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  • Data Visualization using Tableau | How to visualize data in Tableau | Intellipaat

    26 July - 31 October 2020

    Data Visualization using Tableau | How to visualize data in Tableau | Intellipaat https://tess.elixir-europe.org/events/data-visualization-using-tableau-how-to-visualize-data-in-tableau-intellipaat In this data visualization using tableau video you will learn fundamentals of data visualization, essential design principles in tableau, visual analytics in tableau and hands on - creating dashboard using tableau in detail. Link: https://www.youtube.com/watch?v=8qQRD0Z0CH4 2020-07-26 16:53:00 UTC 2020-10-31 23:00:00 UTC Intellipaat [] [] [] workshops_and_courses [] []
  • What is Genetic Counselling?

    3 August - 25 October 2020

    What is Genetic Counselling? https://tess.elixir-europe.org/events/what-is-genetic-counselling # Overview * **Duration:** 6 weeks live, 2 hours per week * **Free** * **Certificate of achievement** available on satisfactory completion * **Start Date:** The course is run ‘live’ for 6 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? Who are genetic counsellors? Who has genetic counselling and what does a genetic counsellor do? On this course, you will find the answers to these questions whilst learning about the role of genetic counselling in healthcare and the genomic era. You will discover why people seek genetic counselling and how it compares in different contexts and countries. You will explore the main skills and knowledge needed of a genetic counsellor, as well as their key responsibilities to patients. You will also discuss the ethical issues of genetic counselling, and its varied opportunities and challenges for the future. ### Who is the course for? This course is designed for healthcare professionals, clinicians, biomedical research scientists, and anyone curious about genetic counselling. Although not required, a basic knowledge of genetics, genetic testing technologies, and inheritance patterns would help support your learning on this course. ### What do people say about this course? _"What a great course. Perfect introduction to genetic counseling. This has given me a very real insight into the work that is carried out prior to my role in a genetic testing laboratory. Also overwhelming to think of the hours that go into the counselling sessions, ensuring patients are prepared, informed and able to make their own decisions." - Previous Participant_ _"Thank you very much for such an informative, enjoyable and though-provoking course. I have learnt a lot during these six weeks and I definitely know more now than I did prior to starting! I am glad to say that this has increased my interest in Genetic counselling as a profession and am very likely going to pursue it as a career." - Previous Participant_ _"Thank you Anna and Jonathan for a very interesting course, I have enjoyed the role play as it allowed me to be in the GC and clients shoes, and discussing my thoughts/comments with my fellow learners, and learning about the difference in other countries that was shared. Kept me gripped learning something new." _- _Previous Participant_ _"It has been a great and interesting time in the last six weeks. Understanding the personal feelings/ views of patients (autonomy, empathy, patience, etc), professional ways of communication in GC, ethics of GC, with the professional know how of the Genetic Counsellors; the different contexts of Genetic Services in different countries,and also sharing the view of my co-learners, has been a great experience._ _These will greatly assist in the discharge of my duties to the the patients as I come across them whether at my duty post or elsewhere."_ - Previous Participant # Programme ### What topics will you cover? * Why people would see a genetic counsellor * Some of a genetic counsellor’s key tasks * A genetic counsellor’s key skills and knowledge: counselling skills, medical and scientific knowledge * Ethical issues in genetic counselling * What the future might hold for genetic counsellors ### What will you achieve? By the end of the course, you'll be able to... * Identify why people have genetic counselling and the different contexts in which people receive genetic counselling * Describe the different skills and knowledges needed by genetic counsellors * Compare genetic counselling in different contexts and different countries * Reflect on some ethical issues that arise in genetic counselling * Discuss the role of genetic counselling in healthcare as we enter the ‘genomic era'. ### What software or tools do you need? No specific software, hardware or other resources are required to complete the course. # Educators ## Lead Educators ### Anna Middleton I am the Chair of the Association of Genetic Nurses and Counsellors in the UK and ROI (2018/19) and Head of Society and Ethics Research at the Wellcome Genome Campus, Connecting Science, Cambridge, UK ### Jonathan Roberts I am a pre-registration genetic counsellor at Addenbrooke’s Hospital, Cambridge. I am also a Staff Scientists at the Wellcome Genome Campus. I conduct my research within the Society and Ethics Research group. # 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 2020-08-03 09:00:00 UTC 2020-10-25 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] geneticcounsellingHDRUK
  • Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance

    31 August 2020 - 3 January 2021

    Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance https://tess.elixir-europe.org/events/bacterial-genomes-disease-outbreaks-and-antimicrobial-resistance-2aa0df3a-e74c-4f5c-acc3-8c2ee0847f71 # 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 2020-08-31 09:00:00 UTC 2021-01-03 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesAMRHDRUK
  • Metabolomics: Understanding Metabolism in the 21st Century

    14 September - 4 December 2020

    Elixir node event
    Metabolomics: Understanding Metabolism in the 21st Century https://tess.elixir-europe.org/events/metabolomics-understanding-metabolism-in-the-21st-century-9e853a8f-6a6f-40e7-9854-021aa2c07370 Metabolomics is 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 genome and its interaction with the environment. Metabolomics has a wide application area across the medical and biological sciences. The course provides an introduction to metabolomics, describes the tools and techniques we use to study the metabolome and explains why we want to study it. By the end of the course you will understand how metabolomics can revolutionise our understanding of metabolism. This course is designed as a 4-week course and the Educators will support discussions and learning in weeks 1 to 4 responding to questions and comments. The course will remain open for 12 weeks in total; if you join the course after week 5 we encourage you to read posts / comments on the platform to aid your learning. The Educators will answer comments and questions at a lower frequency in weeks 5 to 12. 2020-09-14 09:00:00 UTC 2020-12-04 23:59:00 UTC Birmingham Metabolomics Training Centre Metabolomics University of Birmingham bmtc@contacts.bham.ac.uk [] ScientistsPhD studentsMaster studentsUndergraduate students workshops_and_courses [] Metabolomics
  • Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2020

    21 - 23 September 2020

    Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2020 https://tess.elixir-europe.org/events/hdhd Educators: Axel von Kamp, Steffen Klamt, Sven Thiele (MPI Magdeburg), Frank T. Bergmann, Ursula Kummer (University of Heidelberg), Wolfgang Müller, Maja Rey, Andreas Weidemann, Ulrike Wittig (HITS) (de.NBI-SysBio) Date: 21. - 23 September 2020 Location: MPI Magdeburg Sandtorstrasse 1 39106 Magdeburg or online Contents: Key concepts of stoichiometric and kinetic modeling of biochemical networks: - stoichiometric matrix and stoichiometric networks - steady state flux distributions - principles of constraint-based modeling - metabolic flux analysis and flux optimization (flux balance analysis) - metabolic pathway analysis with elementary flux modes - metabolic network design via minimal cut sets - simulation of dynamic (kinetic) models - sensitivity analysis - carrying out parameter estimation tasks - model exchange using SBML Data and model management: - manual/programmatic access to reaction kinetics data from SABIO-RK - storage and exchange of data and models using FAIRDOMHub/SEEK - modeling specific functionalities in FAIRDOMHub/SEEK Learning goals: During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day SABIO-RK is used as a resource for kinetic data and FAIRDOMHub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists. The second day introduces principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The third day continues with kinetic modeling techniques which will be illustrated and exercised with COPASI The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks. Prerequisites: Some knowledge of mathematical modeling will be advantageous. The participants should bring their own laptop with MATLAB installed (if you do not have MATLAB please let us know during registration). Download and preinstallation of COPASI and CellNetAnalyzer is recommended but not mandatory. Keywords: CellNetAnalyzer (CNA), COPASI, SBML, FAIR, modeling, kinetic data access, database, data and model management Tools: CellNetAnalyzer, COPASI, Matlab, SABIO-RK, FAIRDOMHub/SEEK 2020-09-21 09:00:00 UTC 2020-09-23 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • Computational genomics course for hands-on data analysis 2020

    23 - 25 September 2020

    Computational genomics course for hands-on data analysis 2020 https://tess.elixir-europe.org/events/computational-genomics-course-for-hands-on-data-analysis-2020 Educators: Altuna Alkalin, Verdan Franke, Bora Uyar (RBC/deNBI-epi Scientists from Berlin) Date: 23-25 September 2020 Location: Online Contents: The general aim of the course is to equip participants with practical and technical knowledge to analyze single cell RNA-seq data. With this aim in mind, we will go through unsupervised machine learning methods to analyze high-dimensional data sets, and move on to statistical methods developed to analyze bulk RNA-seq. Lastly, we will introduce analysis techniques used for single cell RNA-seq. There will be theoretical lectures followed by practical sessions where students directly apply what they have learned. The programming will be mainly done in R. Day 1: Intro to machine learning & data visualization for genomics Day 2: Bulk RNA-seq analysis Day 3: Single cell RNA-seq analysis Learning goals: The course will be beneficial for first year computational biology PhD students, and experimental biologists and medical scientists who want to begin data analysis or are seeking a better understanding of computational genomics and analysis of popular sequencing methods.r Prerequisites: Some statistics and R programming experience will be good to keep up with the course. Practicals will be done in R. Keywords: Computational genomics, RNA-seq, Machine learing, Tools: R/Bioconductor 2020-09-23 09:00:00 UTC 2020-09-25 17:00:00 UTC de.NBI Berlin, Berlin, Germany Berlin Berlin Germany [] [] [] workshops_and_courses [] []
  • International Summer School on Rare Disease Registries and FAIRification of Data

    28 September - 2 October 2020

    International Summer School on Rare Disease Registries and FAIRification of Data https://tess.elixir-europe.org/events/international-summer-school-on-rare-disease-registries-and-fairification-of-data-810a68d3-7fff-4daa-86bc-f2e6ea7a4603 Registries are key resources in order to increase timely and accurate diagnosis, improve patients management, tailor treatments, facilitate clinical trials, support healthcare planning and speed up research. This course is composed of two training modules: - during the first three days module *28-30 September 2020*, participants will learn (a) what resources are needed for the establishment/maintenance of a high quality registry (b) the features of successful strategies to ensure (i) long-time sustainability of the registry, (ii) quality, (iii) legal and ethical issues in compliance with the EU General Data Protection Regulation - during the second two days module “FAIRification of data”, *1-2 October 2020*, participants will deepen their knowledge on the single steps of the FAIRification of data and will discover the potential of FAIR registries. In this part a time slot will be allocated to discuss FAIR data management and FAIR project planning. 2020-09-28 14:00:00 UTC 2020-10-02 17:30:00 UTC European Joint Programme on Rare Diseases (EJP-RD), Istituto Superiore di Sanità of Italy Rare diseases Istituto Superiore di Sanità claudio.carta@iss.it [] Cliniciansmedical specialistsregistry curatorsdatabase managershealthcare professionals rare disease patients representatives 30 workshops_and_courses first_come_first_servedregistration_of_interest Rare Diseasesdata FAIRnessRegistryethical issues
  • UK Conference of Bioinformatics and Computational Biology 2020

    29 - 30 September 2020

    UK Conference of Bioinformatics and Computational Biology 2020 https://tess.elixir-europe.org/events/uk-conference-of-bioinformatics-and-computational-biology-2020 The UK-CBCB conference is designed to bring together biologists, bioinformaticians, computer scientists, software engineers and data scientists across the life sciences to share innovations, applications and best practice in their fields. The conference will be applicable to bioinformatics researchers working on core services or in research teams as well as computer scientists or bioinformaticians developing tools or maintaining data resources. 2020-09-29 09:00:00 UTC 2020-09-30 17:00:00 UTC Earlham Institute Data management Bioinformatics Metabolomics Earlham Institute Training@earlham.ac.uk [] [] meetings_and_conferences registration_of_interest Bioinformaticslife sciencesMetabolomicsSingle Cell GenomicsMicrobial evolution
  • Bioinformatics for Lipidomics – Online Workshop

    1 October 2020

    Bioinformatics for Lipidomics – Online Workshop https://tess.elixir-europe.org/events/bioinformatics-for-lipidomics-online-workshop Educators: Jacobo Miranda Ackerman, Fadi Al Machot, Nils Hoffmann (BioInfra.Prot / LIFS) Date: October 1st, 2020 Deadline for Workshop Registration: September 25th, 2020 Location: Online, virtual workshop as part of the joint European Lipidomics Meeting & Lipidomics Forum 2020. Contents: In the first part of the course, we will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. In the second part of the course, we will apply PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets. The third part of this course will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will inspect, check and normalize the data as well as calculate absolute quantities using internal class-specific standards with lxPostman. We will then perform a qualitative comparison of the lipidomes using the LUX Score lipidome homology. 09:00 – 09:30 Welcome and Introduction 09:30 – 12:00 Targeted Lipidomics with LipidCreator and Skyline 12:00 – 13:00 Break 13:00 – 15:00 Shotgun Lipidomics with PeakStrainer and LipidXplorer 15:00 – 17:00 Downstream processing with lxPostman and lipidome comparison with LUX Score Learning goals: Participants will be able to understand and explain the shotgun MS and targeted LC-MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline. Prerequisites: Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based and desktop applications. Please note that you may need to install software on your computer to fully participate in all exercises which may require the proper rights. The workshop will be a mix of small lecture segments and hands-on exercises. The trainers will be available for questions and assistance during the workshop. We will use Zoom to host the workshop. To participate, please ensure that the Zoom client software is installed on your computer. Keywords: Lipidomics, Shotgun, Targeted, LC-MS Tools: PeakStrainer and LipidXplorer, LipidCreator, Skyline, lxPostman, LUX Score 2020-10-01 09:00:00 UTC 2020-10-01 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • Advanced Python for Biologists 2020

    5 - 16 October 2020

    Advanced Python for Biologists 2020 https://tess.elixir-europe.org/events/advanced-python-for-biologists-2020 Python is a dynamic, readable language that is a popular platform for all types of bioinformatics work, from simple one-off scripts to large, complex software projects. This workshop is aimed at people who already have a basic knowledge of Python and are interested in using the language to tackle larger problems. In it, we will look in detail at the parts of the language which are particularly useful in scientific programming, and at the tools Python offers for making development faster and easier. The workshop will use examples and exercises drawn from various aspects of bioinformatics work. After completing the workshop, students should be in a position to; (1) take advantage of the advanced language features in their own programs, and; (2) use appropriate tools when developing software programs. This event will be delivered virtually, in the following format: The programme will be delivered over ten days, from Monday 5 - Friday 16 October 2020, weekdays only. On each day there will be 3.5 hours of live input (via Zoom) from the trainer (9:00-12:30 UK/GMT+1, including breaks). Morning sessions will comprise: Lectures/input Practical exercises, with the trainer on hand to assist and offer 1-1 support. Slack will be used to share important updates and for asking questions. Lectures/input will be recorded and made available to participants as soon as possible that day for anyone who needs to catch up. 2020-10-05 09:00:00 UTC 2020-10-16 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, United Kingdom Earlham Institute (EI), Colney Lane Norfolk United Kingdom Earlham Institute training@earlham.ac.uk [] [] [] [] PythonPython for Biologists
  • Train-the-Trainer

    6 - 9 October 2020

    Train-the-Trainer https://tess.elixir-europe.org/events/train-the-trainer-a201e364-a145-425c-a820-bf1c53f37461 Importants dates: Course ONLINE sessions: October 6th-9th, 14:00-17:30 CET. Deadline for applications: Sept 28th Decisions communicated intil: October2nd Our Train-the-Trainer courses are for any scientists: - with little or no experience in training - who want to become an instructor or a better one - who believe that their professional development will encompass delivering training proficiently Instructors: Allegra Via, ELIXIR-IT, Patricia Palagi, ELIXIR-CH and Pedro Fernandes, ELIXIR-PT This course will cover four main topics: Learning principles and how they apply to education and training; Teaching techniques that enhance learner engagement and participation; Design of lessons, course and materials; Assessment and feedback in training and teaching. Examples and discussions will also focus on the challenges presented by academic teaching. The four ONLINE sessions will have a maximum duration of 3.5 hours. Participants will be asked to prepare a small amount of homework, OFFLINE between the sessions. No partcipation fee will be charged. A maximum of 12 selected candidates will be accepted. To apply: write an e-mail to bicourses”at”igc.gulbenkian.pt explaining why you would like to attend, mentioning your personal expectations and background knowledge about delivering training, if any. Please provide contact data, specifically full name, affiliation, address and telephone number. 2020-10-06 14:00:00 UTC 2020-10-09 17:30:00 UTC Pedro L Fernandes IGC - Instituto Gulbenkian de CiênciaSIB Swiss Institute of BioinformaticsIBB pfern@igc.gulbenkian.pt ELIXIR [] 12 workshops_and_courses registration_of_interest online learningpedagogyCourse designCourse development
  • 3rd de.NBI Cloud Usermeeting

    8 - 14 October 2020

    3rd de.NBI Cloud Usermeeting https://tess.elixir-europe.org/events/3rd-de-nbi-cloud-usermeeting 3rd de.NBI Cloud Usermeeting Online Educators: de.NBI cloud group including Peter Belmann, Daniel Hübschmann, Peter Ebert, Martin Zurowietz, Kay Schallert, Sven Olaf Twardziok, Jan Krüger, Maximillian Hanussek, Martin Braun, Marius Dieckmann, Björn Grüning etc. Date: 8.10.2020 – 14.10.2020 Location: Online Contents: We are pleased to announce the third de.NBI Cloud User Meeting. In comparison to preceding meetings, this year`s meeting will be organized as an online conference. Over five days users can watch talks of already experienced users and long running projects and thereby learn about best practices in cloud computing. Same as the last years we will try to cover topics for beginners such as virtualization but also topics for software engineers and administrators such as orchestration with Kubernetes. Participants will learn how to scale up their analysis to handle growing input data and how to use workflow managers such as Snakemake in a cloud environment. As every year we are also going to demonstrate the usage of bioinformatics software in the de.NBI Cloud using Docker images or Bioconda packages. Planned Courses: - Running Snakemake Workflows in the de.NBI Cloud - OpenStack Introduction - BioConda and BioContainers - Kubernetes Introduction - Deploying Web Services in the de.NBI Cloud - Extensible Cluster Setup in the Cloud with BibiGrid and Ansible - Using Terraform to define infrastructure as code Learning goals: Working with the de.NBI cloud Prerequisites: We welcome people from all background, no matter if you are new to the de.NBI Cloud or considering to submit a project application, to learn and network in our growing community. Keywords: de.NBI cloud Tools: de.NBI cloud Webpage: https://cloud.denbi.de/3rd-de-nbi-cloud-user-meeting/ 2020-10-08 09:00:00 UTC 2020-10-14 17:00:00 UTC de.NBI [] [] [] meetings_and_conferences [] []
  • Metabolomics Data Processing and Data Analysis

    12 October - 6 November 2020

    Elixir node event
    Metabolomics Data Processing and Data Analysis https://tess.elixir-europe.org/events/metabolomics-data-processing-and-data-analysis-3855a7d7-cf12-44e8-8d22-d6c252487ce0 This online course explores the tools and approaches that are used to process and analyse metabolomics data. You will investigate the challenges that are typically encountered in the analysis of metabolomics data, and provide solutions to overcome these problems. The materials in this course are delivered via the FutureLearn platform over a four week period, with an estimated learning time of four hours per week. Each week you will work through a number of steps to complete the learning material. A step may include a short video, an article, an exercise with step-by-step instructions, a test or a discussion to interact with your peer or the educators. All of the course material is uploaded to the FutureLearn platform so that you can complete the steps at a convenient time for you. We (the educators) support your learning via social discussions where you will be able post questions and comments to the team of educators and the other learners on the course throughout the 4 weeks. In the final week of the course there is a live question and answer session with the entire team of educators. You will be provided with information to join the question and answer session via the FutureLearn platform and you can post questions in advance. The question and answer session will be recorded and a video uploaded to the FutureLearn platform. If you do not have time to complete the course during the 4-week period you will retain access to the course material to revisit, as you are able. 2020-10-12 09:00:00 UTC 2020-11-06 23:59:00 UTC Birmingham Metabolomics Training Centre Bioinformatics Metabolomics University of Birmingham bmtc@contacts.bham.ac.uk [] ScientistsPhD studentsMaster students workshops_and_coursesmeetings_and_conferences [] MetabolomicsData processingData analysis
  • Bacterial Genomes: From DNA to Protein Function Using Bioinformatics

    12 October 2020 - 7 February 2021

    Bacterial Genomes: From DNA to Protein Function Using Bioinformatics https://tess.elixir-europe.org/events/bacterial-genomes-from-dna-to-protein-function-using-bioinformatics-e18aa62a-65f6-478d-ad25-61b757305166 # 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 2020-10-12 09:00:00 UTC 2021-02-07 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesinformaticsHDRUK
  • Online Course - A Practical Introduction to NGS Data Analysis

    14 - 16 October 2020

    Online Course - A Practical Introduction to NGS Data Analysis https://tess.elixir-europe.org/events/online-course-a-practical-introduction-to-ngs-data-analysis Advance your research. Understand NGS and analyze sequenced data yourself. In a nutshell - Learn the essential computing skills for NGS bioinformatics - Understand NGS technology, algorithms and data formats - Use bioinformatics tools for handling sequencing data - Perform first downstream analyses for studying genetic variation The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. The participants will be trained on understanding their own NGS data, finding potential problems/errors therein and finally perform their first downstream analysis (variant calling). In the course we will use a real-life NGS dataset from the current market leader illumina. All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this fast evolving research topic. The online course will make use of a web conferencing system. Hands-on NGS analysis will be performed in an interactive browser-based platform. Before the course, you will get a printed manuscript and a USB key by mail. 2020-10-14 09:00:00 UTC 2020-10-16 17:00:00 UTC ecSeq Bioinformatics GmbH Sequence analysis Sequencing Bioinformatics [] ecSeq Bioinformatics GmbH Sternwartenstr. 29 D-04103 Leipzig Germany Email: events@ecSeq.com [] BiologistsBiologists, Genomicists, Computer ScientistsMolecular BiologistsbioinformaticiansPathologistsPhD Studentspost-docs 15 workshops_and_courses first_come_first_served NGSNGS bioinformaticsDNA-seqVariant calling
  • Computing Skills for Reproducible Research: Software Carpentry Course 2020

    19 - 23 October 2020

    Computing Skills for Reproducible Research: Software Carpentry Course 2020 https://tess.elixir-europe.org/events/computing-skills-for-reproducible-research-software-carpentry-course-2020 Educators: Renato Alves (HD-HuB) Date: 19-10-2020 - 23-10-2020 09:00-18:00 Location: Online Contents: Computation is an integral part of today's research as data has grown too large or too complex to be analysed by hand. An ever-growing fraction of science is performed computationally and many wet-lab biologists spend part of their time on the computer. Many scientists struggle with this aspect of research as they have not been properly trained in the necessary set of skills. The result is that too much time is spent using inefficient tools when progress could be faster. This course provides training in several key tools, with a focus on good development practices that encourage efficient and reproducible research computing. Topics covered include: Introduction to Python scripting Introduction to the Unix shell and usage of cluster resources Version control with Git and Github Analysis pipeline management Scientific Python & working with biological data Literate programming with Jupyter notebooks Learning goals: This course aims to teach software writing skills and best practices to researchers in biology who wish to analyse data, and to introduce a toolset that can help them in their work. The goal is to enable them to be more productive and to make their science better and more reproducible. Prerequisites: This is a course for researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will be familiar with some command line/programmatic computer usage, will want to become more confident using these tools efficiently and reproducibly. A target student will have written a for loop in some language before, but will not know what git is (or at least not be very comfortable using git). Keywords: Programming; Command Line; Version Control; Bioinformatics; Data Analysis; Cluster Computing Tools: Python; Bash; Unix/Linux; Git; GitHub; SnakeMake; Biopython; Pandas; Numpy; SciPy; Matplotlib 2020-10-19 09:00:00 UTC 2020-10-23 17:00:00 UTC de.NBI Heidelberg, Heidelberg, Germany Heidelberg Heidelberg Karlsruhe Germany [] [] [] workshops_and_courses [] []
  • ELIXIR Norway All Hands Meeting 2020

    21 - 23 October 2020

    Elixir node event
    ELIXIR Norway All Hands Meeting 2020 https://tess.elixir-europe.org/events/elixir-norway-all-hands-meeting-2020 Yearly gathering of all hands involved in ELIXIR Norway, including our SAC and stakeholder panel. This year's meeting will be all digital. Registration here by 2 October: https://forms.gle/hprhrTnthstT46E37 2020-10-21 09:00:00 UTC 2020-10-23 16:00:00 UTC ELIXIR Norway Digital, Trondheim, Norway Digital Trondheim Norway [] christine.stansberg@uib.no [] [] meetings_and_conferences [] []
  • 5th Differential analysis of quantitative proteomics data using R

    2 November 2020

    5th Differential analysis of quantitative proteomics data using R https://tess.elixir-europe.org/events/5th-differential-analysis-of-quantitative-proteomics-data-using-r Educators: Michael Turewicz (bioinformatician) and Karin Schork (biostatistician) (BioInfra.Prot) Date: Monday, 2nd Nov 2020 Location: Online Contents: This course will impart knowledge about how to conduct a differential analysis of high-throughput quantitative proteomics data using R. As we start with a basic introduction to the popular statistical programming language, no prior knowledge on R is required. The statistical background on utilized methods is explained in order to enable the participants to assess their own as well as published workflows critically. In this regard the course will touch upon • statistical inference: hypotheses, type I and II error • location tests (t-test) • multiple testing Learning goals: • Independent usage of basic R functions including - data import and export - basic plots - statistical tests • Deeper understanding of statistical methods applied in differential analyses Prerequisites: • Basic understanding of high-dimensional data sets from quantitative proteomics or other life sciences; • No prior knowledge on R required • Computer with stable internet connection, headset and camera Keywords: R; high-throughput data; omics; proteomics; differential analysis Tools: download and more information on R here: https://cran.r-project.org/ We recommend using an editor such as RStudio, see www.rstudio.com 2020-11-02 09:00:00 UTC 2020-11-02 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • 2nd Advanced analysis of quantitative proteomics data using R

    9 November 2020

    2nd Advanced analysis of quantitative proteomics data using R https://tess.elixir-europe.org/events/2nd-advanced-analysis-of-quantitative-proteomics-data-using-r Educators: Michael Turewicz (bioinformatician) and Karin Schork (biostatistician) (BioInfra.Prot) Date: Monday, 9th Nov 2020 Location: Online Contents: In this course you will learn about using R for the analysis of proteomics data. We will focus on data preprocessing methods and advanced methods for data analysis. In this regard the cpurse will touch upon: • data normalization • quality control, handling of missing values • clustering, heatmaps • ROC-curves Please be aware that basic knowledge of R and methods for differential analysis of proteomics data are taught in our course “Differential analysis of quantitative proteomics data” the previous day (Monday, 2nd Nov 2020, http://goo.gl/forms/mpKHnbT1Um) Learning goals: • Independent usage of R functions for - Data preprocessing - Plots and graphs - Statistical methods for data analysis - Use of additional R packages • Deeper understanding of statistical methods applied in differential analyses Prerequisites: • Basic understanding of high-dimensional data sets from quantitative proteomics or other life sciences; • Basic knowledge of R (e.g. data import, basic plots, t-test, for loop) and basic knowledge of differential analysis of proteomics data. Both can for example be gained from our course “Differential analysis of quantitative proteomics data” the previous day (Monday, 2nd Nov 2020, http://goo.gl/forms/mpKHnbT1Um). • Computer with stable internet connection, headset and camera Keywords: R; high-throughput data; omics; proteomics; data analysis, graphics, data preprocessing Tools: download and more information on R here: https://cran.r-project.org/ We recommend using an editor such as RStudio, see www.rstudio.com 2020-11-09 09:00:00 UTC 2020-11-09 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • de.NBI Crop Analysis Tool Suite (Part I) training course – Explore the barley genome

    16 November 2020

    de.NBI Crop Analysis Tool Suite (Part I) training course – Explore the barley genome https://tess.elixir-europe.org/events/de-nbi-crop-analysis-tool-suite-part-i-training-course-explore-the-barley-genome Educators: Uwe Scholz (GCBN), Sebastian Beier (GCBN) Date: 16th November 2020, 10:00 a.m. – 11:30 a.m. Location: Online Contents: Complex plant genomes impose high demands on analytical software and the knowledge of biologists to interpret these results. The service centre GCBN offers CATS (Crop Analysis Tool Suite), which provides various tools for sequence analysis. In this first of three courses the main focus is on the operation of the BLAST Server and the integration with BARLEX (Barley Genome Explorer). There will be two short presentations on the two topics and two online live demonstrations with examples. Together the whole training course will last about 90 minutes. Learning goals: The primary objective of this training course is to introduce tools for sequence analysis for crops (in particular barley). The theoretical basics as well as some examples will be shown by using online demonstrations, which will enable the participants to design and perform their own analyses. Prerequisites: The training course is designed for early career scientists such as PhD students and postdocs, but also for experienced scientists who want to learn more about the analysis and handling of sequence data for complex plant genomes like barley. Keywords: Sequence analysis, genomics, transcriptomics, annotation, Morex v2 assembly Tools: IPK WebBlast - https://webblast.ipk-gatersleben.de/barley_ibsc/ BARLEX - http://barlex.barleysequence.org/ 2020-11-16 10:00:00 UTC 2020-11-16 11:30:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • de.NBI – e!DAL-PGP training course – Sharing and Publishing Comprehensive Plant Research Data

    19 November 2020

    de.NBI – e!DAL-PGP training course – Sharing and Publishing Comprehensive Plant Research Data https://tess.elixir-europe.org/events/de-nbi-e-dal-pgp-training-course-sharing-and-publishing-comprehensive-plant-research-data Educator: Daniel Arend (GCBN) Date: 19th November 2020, 10:00 a.m. – 11:30 a.m. Location: Online Contents: In the context of a growing global demand for food and feed the need for improved crop yield and the identification of more efficient and better adapted crops to answer the world's growing population is an important driving force for high-throughput plant genotyping and phenotyping studies which comprise comprehensive and data-intense experiments. As formulated in current funding policies, research data should be published under consideration of the FAIR (findable, accessible, interoperable, and reusable) data principles. Contrarily, they remain frequently unpublished due to organizational reasons or missing infrastructures. Therefore, the reproducibility and the preservation of research data depend on the scientists or the journal to which they want to publish their results. The eDAL-PGP repository provide a powerful infrastructure to easily share and publish comprehensive and cross-domain plant research data. Learning goals: The major goal of this trainings course is to get a general understanding how to publish plant research data that do not fit into the scope of existing databases in a FAIR way by using the eDAL-PGP repository. Prerequisites: The training course is designed for early career scientists such as PhD students and postdocs, but also for experienced scientists who want to learn more about the analysis and handling of sequence data for complex plant genomes like barley. Keywords: FAIR research data, Digital Object Identifier, Research Data Publication, Genomics, Phenomics Tools: e!DAL-PGP - http://edal-pgp.ipk-gatersleben.de/ 2020-11-19 10:00:00 UTC 2020-11-19 11:30:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • de.NBI Crop Analysis Tool Suite (Part II) training course – Working with repetitive sequences

    20 November 2020

    de.NBI Crop Analysis Tool Suite (Part II) training course – Working with repetitive sequences https://tess.elixir-europe.org/events/de-nbi-crop-analysis-tool-suite-part-ii-training-course-working-with-repetitive-sequences Educator: Sebastian Beier (GCBN) Date: 20th November 2020, 10:00 a.m. – 11:30 a.m. Location: Online Contents: Complex plant genomes impose high demands on analytical software and the knowledge of biologists to interpret these results. The service centre GCBN offers CATS (Crop Analysis Tool Suite), which provides various tools for sequence analysis. In this second of three courses the main focus is on the operation of repeat analysis and masking with the tools Kmasker plants (mathematically defined repeats) and MISA-Web (microsatellites). There will be two short presentations on the two topics and two online live demonstrations with examples. Together the whole training course will last about 90 minutes. Learning goals: The primary objective of this training course is to introduce tools for sequence analysis for crops. The theoretical basics as well as some examples will be shown by using online demonstrations, which will enable the participants to design and perform their own analyses. Prerequisites: The training course is designed for early career scientists such as PhD students and postdocs, but also for experienced scientists who want to learn more about the repeat analysis and masking of sequence data for complex plant genomes. Keywords: Microsatellite, Mathematically Defined Repeat, K-mer, SSR Tools: Kmasker Plants - https://kmasker.ipk-gatersleben.de/ MISA-Web - https://webblast.ipk-gatersleben.de/misa/ 2020-11-20 10:00:00 UTC 2020-11-20 11:30:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • Introduction to the Cloud for Proteomics Analyses

    23 November 2020

    Introduction to the Cloud for Proteomics Analyses https://tess.elixir-europe.org/events/introduction-to-the-cloud-for-proteomics-analyses Educators: Dominik Kopczynski, Markus Stepath, Michael Turewicz and Julian Uszkoreit (BioInfra.Prot) Date: Monday, 2020-11-23 Location: online Contents: In this one day course we will show some of BioInfra.Prot's tools provided by de.NBI, namely “PIA - Protein Inference Algorithms”, “BIONDA – A Free Biomarker Database” and “CalibraCurve”. Besides the tool based sessions we offer a "Proteomics in the Cloud" session where we show advantages of cloud based bioinformatics and give a tutorial how to access the de.NBI cloud. PIA allows to inspect and combine the results of proteomics search engines. The main focus lays on the integrated inference algorithms for identification and quantification purposes. BIONDA is a free, up-to-date and user-friendly biomarker and biomarker candidate database that facilitates any kind of research on protein biomarkers and the corresponding diseases. CalibraCurve is a tool intended for the generation of calibration curves in the context of MRM (targeted proteomics) experiments. Such calibration curves are necessary for the selection of suitable transitions. In addition the web service STAMPS will be part of this course. It is a pathway-centric service for the development of targeted proteomics assays. In combination with Skyline, it offers a streamlined pipeline for identification and quantification in targeted proteomics analyses and development of targeted proteomics assays. Learning goals: Attendees of the course will learn how to use the tools PIA, BIONDA, CalibraCurve and STAMPS effectively for their daily proteomics tasks. Additionally they will learn how to use the de.NBI cloud. Prerequisites: This course is for all researches in the field of proteomics. The attendees should have basic knowledge of LC-MS proteomics, but no prior bioinformatics skills are required. Basic knowledge of how to analyse LC-MS data are sufficient. Attendees are required to bring their own laptops. If this is not possible or laptops have very low computing capacities, please contact the organizers. Keywords: Proteomics; Data Analysis; Assay Development; Biomarkers; de.NBI Cloud 2020-11-23 09:00:00 UTC 2020-11-23 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • de.NBI Crop Analysis Tool Suite (Part III) training course – Explore barley diversity

    24 November 2020

    de.NBI Crop Analysis Tool Suite (Part III) training course – Explore barley diversity https://tess.elixir-europe.org/events/de-nbi-crop-analysis-tool-suite-part-iii-training-course-explore-barley-diversity Educator: Patrick König (GCBN) Date: 24th November 2020, 10:00 a.m. – 11:30 a.m. Location: Online Contents: The service centre GCBN offers CATS (Crop Analysis Tool Suite), which includes a web application for exploratory data analysis of the genomic diversity data derived from studies based on the concept of gene bank genomics. The concept of gene bank genomics is about to gain insight into the diversity of genetic resources stored in gene banks and to allow the utilisation of this mainly untapped diversity for breeding and further research and exploitation. BRIDGE is an interactive web tool for exploratory data analysis of a gene bank genomics study of more than 20,000 barley accessions. The tool helps researchers and breeders to keep the overview about the massive amount of data and to derive a benefit from diversity data through context-based data visualisation and data export. Learning goals: The goal of this training course is to provide an introduction into the BRIDGE web application, its available data domains and its use for data visualisation, exploratory data analysis and data export for different use cases of specific research interests. Prerequisites: The training course is aimed at young scientists such as PhD students and postdocs, but also at experienced scientists who want to learn more about exploratory data analysis, visualization and exploitation of plant diversity data for use in breeding and research. Keywords: Barley, Gene bank genomics, Exploratory data analysis, Visual analytics, Data visualisation, Data warehouse, Tools: BRIDGE (https://doi.org/10.3389/fpls.2020.00701 2020-11-24 10:00:00 UTC 2020-11-24 11:30:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • Quality Assurance and Quality Control in Metabolomics

    30 November - 18 December 2020

    Elixir node event
    Quality Assurance and Quality Control in Metabolomics https://tess.elixir-europe.org/events/quality-assurance-and-quality-control-in-metabolomics-fc8eb4e0-eaca-4a9a-8c76-1f3bf559d9a1 The application of quality assurance and quality control in the metabolomics field is vital to ensure the collection of high quality data. In this course you will explore the importance of quality assurance and quality control in both untargeted and targeted metabolomics studies. We will explain the difference between quality control and quality assurance and how to apply in your studies and laboratories. You will evaluate the types of quality control samples that can be applied in metabolomics, what is the most appropriate quality control sample to use in your research, and how to apply the data in your quality assurance procedure to produce robust and reproducible data. The materials in this course are delivered via the FutureLearn platform over a three week period, with an estimated learning time of four hours per week. Each week you will work through a number of steps to complete the learning material. A step may include a short video, an article, an exercise with step-by-step instructions, a discussion to interact with your peer and a selection of quizzes, tests and polls to self-assess your own learning. All of the course material is uploaded to the FutureLearn platform so that you can complete the steps at a convenient time for you. We (the educators) support your learning via social discussions where you will be able post questions and comments to the team of educators and the other learners on the course throughout the three weeks. In the final week of the course we will record a summary video where we will respond to questions posted by you during the course. If you do not have time to complete the course during the 3-week period you will retain access to the course material to revisit, as you are able. 2020-11-30 09:00:00 UTC 2020-12-18 23:59:00 UTC Birmingham Metabolomics Training Centre Metabolomics University of Birmingham [] ScientistsPhD studentsMasters students meetings_and_conferencesworkshops_and_courses [] MetabolomicsQuality AssuranceQuality Control
  • Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT)

    30 November 2020 - 31 January 2021

    Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT) https://tess.elixir-europe.org/events/bacterial-genomes-comparative-genomics-using-artemis-comparison-tool-act-3e9f10a2-bd0a-4af3-bc39-0d11856143e2 # Overview * **Duration**: 3 weeks, 5 hours per week * Free * Certificate of achievement available on satisfactory completion * **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? Disease outbreaks are still a big problem in our modern world. Comparison between two or more bacterial genomes can help improve understanding of the causes of pathogenicity and outbreaks of disease caused by bacteria. On this course you will learn how to use the free Artemis Comparison Tool (ACT). Developed at the Wellcome Sanger Institute, ACT will help you to visualise the comparison of genomes and analyse the results. ### Who is the course for? This course would benefit those interested in learning how to use tools to investigate and research bacterial genomes, and acquire bioinformatics skills to evaluate the role of microbial genes in disease. Learners will gain experience in comparative genomics, using the Artemis Comparison Tool to probe, visualise and compare genomes, and analyse the results. This course will be of interest to anyone interested in microbiology, including undergraduates, post-graduates, biomedical researchers, microbiologists, bioinformaticians, teachers, and healthcare professionals. The opportunity to gain experience in using the Artemis Comparison Tool, a computational tool designed for comparative genomics, will also be of interest to all those who have studied our pre-requisite courses: those with an interest in genomics and disease outbreaks, teachers and their 16-18-year-old science and computing students. Ideally, you will have completed [Bacterial Genomes: From DNA to Protein Function Using Bioinformatics][1] and [Bacterial Genomes: Accessing and Analysing Microbial Genome Data][2] before joining this course. [1]: /our-events/bacterial-genomes-dna-protein-function-bioinformatics-online-sep19/ [2]: /our-events/bacterial-genomes-accessing-analysing-microbial-genome-data-feb19/ # Programme ### What topics will you cover? Week 1 * Introduction to comparative genomics * Introduction to ACT Week 2 * Analyse available data * Generate your own comparison files * Make your own comparisons in ACT Week 3 * Identify pseudogenes in Mycobacterium leprae using ACT * Peer review project: Comparative genomics on two clinically relevant plasmids from Shigella ### What will you achieve? By the end of the course, you'll be able to... * Explain the advantages of comparative genomics * Explore basic tools of ACT * Interpret results from already generated comparison files * Produce new comparisons and analyse results * Develop hypothesis based on results observation ### What software or tools do you need? This course will give you an opportunity to learn about and use Artemis Comparison Tool (ACT), a free tool used to display pairwise comparisons between two DNA sequences. To run this software effectively, you will require a computer (Windows, Mac or Linux) with 2GB RAM. The current version of ACT requires version 11 of Java to run successfully. Java 11 can be downloaded from [this link][1]. Older versions of ACT require Java 8 to run successfully. Java 8 can be downloaded from [this link][2]. [1]: https://www.oracle.com/technetwork/java/javase/downloads/jdk11-downloads-5066655.html [2]: https://www.java.com/en/download/ # 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. ### 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. ### Dr. Ulrike Böhme I am a researcher in parasitology at the Wellcome Sanger Institute where I work as biocurator for Plasmodium genomes. ### Dr. Pablo Tsukayama I am a professor of microbiology at Universidad Peruana Cayetano Heredia and a visiting research scholar at the Wellcome Sanger Institute. I study how pathogen populations evolve and spread in Peru. ### 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. ### 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 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. # 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 2020-11-30 09:00:00 UTC 2021-01-31 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] comparativegenomicsHDRUK
  • Data visualization using R

    7 December 2020

    Data visualization using R https://tess.elixir-europe.org/events/data-visualization-using-r Educators: Markus Stepath, Karin Schork, Nils Hoffmann (BioInfra.Prot / LIFS) Date: Monday, 7th Dec 2020 Location: Online training Contents: In this course you will learn how to use the ggplot2 package in R to create informative and beautiful figures to communicate your omics data and analysis results. We will cover the following topics: - Usage of the tidyverse for data preprocessing - Usage of the ggplot2 R package - Presentation of different types of graphics and when to use them - Customization of graphics Please be aware that basic knowledge of R is taught in our course “Differential analysis of quantitative proteomics data” on Monday, 2nd Nov 2020 (http://goo.gl/forms/mpKHnbT1Um). Learning goals: - Using the ggplot2 R package to create graphics for omics data - Decide which type of graph is appropriate for the given data - Ability to costumize the graphics using ggplot2 Prerequisites: - Basic understanding of high-dimensional data sets from quantitative proteomics or other life sciences; - Basic knowledge of R (e.g. data import, basic plots. This can for example be gained from our course “Differential analysis of quantitative proteomics data” (Monday, 2nd Nov 2020, http://goo.gl/forms/mpKHnbT1Um). - Computer with stable internet connection, headset and camera Keywords: R; tidyverse; ggplot2; high-throughput data; omics; proteomics; data analysis, graphics, data preprocessing Tools: Download and more information on R here: https://cran.r-project.org/ We recommend using an editor such as RStudio, see www.rstudio.com 2020-12-07 09:00:00 UTC 2020-12-07 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []
  • Online Course - A Practical Introduction to NGS Data Analysis

    9 - 11 December 2020

    Online Course - A Practical Introduction to NGS Data Analysis https://tess.elixir-europe.org/events/online-course-a-practical-introduction-to-ngs-data-analysis-2523f702-4ade-4c7e-a782-cec42fbeec49 Advance your research. Understand NGS and analyze sequenced data yourself. In a nutshell - Learn the essential computing skills for NGS bioinformatics - Understand NGS technology, algorithms and data formats - Use bioinformatics tools for handling sequencing data - Perform first downstream analyses for studying genetic variation The purpose of this workshop is to get a deeper understanding in Next-Generation Sequencing (NGS) with a special focus on bioinformatics issues. Advantages and disadvantages of current sequencing technologies and their implications on data analysis will be discovered. The participants will be trained on understanding their own NGS data, finding potential problems/errors therein and finally perform their first downstream analysis (variant calling). In the course we will use a real-life NGS dataset from the current market leader illumina. All workshop attendees will be enabled to perform important first tasks of NGS data analysis themselves. The course layout has been adapted to the needs of beginners in the field of NGS bioinformatics and allows scientists with no or little background in computer science to get a first hands-on experience in this fast evolving research topic. The online course will make use of a web conferencing system. Hands-on NGS analysis will be performed in an interactive browser-based platform. Before the course, you will get a printed manuscript and a USB key by mail. 2020-12-09 09:00:00 UTC 2020-12-11 17:00:00 UTC ecSeq Bioinformatics GmbH Sequencing Sequence analysis Bioinformatics [] ecSeq Bioinformatics GmbH Sternwartenstr. 29 D-04103 Leipzig Germany Email: events@ecSeq.com [] BiologistsMolecular BiologistsPathologistsBiologists, Genomicists, Computer Scientistspost-docsPhD studentsbioinformaticians 15 workshops_and_courses first_come_first_served NGS bioinformaticsNGSVariant callingDNA-seq

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