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  • Executive Masters in Management of Research Infrastructures

    13 November 2018 - 26 June 2020

    Milan, Italy

    Elixir node event
    Executive Masters in Management of Research Infrastructures https://tess.elixir-europe.org/events/executive-masters-in-management-of-research-infrastructures-12abb26e-f3b7-45ac-92c6-24008017292d This Masters development programme is aimed at current Research Infrastructures managers and leaders who wish to develop the competencies required to meet the needs of Research Infrastructures in the planning, construction and operation phases. 2018-11-13 12:00:00 UTC 2020-06-26 12:00:00 UTC University of Milano-Bicocca, Milan, Italy University of Milano-Bicocca Milan Italy 20126 [] Claire Johnson [] [] [] [] HDRUK

  • eLife Innovation Leaders 2020

    1 February - 30 June 2020

    eLife Innovation Leaders 2020 https://tess.elixir-europe.org/events/elife-innovation-leaders-2020 *eLife Innovation Leaders* is a 14-week mentorship and open leadership training programme designed for innovators developing open-source tools and projects for open research communication. Key takeaways: - A personalised experience with one-on-one mentorship - A shared co-learning journey - Theory and practice in project design, community engagement, and more - Opportunities to be supported beyond the programme The programme will take place between February and June 2020. We invite you to find out more and apply by December 8 here: [elifesci.org/innovationleaders](https://elifesci.org/innovationleaders) If you have any specific requirements to enable your participation, please don't hesitate to let us know through the application form or through email, we're happy to discuss potential arrangements. 2020-02-01 09:00:00 UTC 2020-06-30 23:59:00 UTC Emmy Tsang, Innovation Community Manager @ eLife [] Emmy at innovation [at] elifesciences [dot] org [] research software engineers and research data managers working with ELIXIR-supported tools and resourcestool authorssoftware developers, bioinformaticians workshops_and_courses [] Open scienceopen sourceCommunication

  • DIPLÔME UNIVERSITAIRE EN BIOINFORMATIQUE INTÉGRATIVE : DU-BII 2020

    2 March - 19 June 2020

    Elixir node event
    DIPLÔME UNIVERSITAIRE EN BIOINFORMATIQUE INTÉGRATIVE : DU-BII 2020 https://tess.elixir-europe.org/events/diplome-universitaire-en-bioinformatique-integrative-du-bii-2020 No description available 2020-03-02 09:00:00 UTC 2020-06-19 00:00:00 UTC [] [] [] [] [] []

  • Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance

    9 March - 12 July 2020

    Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance https://tess.elixir-europe.org/events/bacterial-genomes-disease-outbreaks-and-antimicrobial-resistance-9b6d1f32-b676-422b-93fe-ad935f02bf74 # Overview * **Duration**: 3 weeks, 3 hours per week * Free * Certificate of achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (9 credits), Royal College of Nursing (9 credits) * **Start Date**: The course is run ‘live’ for 3 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join the course? The increase in resistance of harmful bacteria to antibiotics is a major global threat to health. Here we explore bacterial genomes and the use of genome sequencing to identify and track these drug resistant bacteria. Join us to discover how genome research is helping scientists and healthcare professionals track disease outbreaks and prevent the rise of antibiotic resistant ‘superbugs’. ### Who is the course for? This course will be of interest to scientists, healthcare professionals, biomedical researchers and bioinformaticians. The course offers all learners an opportunity to learn about genomes, disease, and antimicrobial resistance. You require no previous knowledge of genome science to complete the course. ### What do people say about this course? "_I would definitely point students to this resource. Text, videos, and figures were all very well done._" Pablo Tsukayama, Assistant Professor of Microbiology "_A highlight of the course was the introduction to whole genome sequencing – new information for me._" Christine Laws, Medical Doctor “_Exchanging genetic information quickly throughout the world is clearly going to revolutionise the ability to combat disease._” Prue van der Hoorn, Artist # Programme and start dates ### Course start dates This course is repeated twice a year. ### What topics will you cover? * Diseases caused by bacteria * What bacterial genomes look like * Genome sequencing technology * Mechanisms of transmission and resistance * Genomic epidemiology – tracking the spread of bacterial pathogens * Antimicrobial resistance ### What will you achieve? By the end of the course, you'll be able to... * Explain why some bacteria are pathogenic * Explore the structure of bacterial genomes * Describe the uses of different genome sequencing technologies * Investigate how genome data are used to track the spread of bacterial disease * Discuss the role of genome sequencing in stopping the spread of antimicrobial resistance # Educators ## **Lead Educators** **[Dr Adam Reid][1]** I am a senior staff scientist at the Wellcome Sanger Institute near Cambridge in the United Kingdom. I'm interested in using genomics and bioinformatics to better understand infectious diseases. **[Dr Josie Bryant][2]** I am a Henry Wellcome Postdoctoral Fellow in the University of Cambridge, Department of Medicine. I am working on bacterial genomics and evolution with a focus on within-patient microbial diversity ### Dr Francesca Short I am a scientist at the Wellcome Sanger Institute. I am interested in using functional genomics techniques to understand infections caused by the bacterium _Klebsiella pneumoniae_. ## **Programme Lead Educator** **[Professor Nicholas Thomson][3]** I am a Group Leader at the Wellcome Sanger Institute. I provide scientific oversight for this course. I am interested in bacterial evolution and the spread of infectious disease. ### The course also features interviews with distinguished scientists, including: * **[Mathew Beale][4]** - Wellcome Sanger Institute * **[Daryl Domman][5]** - Wellcome Sanger Institute * **[Gal Horesh][6]** - Wellcome Sanger Institute * **[Catherine Ludden][7]** - London School of Hygiene and Tropical Medicine * **[Tapoka Mkandawire][8]** - Wellcome Sanger Institute * **[Julian Parkhill][9]** - Wellcome Sanger Institute * **Lindsay Pike** - Wellcome Sanger Institute * **[Michael Quail][10]** - Wellcome Sanger Institute * **[Susannah J. Salter][11]** - Wellcome Sanger Institute * **[Estee Torok][12]** - Addenbrooke’s Hospital and University of Cambridge [1]: http://www.sanger.ac.uk/people/directory/reid-adam-james [2]: https://www.infectiousdisease.cam.ac.uk/directory/josie-bryant [3]: http://www.sanger.ac.uk/people/directory/thomson-nicholas-robert [4]: http://www.sanger.ac.uk/people/directory/beale-mathew [5]: http://www.sanger.ac.uk/people/directory/domman-daryl [6]: http://www.sanger.ac.uk/people/directory/horesh-gal [7]: https://www.lshtm.ac.uk/aboutus/people/ludden.catherine [8]: http://www.sanger.ac.uk/people/directory/mkandawire-tapoka-t [9]: http://www.sanger.ac.uk/people/directory/parkhill-julian [10]: http://www.sanger.ac.uk/people/directory/quail-michael-andrew [11]: http://www.sanger.ac.uk/people/directory/salter-susannah-j [12]: https://www.infectiousdisease.cam.ac.uk/directory/et317@medschl.cam.ac.uk # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible # CDP Approval 2020-03-09 09:00:00 UTC 2020-07-12 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesAMRHDRUK

  • Introduction to high throughput screening

    24 March - 31 December 2020

    Elixir node event
    Introduction to high throughput screening https://tess.elixir-europe.org/events/introduction-to-high-throughput-screening-791e68be-3d9a-424b-b170-8fcf71b03139 2020-03-24 09:00:00 UTC 2020-12-31 00:00:00 UTC [] [] [] workshops_and_courses [] []

  • Bacterial Genomes: From DNA to Protein Function Using Bioinformatics

    20 April - 16 August 2020

    Bacterial Genomes: From DNA to Protein Function Using Bioinformatics https://tess.elixir-europe.org/events/bacterial-genomes-from-dna-to-protein-function-using-bioinformatics-92c9e794-2186-4766-8435-3273e0756322 # Overview * **Duration**: 2 weeks, 5 hours per week * Free * Certificate of Achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (10 credits) * **Start Date**: The course is run ‘live’ for 2 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join the course? Join us in our quest to discover what makes microbes dangerous. Use bioinformatics to probe genomes, to explore and represent DNA and protein sequences. Then, use databases to find protein sequences’ conserved domains and investigate their functions. ### Who is the course for? The course will be of interest to undergraduates, post-graduates, researchers, bioinformaticians, biomedical researchers, microbiologists, healthcare professionals and all those who are interested in learning about the underlying mechanisms of bacterial disease, DNA sequences and protein data, or how to use online analytical tools to probe genomes. The topics covered in this course are applicable to the genomes of all organisms. It is not essential to have previous knowledge or experience in bioinformatics. Scientific terminology is explained. The opportunity to use online computational tools in the context of bacterial genomes will also be of interest to teachers and their 16-18-year-old science and computing students. ### What do people say about this course? "_Clear introduction of the – often viewed as complex – field of bioinformatics_." Mqondisi Tshabalala, PhD student, Institute for Cellular and Molecular Medicine, University of Pretoria, South Africa "_Highlights of the course were the investigations with the databases - these reinforced the learning._" Dr. Alan McLintic, Anaesthesiologist, Faculty of Medicine and Health Scientists, University of Auckland, New Zealand # Programme and start dates ### Course start dates This course will be repeated: Next start dates: * September 2019 (date TBC) ### What topics will you cover? * Bioinformatics tools, DNA and protein sequences * Retrieving DNA and protein sequences from repositories * Databases for protein annotation * Inferring function from sequence ### What will you achieve? By the end of the course, you'll be able to... * assess DNA representations and protein sequences * perform searches in primary databases (repositories) and retrieve gene/protein data * interpret different repository submission formats * investigate biological databases for research * identify the putative function of proteins based on their conserved domains # Educators ## **Lead Educators** ### Dr Anna Protasio I am a researcher in parasitology and life sciences. I am passionate about bioinformatics and how we can use these tools to answer questions in biology. ### Martin Aslett I am the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests lie in bioinformatics and its application to microbial genomics. ### Dr Christine Boinett I am a researcher in bacterial genetics and my interest is in understanding the development of resistance in bacterial pathogens using next generation sequencing techniques. ## **Educator** ### Matthew Dorman I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens as part of the Infection Genomics programme. ## **Programme Lead Educator** ### Professor Nicholas Thomson Group Leader at the Wellcome Sanger Institute, interested in bacterial evolution and the spread of infectious disease; provides scientific oversight for this course. The course also features interviews with two distinguished experts: ### Dr Rob Finn Team Leader of EMBL-EBI Sequence Families Team ### Dr Claire Chewapreecha Sir Henry Wellcome Fellow and Lecturer, University of Cambridge, UK, and King Mongkut University of Technology, Thailand. # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible # CPD Approval 2020-04-20 09:00:00 UTC 2020-08-16 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesinformaticsHDRUK

  • Bacterial Genomes: From DNA to Protein Function Using Bioinformatics

    20 April - 16 August 2020

    Bacterial Genomes: From DNA to Protein Function Using Bioinformatics https://tess.elixir-europe.org/events/bacterial-genomes-from-dna-to-protein-function-using-bioinformatics-58453edc-686a-4baa-87e1-e8f5dbab3cb1 # Overview * **Duration**: 2 weeks, 5 hours per week * Free * Certificate of Achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (10 credits) * **Start Date**: The course is run ‘live’ for 2 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join the course? Join us in our quest to discover what makes microbes dangerous. Use bioinformatics to probe genomes, to explore and represent DNA and protein sequences. Then, use databases to find protein sequences’ conserved domains and investigate their functions. ### Who is the course for? The course will be of interest to undergraduates, post-graduates, researchers, bioinformaticians, biomedical researchers, microbiologists, healthcare professionals and all those who are interested in learning about the underlying mechanisms of bacterial disease, DNA sequences and protein data, or how to use online analytical tools to probe genomes. The topics covered in this course are applicable to the genomes of all organisms. It is not essential to have previous knowledge or experience in bioinformatics. Scientific terminology is explained. The opportunity to use online computational tools in the context of bacterial genomes will also be of interest to teachers and their 16-18-year-old science and computing students. ### What do people say about this course? "_Clear introduction of the – often viewed as complex – field of bioinformatics_." Mqondisi Tshabalala, PhD student, Institute for Cellular and Molecular Medicine, University of Pretoria, South Africa "_Highlights of the course were the investigations with the databases - these reinforced the learning._" Dr. Alan McLintic, Anaesthesiologist, Faculty of Medicine and Health Scientists, University of Auckland, New Zealand # Programme and start dates ### Course start dates This course will be repeated: Next start dates: * September 2019 (date TBC) ### What topics will you cover? * Bioinformatics tools, DNA and protein sequences * Retrieving DNA and protein sequences from repositories * Databases for protein annotation * Inferring function from sequence ### What will you achieve? By the end of the course, you'll be able to... * assess DNA representations and protein sequences * perform searches in primary databases (repositories) and retrieve gene/protein data * interpret different repository submission formats * investigate biological databases for research * identify the putative function of proteins based on their conserved domains # Educators ## **Lead Educators** ### Dr Anna Protasio I am a researcher in parasitology and life sciences. I am passionate about bioinformatics and how we can use these tools to answer questions in biology. ### Martin Aslett I am the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests lie in bioinformatics and its application to microbial genomics. ### Dr Christine Boinett I am a researcher in bacterial genetics and my interest is in understanding the development of resistance in bacterial pathogens using next generation sequencing techniques. ## **Educator** ### Matthew Dorman I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens as part of the Infection Genomics programme. ## **Programme Lead Educator** ### Professor Nicholas Thomson Group Leader at the Wellcome Sanger Institute, interested in bacterial evolution and the spread of infectious disease; provides scientific oversight for this course. The course also features interviews with two distinguished experts: ### Dr Rob Finn Team Leader of EMBL-EBI Sequence Families Team ### Dr Claire Chewapreecha Sir Henry Wellcome Fellow and Lecturer, University of Cambridge, UK, and King Mongkut University of Technology, Thailand. # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible # CPD Approval 2020-04-20 09:00:00 UTC 2020-08-16 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesinformaticsHDRUK

  • Bacterial Genomes: From DNA to Protein Function Using Bioinformatics

    20 April - 16 August 2020

    Bacterial Genomes: From DNA to Protein Function Using Bioinformatics https://tess.elixir-europe.org/events/bacterial-genomes-from-dna-to-protein-function-using-bioinformatics-f8f943e2-2214-43f4-80a9-0215800cbed1 # Overview * **Duration**: 2 weeks, 5 hours per week * Free * Certificate of Achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (10 credits) * **Start Date**: The course is run ‘live’ for 2 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join the course? Join us in our quest to discover what makes microbes dangerous. Use bioinformatics to probe genomes, to explore and represent DNA and protein sequences. Then, use databases to find protein sequences’ conserved domains and investigate their functions. ### Who is the course for? The course will be of interest to undergraduates, post-graduates, researchers, bioinformaticians, biomedical researchers, microbiologists, healthcare professionals and all those who are interested in learning about the underlying mechanisms of bacterial disease, DNA sequences and protein data, or how to use online analytical tools to probe genomes. The topics covered in this course are applicable to the genomes of all organisms. It is not essential to have previous knowledge or experience in bioinformatics. Scientific terminology is explained. The opportunity to use online computational tools in the context of bacterial genomes will also be of interest to teachers and their 16-18-year-old science and computing students. ### What do people say about this course? "_Clear introduction of the – often viewed as complex – field of bioinformatics_." Mqondisi Tshabalala, PhD student, Institute for Cellular and Molecular Medicine, University of Pretoria, South Africa "_Highlights of the course were the investigations with the databases - these reinforced the learning._" Dr. Alan McLintic, Anaesthesiologist, Faculty of Medicine and Health Scientists, University of Auckland, New Zealand # Programme and start dates ### Course start dates This course will be repeated twice a year. ### What topics will you cover? * Bioinformatics tools, DNA and protein sequences * Retrieving DNA and protein sequences from repositories * Databases for protein annotation * Inferring function from sequence ### What will you achieve? By the end of the course, you'll be able to... * assess DNA representations and protein sequences * perform searches in primary databases (repositories) and retrieve gene/protein data * interpret different repository submission formats * investigate biological databases for research * identify the putative function of proteins based on their conserved domains # Educators ## **Lead Educators** ### Dr Anna Protasio I am a researcher in parasitology and life sciences. I am passionate about bioinformatics and how we can use these tools to answer questions in biology. ### Martin Aslett I am the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests lie in bioinformatics and its application to microbial genomics. ### Dr Christine Boinett I am a researcher in bacterial genetics and my interest is in understanding the development of resistance in bacterial pathogens using next generation sequencing techniques. ## **Educator** ### Matthew Dorman I am a graduate student at the Wellcome Sanger Institute, where I research the virulence and the molecular genetics of bacterial pathogens as part of the Infection Genomics programme. ## **Programme Lead Educator** ### Professor Nicholas Thomson Group Leader at the Wellcome Sanger Institute, interested in bacterial evolution and the spread of infectious disease; provides scientific oversight for this course. The course also features interviews with two distinguished experts: ### Dr Rob Finn Team Leader of EMBL-EBI Sequence Families Team ### Dr Claire Chewapreecha Sir Henry Wellcome Fellow and Lecturer, University of Cambridge, UK, and King Mongkut University of Technology, Thailand. # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible # CPD Approval 2020-04-20 09:00:00 UTC 2020-08-16 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesinformaticsHDRUK

  • Systems Medicine - Virtual Spring Seminar Series 2020

    29 April - 27 May 2020

    Elixir node event
    Systems Medicine - Virtual Spring Seminar Series 2020 https://tess.elixir-europe.org/events/systems-medicine-virtual-spring-seminar-series-2020 ELIXIR Slovenia will organize a **Virtual Spring Seminar Series 2020** where experts from all over the world will share their experiences with systems medicine. Systems medicine is a field that will enable the translation of recent technological and scientific advances into the clinical practice. With systems medicine we will boost our understanding of disease mechanisms and the efficacy of treatments. Ultimately, systems medicine will bring a more personalised approach to healthcare, which may radically change the interaction between patients, doctors and other healthcare professionals. New healthcare approaches are an urging need, even accelerated in the Covid-19 era. The webinars will be hosted by **Prof. Dr. Damjana Rozman, Faculty of Medicine, University of Ljubljana, Slovenia**. You can join the webinars on **Zoom** by [following this link](https://us02web.zoom.us/j/89751733107?pwd=REJ5ak1DUllyU2xvMHFpR2ZPNWhZdz09). **Programme:** **Wednesday, 29 April 2020, 16h – 17h CEST** Prof. Dr. Sona Vasudevan, Georgetown University, Washington D.C, USA Title: Systems Medicine with Three-dimensional Insights **Thursday, 30 April 2020, 16h – 18h CEST** Henning Hermjakob, EMBL-EBI, Cambridge, UK Johannes Griss, Medical University of Vienna, Austria Title: Reactome Pathway Analysis and Visualization **Thursday, 7 May 2020, 16h – 17h CEST** Prof. Dr. Josep Roca, University of Barcelona, Spain Title: Digital Health for Enhanced Understanding and Management of Health Events: COPD and COVID-19 as Use Cases **Wednesday, 13 May 2020, 16h – 17h CEST** Prof. Dr. Anke-Hilse Maitland-van der Zee, Amsterdam UMC, the Netherlands Title: Precision Medicine in Respiratory Medicine, Translation into Clinical Practice **Wednesday, 20 May 2020, 16h – 17h CEST** Prof. Dr. Kristel van Steen, KU Leuven, Belgium Title: TBA **Wednesday, 27 May 2020, 16h – 17h CEST** TBA 2020-04-29 16:00:00 UTC 2020-05-27 17:00:00 UTC University of Ljubljana, Faculty of Medicine Systems medicine Personalised medicine University of Ljubljana, Faculty of Medicine ELIXIR Slovenia PhysiciansLife Science ResearchersbioinformaticiansClinicians workshops_and_courses [] systems medicinepersonalized medicineWebinareLearning

  • Galaxy-ELIXIR webinar series: FAIR data and Open Infrastructures to tackle the COVID-19 pandemic

    30 April - 28 May 2020

    Galaxy-ELIXIR webinar series: FAIR data and Open Infrastructures to tackle the COVID-19 pandemic https://tess.elixir-europe.org/events/galaxy-elixir-webinar-series-fair-data-and-open-infrastructures-to-tackle-the-covid-19-pandemic The Galaxy Community and ELIXIR organise a webinar series to demonstrate how open software and public research infrastructures can be used in analysing and publishing SARS-CoV2 data. In a series of five webinar sessions, experts from ELIXIR and the Galaxy community in the US and Europe will demonstrate how open access and open science are fundamental for fast and efficient response to public health crises. The focus will be on research reproducibility and transparency, using exclusively open source tools and the Galaxy platform. The goal of the series is to demonstrate publicly accessible infrastructure and workflows for SARS-CoV-2 data analyses. The webinar sessions will guide participants step-by-step through setting up and executing the SARS-CoV-2 data analyses workflows developed by the global Galaxy community. After completing the series, participants will be able to fully reproduce the workflows and conduct their own analyses of SARS-CoV-2 data. The webinar series will start on 30 April 2020 with the first introductory session. Subsequent sessions will take place in weekly intervals. More information about Galaxy analyses of COVID-19 data: covid19.galaxyproject.org Programme: Session 1: Introduction to Galaxy and the Galaxy workflows for SARS-CoV-2 data analysis 30 April 2020, 17.00-18.00 CEST (starts at 16.00 BST, 11.00 EDT, 8.00 PDT) The first session will introduce the Galaxy platform and other public research infrastructure to be used throughout the webinar series. It will also explain the motivation behind the Galaxy COVID-19 projects and explain the benefits of open reproducible research and transparent and interoperable analytics. Speakers: Anton Nekrutenko, Professor of Biochemistry and Molecular Biology at Penn State University (USA) and co-founder of the Galaxy Project. Sergei Pond, Professor of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, US Frederik Coppens,  Head of Node of ELIXIR Belgium and Co-Lead of the ELIXIR Galaxy Community Björn Grüning, Technical Coordinator of ELIXIR Germany and Co-Lead of the ELIXIR Galaxy Community Register Session 2: Genomics/Variant Calling  7 May 2020, 17.00-18.00 CEST (starts at 16.00 BST, 11.00 EDT, 8.00 PDT) The second session will present the initial analysis of the SARS-CoV-2 genome, published on bioRxiv. It will guide the participants through accessing and collecting the available datasets, the genome assembly and the analysis of the  within-sample sequence variants. It will also explain how to deploy on a Galaxy instance all the tools and workflows needed to reproduce the analysis. Speakers: Anton Nekrutenko, Professor of Biochemistry and Molecular Biology at Penn State University (USA) and co-founder of the Galaxy Project. Wolfgang Maier, PostDoc at the University of Freiburg and member of the European Galaxy team Register Session 3: Cheminformatics: Screening of the main protease 14 May 2020, 17.00-18.00 CEST (starts at 16.00 BST, 11.00 EDT, 8.00 PDT) This session will present the Galaxy workflow to identify candidate molecules for COVID-19 drug treatment, using molecular docking simulation of the SARS-CoV-2 main protease. These simulations are used to predict the binding positions of the candidate molecules in the protease binding site, score the quality of each pose, and compare the results with experimental crystallographic data. The computationally intensive workflow was executed through a distributed compute network available via the Galaxy Europe platform. The webinar will present methods and workflows for the identification of potential COVID-19 drug candidates. Special emphasis will be given to the complex methods that have been applied and that have consumed more than 25 years of CPU and GPU time. Speakers: Tim Dudgeon, Founder and CEO of Informatics Matters Simon Bray, PhD at the University of Freiburg and member of the European Galaxy team Register Session 4: Evolution of the Virus 20 May 2020, 17.00-18.00 CEST (starts at 16.00 BST, 11.00 EDT, 8.00 PDT) Speakers: Sergei Pond, Professor of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, US Register Session 5: Behind the scenes: Global Open Infrastructures at work  28 May 2020, 17.00-18.00 CEST (starts at 16.00 BST, 11.00 EDT, 8.00 PDT) This session will guide the participants how they can use the Galaxy compute capacities to run their own analysis. It will present the Pulsar network that connects data centres and High Performance Computing clusters to share their computation power in support of the Galaxy Europe users and provide examples of how to submit an analysis job from the user’s perspective. Speakers: TBC Register Acknowledgement The analyses have been performed using the Galaxy platform and open source tools from BioConda. Tools were run using XSEDE resources maintained by the Texas Advanced Computing Center (TACC ), Pittsburgh Supercomputing Center (PSC), and Indiana University in the U.S., de.NBI,  VSC   cloud resources and  IFB cluster resources on the European side, STFC-IRIS at the Diamond Light Source, and ARDC cloud resources in Australia.                                       2020-04-30 16:00:00 UTC 2020-05-28 17:00:00 UTC [] [] [] [] [] []

  • Galaxy-ELIXIR webinar series

    30 April - 28 May 2020

    Galaxy-ELIXIR webinar series https://tess.elixir-europe.org/events/galaxy-elixir-webinar-series The Galaxy-ELIXIR webinar series will demonstrate how open software and public research infrastructures can be used in analysing and publishing SARS-CoV2 data. In a series of five webinar sessions, experts from ELIXIR and the Galaxy community in the US and Europe will demonstrate how open access and open science are fundamental for fast and efficient response to public health crises. The focus will be on research reproducibility and transparency, using exclusively open source tools and the Galaxy platform. The goal of the series is to demonstrate publicly accessible infrastructure and workflows for SARS-CoV-2 data analyses. The webinar sessions will guide participants step-by-step through setting up and executing the SARS-CoV-2 data analyses workflows developed by the global Galaxy community. After completing the series, participants will be able to fully reproduce the workflows and conduct their own analyses of SARS-CoV-2 data. 2020-04-30 17:00:00 UTC 2020-05-28 18:00:00 UTC Galaxy Community and ELIXIR Computer science Cheminformatics Genomics Bioinformatics Computational chemistry Computational biology [] [] ResearchersbioinformaticiansBiologistsBiologists, Genomicists, Computer Scientistssoftware developers, bioinformaticiansComputational biologists 500 workshops_and_courses first_come_first_served []

  • WEBINAR SERIES: FAIR data and Open Infrastructures to tackle the COVID-19 pandemic

    1 - 29 May 2020

    WEBINAR SERIES: FAIR data and Open Infrastructures to tackle the COVID-19 pandemic https://tess.elixir-europe.org/events/webinar-series-fair-data-and-open-infrastructures-to-tackle-the-covid-19-pandemic 2020-05-01 01:00:00 UTC 2020-05-29 02:00:00 UTC Australian BioCommons Bioinformatics Australian Biocommons [] [] [] [] bioinformaticslife sciences

  • Data Carpentry - University of California Santa Barbara

    22 - 29 May 2020

    United States of America

    Data Carpentry - University of California Santa Barbara https://tess.elixir-europe.org/events/data-carpentry-university-of-california-santa-barbara Data Carpentry trains researchers in the core data skills for efficient, shareable, and reproducible research practices. We run accessible, inclusive training workshops; teach openly available, high-quality, domain-tailored lessons; and foster an active, inclusive, diverse instructor community that promotes and models reproducible research as a community norm. 2020-05-22 09:00:00 UTC 2020-05-29 00:00:00 UTC University of California Santa Barbara, United States of America University of California Santa Barbara United States of America University of California Santa Barbara [] [] workshops_and_courses [] []

  • [POSTPONED] 34th VI-HPS Tuning Workshop @ HLRS

    25 - 29 May 2020

    [POSTPONED] 34th VI-HPS Tuning Workshop @ HLRS https://tess.elixir-europe.org/events/35th-vi-hps-tuning-workshop-hlrs   (updated 20. May) Workshop has to be postponed again Access to HLRS systems is currently not possible due to a worldwide security incident affecting HPC centers in particular. Therefore, the 34th VI-HPS Tuning Workshop will NOT take place on 25.-29. May as planned and is postponed to a later time. (updated 29. April) This course is postponed to 25. - 29. May. It will be held online using zoom. (updated 16. March) Due to corona virus we are not able to guarantee that the course will go ahead as scheduled. We recommend to book cancellable train tickets and accomodations only! This workshop organized by VI-HPS for the German Prace Advanced Training Centre hosted by  HLRS will: give an overview of the VI-HPS programming tools suite explain the functionality of individual tools, and how to use them effectively offer hands-on experience and expert assistance using the tools For more information about the programme please visit the VI-HPS course site.   Prerequisites Familiarity with Linux and Linux editors is recommended. Programming experience in Fortran or C, some knowledge about parallel programming. For further information and registration please visit the HLRS course page. https://events.prace-ri.eu/event/1002/ 2020-05-25 07:00:00 UTC 2020-05-29 16:00:00 UTC [] [] [] workshops_and_courses [] []

  • 9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis

    26 - 29 May 2020

    České Budějovice, Czechia

    9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis https://tess.elixir-europe.org/events/7th-repeatexplorer-workshop-on-the-application-of-next-generation-sequencing-to-repetitive-dna-analysis The workshop will focus on theoretical and practical aspects of using next generation sequencing (NGS) data for analyzing repeat composition of plant genomes. Special emphasis will be given to repeat characterization methods implemented in the RepeatExplorer pipeline, including practical training in using the pipeline. The workshop should also serve as a platform for exchange of ideas and latest results with ample time dedicated to open discussions. Participants are encouraged to make short presentations of their research related to the workshop topic and/or bring their own data for practical training. The workshop is organized by the Laboratory of Molecular Cytogenetics of the Biology Centre AS CR. It will take place at the Academy of Sciences / University campus in Ceske Budejovice, Czech Republic. The meeting programme will include theoretical lectures and research reports combined with hands-on training (no programming skills required). Registration if open till 5th May. In case of any questions or comments please contact Jiri Macas. 2020-05-26 09:00:00 UTC 2020-05-29 00:00:00 UTC Institute of Plant Molecular Biology, České Budějovice, Czech Republic Branišovská 1160/31, 31, Branišovská, České Budějovice, Czechia Branišovská 1160/31, 31, Branišovská České Budějovice České Budějovice Czechia [] Jiri Macas ELIXIR: The Czech Republic Node PhD StudentspostdocsResearchers workshops_and_courses first_come_first_served []

  • 9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis - CANCELLED

    26 - 29 May 2020

    České Budějovice, Czechia

    9th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis - CANCELLED https://tess.elixir-europe.org/events/repeatexplorer-workshop The workshop will focus on theoretical and practical aspects of using next generation sequencing (NGS) data for analyzing repeat composition of plant genomes. Special emphasis will be given to repeat characterization methods implemented in the RepeatExplorer pipeline, including practical training in using the pipeline. The workshop should also serve as a platform for exchange of ideas and latest results with ample time dedicated to open discussions. Participants are encouraged to make short presentations of their research related to the workshop topic and/or bring their own data for practical training. The workshop is organized by the Laboratory of Molecular Cytogenetics of the Biology Centre AS CR. It will take place at the Academy of Sciences / University campus in Ceske Budejovice, Czech Republic. The meeting programme will include theoretical lectures and research reports combined with hands-on training (no programming skills required). In case of any questions or comments please contact Jiri Macas. 2020-05-26 09:00:00 UTC 2020-05-29 00:00:00 UTC Institute of Plant Molecular Biology building at the Academy of Sciences and University campus in České Budějovice Branišovská 1160/31, 31, Branišovská, České Budějovice, Czechia Branišovská 1160/31, 31, Branišovská České Budějovice České Budějovice Czechia [] Jiri Macas [] Life Science Researchersbioinformaticians workshops_and_courses first_come_first_served []

  • [ONLINE] Scientific computing in R @ SNIC

    27 May 2020

    [ONLINE] Scientific computing in R @ SNIC https://tess.elixir-europe.org/events/online-course-scientific-computing-in-r This one-day, online course will help users of R get started in High Performance Computing (HPC).  In the course, you will learn how to improve your code so that it could run more efficiently on a Desktop and also in an HPC environment. We will use ML models as one of the examples to show how to run more efficiently at an HPC cluster like HPC2N's Kebnekaise cluster. Part of the course will be done on your own computer and part will be done on HPC2N's cluster Kebnekaise. Thus, you will need accounts at SUPR/HPC2N in order to participate in the hands-ons. If you do not have such accounts, you will be contacted about creating them. More information, schedule, and registration can be found on the course webpage at HPC2N, Umeå University. https://events.prace-ri.eu/event/1024/ 2020-05-27 06:00:00 UTC 2020-05-27 15:00:00 UTC [] [] [] workshops_and_courses [] []

  • [ONLINE] Introduction to MPI @ SNIC

    27 May 2020

    [ONLINE] Introduction to MPI @ SNIC https://tess.elixir-europe.org/events/online-course-introduction-to-mpi Message Passing is presently the most widely deployed programming model in massively parallel high performance computing. Message passing is suitable for programming a wide range of current computer architectures, ranging from multi-core desktop equipment to the fastest HPC systems in the world, offering several hundred thousand processing elements. Description This online course will teach you how to write parallel programs using MPI. The course will be delivered by PDC staff. The course is at beginners level and assumes no prior experience in parallel computing. The concepts behind message passing and distributed memory computing will be introduced and the syntax of the key MPI calls will be explained. The course will include point-to-point communications, non-blocking communication and collective communications calls.  Presentations and type-along sessions will be interspersed with practical exercises where participants get experience in writing MPI programs and gain an understanding different parallelisation strategies. Code examples and exercises will be available in C, Fortran and Python. At the end of the course, participants should be able to write their own MPI programs at a basic level. The teaching language for the course will be English. Prerequisites Participants can choose between setting up an MPI environment on their own computers or using PDC clusters if they already have a PDC account. Installation instructions will be sent out to registered participants. Participants should be able to write programs in either C, Fortran or Python. Agenda 08:30    0. (Optional) Software installation help 09:00    1. Introduction to Parallel Computing 09:45    2. Serial and Parallel Regions 10:05    3. MPI_Send and MPI_Recv 10:30    4. Coffee Break 10:50    5. Parallel Paradigms and Parallel Algorithms 11:10    6. Non-blocking Communication 11:40    7. Collective Operations 12:10    8. Lunch Break 13:10    9. Serial to Parallel 14:10    10. Tips and Best Practices 14:30    11. Discussion and independent work 15:00    Finish Course material The course material can be found at https://pdc-support.github.io/introduction-to-mpi.  Contact For more information, contact PDC Support: support@pdc.kth.se.   https://events.prace-ri.eu/event/1023/ 2020-05-27 07:00:00 UTC 2020-05-27 13:00:00 UTC [] [] [] workshops_and_courses [] []

  • Analyse Traitement bioinformatique et analyse différentielle de données d'expression RNA-seq sous Galaxy - POSTPONED

    27 - 30 May 2020

    Analyse Traitement bioinformatique et analyse différentielle de données d'expression RNA-seq sous Galaxy - POSTPONED https://tess.elixir-europe.org/events/analyse-traitement-bioinformatique-et-analyse-differentielle-de-donnees-d-expression-rna-seq-sous-galaxy 2020-05-27 09:00:00 UTC 2020-05-30 00:00:00 UTC [] Véronique Martin [] [] [] [] []

  • Data Carpentry - Curtin University

    27 - 28 May 2020

    Australia

    Data Carpentry - Curtin University https://tess.elixir-europe.org/events/data-carpentry-curtin-university Data Carpentry trains researchers in the core data skills for efficient, shareable, and reproducible research practices. We run accessible, inclusive training workshops; teach openly available, high-quality, domain-tailored lessons; and foster an active, inclusive, diverse instructor community that promotes and models reproducible research as a community norm. 2020-05-27 09:00:00 UTC 2020-05-28 00:00:00 UTC Curtin University, Australia Curtin University Australia Curtin University [] [] workshops_and_courses [] []

  • Advanced topics in single-cell transcriptomics - streamed

    27 - 29 May 2020

    Streamed from Basel, Switzerland

    Elixir node event
    Advanced topics in single-cell transcriptomics - streamed https://tess.elixir-europe.org/events/advanced-topics-in-single-cell-transcriptomics This course is now full with a waiting list. Due to the COVID-19 situation, this course will be streamed only for the registered participants. 2020-05-27 09:00:00 UTC 2020-05-29 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • PDBe Graph Database: A Neo4J-driven integrative knowledge graph for structural data

    27 May 2020

    Elixir node event
    PDBe Graph Database: A Neo4J-driven integrative knowledge graph for structural data https://tess.elixir-europe.org/events/pdbe-graph-database-a-neo4j-driven-integrative-knowledge-graph-for-structural-data This webinar will introduce the concepts of a graph database and describe how we used a graph-approach for integrating the structural data of the Protein Data Bank. 2020-05-27 15:30:00 UTC 2020-05-27 15:30:00 UTC [] Ajay Mishra [] [] [] [] HDRUK

  • Basic statistics in R, Leuven - online

    28 May - 18 June 2020

    Zwijnaarde, Belgium

    Elixir node event
    Basic statistics in R, Leuven - online https://tess.elixir-europe.org/events/basic-statistics-in-r-leuven-91de71fa-c67c-49e8-b2b6-fcce11a5f551 Get an idea of what R and Rstudio is Use R to handle data: creating, reading, reformatting and writing data Use R to create graphics Use basic statistical techniques in R : normality tests, t-tests, wilcoxon tests, chi square tests, correlations, survival analysis... Write and use R scripts 2020-05-28 09:00:00 UTC 2020-06-18 00:00:00 UTC VIB Bioinformatics Core Bio-Accelerator Meeting Center Ghent, Zwijnaarde, Belgium Bio-Accelerator Meeting Center Ghent Zwijnaarde Belgium 9052 [] [] [] [] [] []

  • Galaxy Deployment

    28 - 29 May 2020

    Galaxy Deployment https://tess.elixir-europe.org/events/galaxy-deployment 2020-05-28 09:00:00 UTC 2020-05-29 00:00:00 UTC [] TBD [] [] [] [] []

  • Open Targets at American University in Cairo

    28 May 2020

    United Kingdom

    Open Targets at American University in Cairo https://tess.elixir-europe.org/events/open-targets-at-its-translational-data-academy-sanofi In this webinar, we introduce the Open Targets consortium, its underlying projects and its bioinformatics tools, namely Open Targets Platform and Open Targets Genetics, comprehensive and robust data integration resources for access and visualisation of biological data in drug target identification and discovery. 2020-05-28 09:00:00 UTC 2020-05-28 00:00:00 UTC Hinxton, United Kingdom Hinxton United Kingdom [] [] [] workshops_and_courses [] Open Targets

  • ELIXIR Bioinformatics Industry Forum: Open source Software in the Life Sciences

    28 May 2020

    ELIXIR Bioinformatics Industry Forum: Open source Software in the Life Sciences https://tess.elixir-europe.org/events/elixir-bioinformatics-industry-forum-open-source-software-in-the-life-sciences PROGRAMME: 1. Introduction to the ELIXIR tools platformand development of software FAIR metrics 2. How We Are Supporting Essential Open Source Scientific Software: CZI’s EOSS Program The majority of open source software for science is undervalued and lacks funding for maintenance, growth, development, and community engagement—especially after the initial phase when it’s linked to original research. At the Chan Zuckerberg Initiative we aim to support the people that work on this software to ensure long-term utility and value. The Essential Open Source Software for Science program supports domain-specific and foundational tools essential to conducting biomedical research. We will cover the current and future status of the program and our plans for community building and support beyond funding.    2020-05-28 16:00:00 UTC 2020-05-28 17:00:00 UTC [] [] [] [] [] []

  • Data Science in Python (ONLINE LIVE TRAINING)

    1 - 2 June 2020

    Cambridge, United Kingdom

    Elixir node event
    Data Science in Python (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/data-science-in-python-online-live-training PLEASE NOTE that until further notice, due to the evolving situation with Coronavirus no courses will be offered as classroom based at the Training Facility. The Bioinformatics Team be teaching the course live online, with tutors available to help you work through the course material on a personal copy of the course environment. We will be aiming to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. 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. 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=3414283&course-title=Data%20Science%20in%20Python).'' 2020-06-01 08:30:00 UTC 2020-06-02 15:30:00 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 Manipulation and Visualisation

    1 June 2020

    United Kingdom

    Data Manipulation and Visualisation https://tess.elixir-europe.org/events/data-manipulation-and-visualisation-588646eb-6b41-45a6-96da-c00750c9f120 R is a highly-regarded, free, software environment for statistical analysis, with many useful features that promote and facilitate reproducible research. In this course, we give an introduction to the R environment and explain how it can be used to import, manipulate and analyse tabular data. After the course you should feel confident to start exploring your own dataset using the materials and references provided. 2020-06-01 08:30:00 UTC 2020-06-01 16:00:00 UTC Bartolome House, Seminar Room EG03, United Kingdom Bartolome House, Seminar Room EG03 United Kingdom S10 2HQ [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []

  • Data Carpentry - SADiLaR (online)

    1 - 5 June 2020

    South Africa

    Data Carpentry - SADiLaR (online) https://tess.elixir-europe.org/events/data-carpentry-sadilar Data Carpentry trains researchers in the core data skills for efficient, shareable, and reproducible research practices. We run accessible, inclusive training workshops; teach openly available, high-quality, domain-tailored lessons; and foster an active, inclusive, diverse instructor community that promotes and models reproducible research as a community norm. 2020-06-01 09:00:00 UTC 2020-06-05 00:00:00 UTC SADiLaR (online), South Africa SADiLaR (online) South Africa South African Centre for Digital Language Resources (SADiLaR) [] [] workshops_and_courses [] []

  • Starting single cell RNA-seq analysis (Virtual)

    1 - 5 June 2020

    Cambridge, United Kingdom

    Elixir node event
    Starting single cell RNA-seq analysis (Virtual) https://tess.elixir-europe.org/events/starting-single-cell-rna-seq-analysis-virtual The delivery of this course has changed from face-to-face to virtual. This course trains participants to analyse single cell RNA-seq data utilising Galaxy pipelines, an online open-access resource for the computer-phobic. 2020-06-01 10:15:00 UTC 2020-06-05 13:30:00 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

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