basic structure of the UNIX operating system and how we can interact with it using a basic set of commands. Applying this, we will learn how to navigate the filesystem, manipulate text-based data and structure simple pipelines out of these commands. Building on this foundation, the course will use a bioinformatics example to demonstrate how the skills learnt can be applied to connecting to external resources/servers, installing specialist tools and ultimately combining commands into scripts for automation and reproducibility. This course is targeted at participants with no prior experience working with UNIX-like systems (OSX, Linux) or command line interfaces. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to Book or register Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3117357&amp;course-title=Introduction%20to%20working%20with%20Unix%20and%20bash).'' 2019-09-30 08:30:00 UTC 2019-09-30 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Reproducible Research with R

    1 October 2019

    Cambridge, United Kingdom

    Elixir node event
    Reproducible Research with R https://tess.elixir-europe.org/events/reproducible-research-with-r This course introduces concepts about reproducibility that can be used when you are programming in R. We will explore how to create notebooks - a way to integrate your R analyses into reports using Rmarkdown. The course also introduces the concept of version control. We will learn how to create a repository on GitHub and how to work together on the same project collaboratively without creating conflicting versions of files. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3114638&amp;course-title=Reproducible%20Research%20with%20R).'' 2019-10-01 08:30:00 UTC 2019-10-01 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • An Introduction to Machine Learning

    2 - 4 October 2019

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Machine Learning https://tess.elixir-europe.org/events/an-introduction-to-machine-learning-c4f53d48-57b9-468c-bf48-8107350d6d40 Machine learning gives computers the ability to learn without being explicitly programmed. It encompasses a broad range of approaches to data analysis with applicability across the biological sciences. Lectures will introduce commonly used algorithms and provide insight into their theoretical underpinnings. In the practicals students will apply these algorithms to real biological data-sets using the R language and environment. Please be aware that the course syllabus is currently being updated following feedback from the last event; therefore the agenda below will be subjected to changes. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3043850&amp;course-title=An%20Introduction%20to%20Machine%20Learning).'' 2019-10-02 08:30:00 UTC 2019-10-04 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Machine learning Data mining Bioinformatics University of Cambridge Bioinformatics Training [] This is aimed at life scientists with little or no experience in machine learning and that are looking at implementing these approaches in their research.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • EMBL-EBI Workshop: Mathematics of life workshop: “Modelling molecular mechanisms: from basic science to drug discovery”

    2 October 2019

    Cambridge, United Kingdom

    Elixir node event
    EMBL-EBI Workshop: Mathematics of life workshop: “Modelling molecular mechanisms: from basic science to drug discovery” https://tess.elixir-europe.org/events/embl-ebi-workshop-mathematics-of-life-workshop-modelling-molecular-mechanisms-from-basic-science-to-drug-discovery The one-day workshop includes scientific talks from 3 distinguished speakers who will showcase how modelling is useful in fundamental research as well as pharmaceutical industry, a tutorial session on modelling of normal and disease pathways using simulation software, COPASI, and an extended afternoon hands-on training workshop / group project. 2019-10-02 08:30:00 UTC 2019-10-02 18:30:00 UTC Sanders Hall, Postdoc Centre @ Eddington, Cambridge, United Kingdom Sanders Hall, Postdoc Centre @ Eddington Cambridge United Kingdom CB3 1AS [] Rahuman Sheriff [] [] [] [] HDRUK
  • Exploring Biological Sequences

    8 - 10 October 2019

    Cambridge, United Kingdom

    Elixir node event
    Exploring Biological Sequences https://tess.elixir-europe.org/events/exploring-biological-sequences-0cf6b334-a619-4ea1-b8e1-7f229c9e58ab This course will introduce you to approaches used for finding, analysing and using biological sequences. 2019-10-08 09:00:00 UTC 2019-10-10 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 1, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 1 Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • First steps with R in Life Sciences

    8 - 9 October 2019

    Lausanne, Switzerland

    Elixir node event
    First steps with R in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-r-in-life-sciences-31722d33-fefc-4aaa-a004-cd69bbab054e The course is now full with a long waiting list. Application is still open but you will be directly put in the waiting list. There will be other sessions next year. Thank you for your understanding. 2019-10-08 09:00:00 UTC 2019-10-09 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • 4th de.NBI Training Course on Metagenome Analysis

    9 - 11 October 2019

    Bielefeld, Germany

    4th de.NBI Training Course on Metagenome Analysis https://tess.elixir-europe.org/events/4th-de-nbi-training-course-on-metagenome-analysis Educators: Sebastian Jünemann (Bielefeld University), Dr. Alex Sczyrba (Bielefeld University), Sebastian Jaenicke (Giessen University), Nils Kleinboelting (Bielefeld University) Location: Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Room V6-113 Date: October the 9th to 11th, 2019 Content: The aim of this 3-day workshop will be to give students a brief overview of the tools and bioinformatics techniques available for the analysis of next generation sequence (NGS) data from microbial communities. The format will comprise a mixture of lectures and hands-on tutorials where students will process example data sets in real-time in the de.NBI cloud environment. After covering general aspects of sequence based analysis (e.g. pre-processing, quality measurements, error handling, and so on) the course is divided into two parts: targeted (16S rRNA gene amplicons) and untargeted (whole-genome shotgun; WGS) metagenome analysis. On demand, a compact introduction into the Linux operating system and the usage of the command line interface will be given upstream to the introducing part to guarantee a consistent baseline for the following lectures. The main aspects of the 16S part are the common pipeline steps beginning with pre-processing and filtering followed by OTU clustering, taxonomic classification, and different statistical measurements. Then, the new ASV/zOTU approach will be introduced followed by similar statistics and both approaches discussed with the attendants in conclusion. In the third part, advantages and disadvantages of whole metagenome sequencing will be illustrated. As WGS metagenomics has the potential to address the full spectra of genome-based issues, the focus here will be on taxonomic and functional analysis with the aid of different bioinformatic tools. Two different techniques to analyze WGS metagenome data are part of this section: (1) in the read-based approach the software solution MGX, an integrated platform for metagenome analysis and data visualization, will be demonstrated. (2) the assembly-based approach to potentially recover near-complete genome by assembling reads into contigs which are subject to binning methods to group individual contigs into genome bins. Prerequisites: - basic knowledge in microbiology and NGS-based analysis - practical experience in a Linux/Unix derivatives, the command line interface and file system required Prerequisites for the workshop plus the optional Linux introduction: - basic knowledge in microbiology and NGS-based analysis Please not that participation to this course does not depend on the actual Linux experience of the applicant. Both, experienced as well as inexperienced Linux users are encouraged to submit an application. However, the Linux introducing session in the morning of the first day is optional only for applicants fulfilling the Linux prerequisite. Application: Please send your application to denbi-courses@cebitec.uni-bielefeld.de (subject MG­course2019) including a short motivation, a few words about your background, your level of experience on the command line (Linux/Unix), and your experience within the field of metagenomic analysis and related bioinformatic tools. There will be no participation fee, yet travel and accommodation expenses need to be paid by the participants. 2019-10-09 09:00:00 UTC 2019-10-11 17:00:00 UTC de.NBI Bielefeld, Bielefeld, Germany Bielefeld Bielefeld Detmold Germany [] [] [] workshops_and_courses [] metagenomics
  • An Introduction to Data Exploration, Experimental Design, and Biomarker Expression Analysis using JMP Software Tools

    10 October 2019

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Data Exploration, Experimental Design, and Biomarker Expression Analysis using JMP Software Tools https://tess.elixir-europe.org/events/an-introduction-to-data-exploration-experimental-design-and-biomarker-expression-analysis-using-jmp-software-tools Through the use of real world examples and the [JMP, JMP Pro, and JMP Genomics software](https://www.jmp.com/en_us/home.html), we will cover best practices used in both industry and academia today to visually explore data, plan biological experiments, detect differential expression patterns, find signals in next-generation sequencing data and easily discover statistically appropriate biomarker profiles and patterns. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3129245&amp;course-title=JMP%20workshop).'' 2019-10-10 12:00:00 UTC 2019-10-10 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Biomarkers Data visualisation Data quality management Omics Genomics Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Introduction to Scientific Figure Design

    11 October 2019

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Scientific Figure Design https://tess.elixir-europe.org/events/introduction-to-scientific-figure-design-3981eee7-417e-4f61-b794-eff8f0e05580 This course provides a practical guide to producing figures for use in reports and publications. It is a wide ranging course which looks at how to design figures to clearly and fairly represent your data, the practical aspects of graph creation, the allowable manipulation of bitmap images and compositing and editing of final figures. The course will use a number of different open source software packages and is illustrated with a number of example figures adapted from common analysis tools. Further information and access to the course materials is [here](http://www.bioinformatics.babraham.ac.uk/training.html#figuredesign). The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3088725&amp;course-title=Introduction%20to%20Scientific%20Figure%20Design).'' 2019-10-11 08:30:00 UTC 2019-10-11 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Data visualisation Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Ensembl Browser workshop - EBI October 2019

    15 October 2019

    Cambridge, United Kingdom

    Elixir node event
    Ensembl Browser workshop - EBI October 2019 https://tess.elixir-europe.org/events/ensembl-browser-workshop-ebi-october-2019 Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart. 2019-10-15 09:30:00 UTC 2019-10-15 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Emily Perry [] [] [] [] HDRUK
  • Ensembl Browser workshop, EBI, 15 October 2019

    15 October 2019

    Cambridge, United Kingdom

    Elixir node event
    Ensembl Browser workshop, EBI, 15 October 2019 https://tess.elixir-europe.org/events/ensembl-browser-workshop-ebi-15-october-2019 Work with the Ensembl Outreach team to get to grips with the Ensembl browser, accessing gene, variation, comparative genomics and regulation data, and mine these data with BioMart. 2019-10-15 09:30:00 UTC 2019-10-15 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Astrid Gall [] [] [] [] HDRUK
  • 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 &amp; 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 [] []
  • Ensembl REST API workshop - EBI October 2019

    16 October 2019

    Cambridge, United Kingdom

    Elixir node event
    Ensembl REST API workshop - EBI October 2019 https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-ebi-october-2019 Work with Ensembl to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments. 2019-10-16 09:30:00 UTC 2019-10-16 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Emily Perry [] [] [] [] HDRUK
  • Ensembl REST API workshop, EBI, 16 October 2019

    16 October 2019

    Cambridge, United Kingdom

    Elixir node event
    Ensembl REST API workshop, EBI, 16 October 2019 https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-ebi-16-october-2019 Work with Ensembl to master the Ensembl REST API and flexibly access genome-wide data, such as genes, variants, regulatory features, homologues and alignments. 2019-10-16 09:30:00 UTC 2019-10-16 15:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Astrid Gall [] [] [] [] HDRUK
  • Open Targets: Integrating genetics and genomics for disease biology and translational medicine

    17 October 2019

    Cambridge, United Kingdom

    Elixir node event
    Open Targets: Integrating genetics and genomics for disease biology and translational medicine https://tess.elixir-europe.org/events/open-targets-integrating-genetics-and-genomics-for-disease-biology-and-translational-medicine Open Targets is a public-private partnership to use human genetics, genomic data and drug information for systematic identification and prioritisation of therapeutic targets. This module introduces the Open Targets partnership, its underlying projects and the bioinformatics resources for researchers studying associations of human genes with diseases. We offer interactive and hands-on experience with Open Targets Platform and Open Targets Genetics, open source tools of integrated biological and chemical data for drug target identification and prioritisation. We cover user cases relevant to the biomedical and pharmaceutical communities and can customise the course according to specific therapeutic areas. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3093271&amp;course-title=OpenTargets%20workshop).'' 2019-10-17 12:00:00 UTC 2019-10-17 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Pharmacogenomics Genotype and phenotype Data visualisation Bioinformatics University of Cambridge Bioinformatics Training [] This course is suitable for anyone who has an interest in biomedical research and therapeutics with a special emphasis on drug discovery and target validation. It is also useful to those who wish to find out how large-scale genomic experimentscellular models of disease and computational techniques are used to identify and validate the causal links between targetspathways and diseases.Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Genomic Data for Surveillance of Communicable Disease

    21 - 25 October 2019

    Cambridge, United Kingdom

    Elixir node event
    Genomic Data for Surveillance of Communicable Disease https://tess.elixir-europe.org/events/genomic-data-for-surveillance-of-communicable-disease This course will introduce participants to genomic approaches used in the detection and monitoring of communicable diseases. 2019-10-21 15:00:00 UTC 2019-10-25 15:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 1, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 1 Cambridge United Kingdom CB10 1SD [] Marina Pujol [] [] [] [] []
  • Analysis of High-Throughput Sequencing Data

    21 - 25 October 2019

    Cambridge, United Kingdom

    Elixir node event
    Analysis of High-Throughput Sequencing Data https://tess.elixir-europe.org/events/analysis-of-high-throughput-sequencing-data-c870b761-2d91-4573-af2b-30783e1c7a55 This course will familiarise participants with methodologies for bioinformatics analysis on next generation sequencing (NGS) data. 2019-10-21 15:00:00 UTC 2019-10-25 15:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 1, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 1 Cambridge United Kingdom CB10 1SD [] EMBL-EBI Training Team [] [] [] [] []
  • ChIP-seq and ATAC-seq analysis

    23 - 24 October 2019

    Cambridge, United Kingdom

    Elixir node event
    ChIP-seq and ATAC-seq analysis https://tess.elixir-europe.org/events/chip-seq-and-atac-seq-analysis-b2a9ec58-3f94-497f-b6a6-d18041934b1f The primary aim of this course is to familiarise participants with the analysis of ChIP-seq and ATAC-seq data and provide hands-on training on the latest analytical approaches. The course starts with an introduction to ChIP-seq experiments for the detection of genome-wide DNA binding sites of transcription factors and other proteins. We first show data quality control and basic analytical steps such as alignment, peak calling and motif analysis, followed by practical examples on how to work with biological replicates and fundamental quality metrics for ChIP-seq datasets. On the second day, we then focus on the analysis of differential binding, comparing between different samples. We will also give an introduction to ATAC-seq data analysis for the detection of regions of open chromatin. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3049814&amp;course-title=ChIP-seq%20and%20ATAC-seq%20analysis).'' 2019-10-23 08:30:00 UTC 2019-10-24 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR ChIP-seq Data mining Data visualisation Functional genomics Epigenomics Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • 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 [] []
  • Data Science in Python

    30 - 31 October 2019

    Cambridge, United Kingdom

    Elixir node event
    Data Science in Python https://tess.elixir-europe.org/events/data-science-in-python-936eab84-71b6-473b-b5e4-ab74565a90d0 This course covers concepts and strategies for working more effectively with Python with the aim of writing reusable code, using function and libraries. Participants will acquire a working knowledge of key concepts which are prerequisites for advanced programming in Python e.g. writing modules and classes. Note: this course is the continuation of the [Introduction to Solving Biological Problems with Python](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-python/); participants are expected to have attended the introductory Python course and/or have acquired some working knowledge of Python. This course is also open to Python beginners who are already fluent in other programming languages as this will help them to quickly get started in Python. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3062424&amp;course-title=Data%20Science%20in%20Python).'' 2019-10-30 09:30:00 UTC 2019-10-31 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Biology Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Data Management Plan

    31 October - 1 November 2019

    Lausanne, Switzerland

    Elixir node event
    Data Management Plan https://tess.elixir-europe.org/events/data-management-plan-812edd6d-94f8-445e-9830-257ec0790d90 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 (Chalmers et al., 2009; Freedman et 2019-10-31 09:00:00 UTC 2019-11-01 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Introduction to R for Biologists

    5 - 6 November 2019

    Cambridge, United Kingdom

    Elixir node event
    Introduction to R for Biologists https://tess.elixir-europe.org/events/introduction-to-r-for-biologists-1288c345-ea99-48e3-be34-00786399b176 R is one of the leading programming languages in Data Science. It is widely used to perform statistics, machine learning, visualisations and data analyses. It is an open source programming language so all the software we will use in the course is free. This course is an introduction to R designed for participants with no programming experience. We will start from scratch by introducing how to start programming in R and progress our way and learn how to read and write to files, manipulate data and visualise it by creating different plots - all the fundamental tasks you need to get you started analysing your data. During the course we will be working with one of the most popular packages in R; tidyverse that will allow you to manipulate your data effectively and visualise it to a publication level standard. The training room is located on the first floor and there is currently no wheelchair or level access available to this level. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3079285&amp;course-title=Introduction%20to%20R%20for%20Biologists).'' 2019-11-05 09:30:00 UTC 2019-11-06 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • 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, &amp; 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 [] []
  • Bioinformatics & Functional Genomics in Zebrafish

    11 - 14 November 2019

    Cambridge, United Kingdom

    Elixir node event
    Bioinformatics & Functional Genomics in Zebrafish https://tess.elixir-europe.org/events/bioinformatics-functional-genomics-in-zebrafish-5f0fa5f9-c6c7-4169-8dd4-50c25518e259 This course has been designed specifically for researchers working within the Zebrafish community, providing an introduction and practical knowledge of tools and resources for working with functional genomics data. 2019-11-11 10:30:00 UTC 2019-11-14 15:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 2, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 2 Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
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