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217 events found
  • NBIS course Lund: Omics integration and Systems biology

    5 - 10 October 2020

    Elixir node event
    NBIS course Lund: Omics integration and Systems biology https://tess.elixir-europe.org/events/nbis-course-lund-omics-integration-and-systems-biology #training #url: https://www.scilifelab.se/event/omics-integration-and-systems-biology-3 email: edu.omics-integration@nbis.se 2020-10-05 09:00:00 UTC 2020-10-10 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] #trainingtraining
  • Introduction to RNA-Seq: From quality control to pathway analysis - streamed

    5 - 6 October 2020

    Streamed from Basel, Switzerland

    Elixir node event
    Introduction to RNA-Seq: From quality control to pathway analysis - streamed https://tess.elixir-europe.org/events/introduction-to-rna-seq-from-quality-control-to-pathway-analysis-a2df060f-df2e-499e-be62-1f68e7b8cb91 This course is over-subscribed with a very long waiting list. We are not accepting applications any more. 2020-10-05 09:00:00 UTC 2020-10-06 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Single cell RNA-seq analysis using R

    5 - 9 October 2020

    Cambridge, United Kingdom

    Elixir node event
    Single cell RNA-seq analysis using R https://tess.elixir-europe.org/events/single-cell-rna-seq-analysis-using-r This course covers the analysis of scRNA-seq data using R and command line tools. 2020-10-05 09:45:00 UTC 2020-10-09 14:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • Shared-memory programming with OpenMP @ EPCC Online

    6 - 15 October 2020

    Shared-memory programming with OpenMP @ EPCC Online https://tess.elixir-europe.org/events/shared-memory-programming-with-openmp-epcc-online Outline Almost all modern computers now have a shared-memory architecture with multiple CPUs connected to the same physical memory, for example multicore laptops or large multi-processor compute servers. This course covers OpenMP, the industry standard for shared-memory programming, which enables serial programs to be parallelised easily using compiler directives. Users of desktop machines can use OpenMP on its own to improve program performance by running on multiple cores; users of parallel supercomputers can use OpenMP in conjunction with MPI to better exploit the shared-memory capabilities of the compute nodes. This course will cover an introduction to the fundamental concepts of the shared variables model, followed by the syntax and semantics of OpenMP and how it can be used to parallelise real programs. Hands-on practical programming exercises will be included, with access to HPC provided for the duration of the course. Pre-requisites This course is aim at attendees with prior experience of programming in C, C++ or Fortran. Some familiarity with HPC systems is helpful but not essential.  Learning outcomes At the end of the course, attendees should be equipped with the skills to write correct parallel programs using the core functionality of OpenMP, and understand the main issues affecting performance of shared memory parallel programs Timetable This course will be held over four 2-hour afternoon sessions: Tue 6th Oct 14:00 - 16:00 BST Thu 8th Oct 14:00 - 16:00 BST Tue 13th Oct 14:00 - 16:00 BST Thu 15th Oct 14:00 - 16:00 BST Full details Register https://events.prace-ri.eu/event/1057/ 2020-10-06 13:00:00 UTC 2020-10-15 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • 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
  • Using the PDBe graph API

    6 October 2020

    Elixir node event
    Using the PDBe graph API https://tess.elixir-europe.org/events/using-the-pdbe-graph-api This webinar will introduce the PDBe graph API, which is generated from the PDBe graph database and contains an even richer level of data than our standard API. We will highlight how this API supports our PDBe-KB aggregated views, with specific case studies that demonstrate the possibilities through this API. 2020-10-06 15:30:00 UTC 2020-10-06 16:30:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • The Ensembl Rapid Release genome browser

    7 October 2020

    Elixir node event
    The Ensembl Rapid Release genome browser https://tess.elixir-europe.org/events/the-ensembl-rapid-release-genome-browser This webinar will introduce you to the data available in the Ensembl Rapid Release site, a new, lightweight genome browser designed to allow quick release of the latest genome annotation for a large number of vertebrate and non-vertebrate species. 2020-10-07 15:30:00 UTC 2020-10-07 16:30:00 UTC [] Ajay Mishra [] [] [] [] HDRUK
  • 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 [] []
  • Challenges in Omics Data Integration

    8 - 9 October 2020

    Elixir node event
    Challenges in Omics Data Integration https://tess.elixir-europe.org/events/challenges-in-omics-data-integration 2020-10-08 09:00:00 UTC 2020-10-09 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
  • FAIR Data Stewardship (basis)

    8 October - 19 November 2020

    Leiden, Netherlands

    Elixir node event
    FAIR Data Stewardship (basis) https://tess.elixir-europe.org/events/fair-data-stewardship-basis Bij onderzoek – in de brede zin van het woord – wordt steeds meer data geproduceerd. Daarbij is de wens dat deze onderzoeksdata bruikbaar blijft voor vervolgonderzoek. In de praktijk gaat dat lastig. Om deze problematiek te adresseren zijn de… The post FAIR Data Stewardship (basis) appeared first on Dutch Techcentre for Life Sciences. 2020-10-08 09:00:00 UTC 2020-11-19 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] [] workshops_and_courses [] []
  • [ONLINE] Parallel Programming Workshop (Train the Trainer) @ HLRS

    12 - 16 October 2020

    [ONLINE] Parallel Programming Workshop (Train the Trainer) @ HLRS https://tess.elixir-europe.org/events/online-parallel-programming-workshop-train-the-trainer-hlrs The Train the Trainer Program is provided in conjunction with the regular course Parallel Programming with MPI and OpenMP and Advanced Parallel Programming. Whereas the regular course teaches parallel programming, this program is an education for future trainers in parallel programming. Too few people can provide parallel programming courses on the level that is needed if scientists and PhD students want to learn how to parallelize a sequential application or to enhance parallel applications. Within Europe, currently only six PATC centres and several other national centres provide such courses on an European or national level. We would like to assist further trainers and centres to also provide such courses for whole Europe or at least within their countries. Prerequisites You are familiar with parallel programming with MPI and OpenMP on an advanced level and skilled in both programming languages C and Fortran. Your goal: You want to provide MPI and OpenMP courses for other scientists and PhD students in your country, i.e., you would like to provide at least the first three days of the regular course as a training block-course to PhD students. Background: (a) Your centre supports you to provide such PhD courses in a course room at your centre. The course room is equipped at least with one computer/laptop per two (or three) students and has access to a HPC resource that allows MPI and OpenMP programming in C and Fortran. Or (b), you as a future trainer would like to co-operate with a centre with the necessary course infrastructure. What does this Train the Trainer Program provide? We provide you with all necessary teaching material on a personal basis, i.e., with the copyright to use it and to provide pdf or paper copies to the students in your PhD courses. We provide all exercise material. You will listen the lectures that you get familiar with the training material. During the exercises, you will help the regular students to correct their errors. The regular students are advised to request help if they were stuck for more than a minute. You will be trained to detect their problems as fast as possible (typically in less than a minute) and to provide the students with the needed help.   The Train the Trainer Program includes the curriculum from Monday until Friday according the course agenda. The Train the Trainer Program starts on Monday with a short introductory meeting at 8:15 am. On Thursday evening we will have an additional meeting and dinner for all participants of this TtT program. For further information and registration please visit the HLRS course page. https://events.prace-ri.eu/event/1031/ 2020-10-12 06:15:00 UTC 2020-10-16 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] Parallel Programming Workshop (MPI, OpenMP and advanced topics) @ HLRS

    12 - 16 October 2020

    [ONLINE] Parallel Programming Workshop (MPI, OpenMP and advanced topics) @ HLRS https://tess.elixir-europe.org/events/online-parallel-programming-workshop-mpi-openmp-and-advanced-topics-hlrs Distributed memory parallelization with the Message Passing Interface MPI (Mon, for beginners – non-PRACE part): On clusters and distributed memory architectures, parallel programming with the Message Passing Interface (MPI) is the dominating programming model. The course gives an introduction into MPI-1. Hands-on sessions (in C and Fortran) will allow users to immediately test and understand the basic constructs of the Message Passing Interface (MPI). Shared memory parallelization with OpenMP (Tue, for beginners – non-PRACE part): The focus is on shared memory parallelization with OpenMP, the key concept on hyper-threading, dual-core, multi-core, shared memory, and ccNUMA platforms. This course teaches shared memory OpenMP parallelization. Hands-on sessions (in C and Fortran) will allow users to immediately test and understand the directives and other interfaces of OpenMP. Race-condition debugging tools are also presented. Intermediate and advanced topics in parallel programming (Wed-Fri – PRACE course): Topics are advanced usage of communicators and virtual topologies, one-sided communication, derived datatypes, MPI-2 parallel file I/O, hybrid mixed model MPI+OpenMP parallelization, parallelization of explicit and implicit solvers and of particle based applications, parallel numerics and libraries, and parallelization with PETSc. MPI-3.0 introduced a new shared memory programming interface, which can be combined with MPI message passing and remote memory access on the cluster interconnect. It can be used for direct neighbor accesses similar to OpenMP or for direct halo copies, and enables new hybrid programming models. These models are compared in the hybrid mixed model MPI+OpenMP parallelization session with various hybrid MPI+OpenMP approaches and pure MPI. Further aspects are domain decomposition, load balancing, and debugging. Hands-on sessions are included on all days. This course provides scientific training in Computational Science, and in addition, the scientific exchange of the participants among themselves. Hands-on sessions are included on all days. This course provides scientific training in Computational Science, and in addition, the scientific exchange of the participants among themselves. For further information and registration please visit the HLRS course page. https://events.prace-ri.eu/event/1030/ 2020-10-12 06:30:00 UTC 2020-10-16 14:30:00 UTC [] [] [] workshops_and_courses [] []
  • [POSTPONED] Performance portability for GPU application using high-level programming approaches with Kokkos @ MdlS/Idris

    12 - 13 October 2020

    [POSTPONED] Performance portability for GPU application using high-level programming approaches with Kokkos @ MdlS/Idris https://tess.elixir-europe.org/events/performance-portability-for-gpu-application-using-high-level-programming-approaches-with-kokkos-mdls-idris When developing a numerical simulation code with high performance and efficiency in mind, one is often compelled to accept a trade-off between using a native-hardware programming model (like CUDA or OpenCL), which has become tremendously challenging, and loosing some cross-platform portability. Porting a large existing legacy code to a modern HPC platform, and developing a new simulation code, are two different tasks that may be benefit from a high-level programming model, which abstracts the low-level hardware details. This training presents existing high-level programming solutions that can preserve at best as possible performance, maintainability and portability across the vast diversity of modern hardware architectures (multicore CPU, manycore, GPU, ARM, ..) and software development productivity. We will  provide an introduction to the high-level C++ programming model Kokkos https://github.com/kokkos, and show basic code examples  to illustrate the following concepts through hands-on sessions: hardware portability: design an algorithm once and let the Kokkos back-end (OpenMP, CUDA, ...) actually derive an efficient low-level implementation; efficient architecture-aware memory containers: what is a Kokkos::view; revisit fundamental parallel patterns with Kokkos: parallel for, reduce, scan, ... ; explore some mini-applications. Several detailed examples in C/C++/Fortran will be used in hands-on session on the high-end hardware platform Jean Zay (http://www.idris.fr/jean-zay/), equipped with Nvidia Tesla V100 GPUs. Prerequisites: Some basic knowledge of the CUDA programming model and of C++. https://events.prace-ri.eu/event/892/ 2020-10-12 07:30:00 UTC 2020-10-13 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • Analyse avancée de séquences

    12 - 14 October 2020

    Elixir node event
    Analyse avancée de séquences https://tess.elixir-europe.org/events/analyse-avancee-de-sequences-061cb459-9688-429e-ad16-cb73bc68c1ff Analyse avancée de séquences 2020-10-12 09:00:00 UTC 2020-10-14 00:00:00 UTC [] [] [] [] [] []
  • 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
  • Bulk RNASeq: from counts to differential expression, autumn session

    12 - 19 October 2020

    Elixir node event
    Bulk RNASeq: from counts to differential expression, autumn session https://tess.elixir-europe.org/events/bulk-rnaseq-from-counts-to-differential-expression-autumn-session The course will show: R tools to generate count files like featureCounts, and summarizeOverlaps are demonstrated Count files from HTSeq-Count, FeatureCounts, Salmon or Kallisto are used to identify differentially expressed genes After the live session participants can analyze their own count files. Issues can be handled during the Q&A session. 2020-10-12 09:00:00 UTC 2020-10-19 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
  • 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
  • Summer School in bioinformatics

    12 - 16 October 2020

    Cambridge, United Kingdom

    Elixir node event
    Summer School in bioinformatics https://tess.elixir-europe.org/events/summer-school-in-bioinformatics-77f7f58f-cee6-430c-b176-c28939aac928 Please note this course has moved from the previous dates of 22-26 June 2020. This course provides an introduction to the use of bioinformatics in biological research, giving participants guidance for using bioinformatics in their work whilst also providing hands-on training in tools and resources appropriate to their research. 2020-10-12 10:00:00 UTC 2020-10-16 15:30:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Scientific Conferences [] [] [] [] HDRUK
  • Summer School in bioinformatics (Virtual)

    12 - 16 October 2020

    Hinxton, United Kingdom

    Elixir node event
    Summer School in bioinformatics (Virtual) https://tess.elixir-europe.org/events/summer-school-in-bioinformatics-virtual The delivery of this course has changed from face-to-face to virtual. Please note this course has moved from the previous dates of 22-26 June 2020. This course provides an introduction to the use of bioinformatics in biological research, giving participants guidance for using bioinformatics in their work whilst also providing hands-on training in tools and resources appropriate to their research. 2020-10-12 10:00:00 UTC 2020-10-16 15:30:00 UTC Virtual, Hinxton, United Kingdom Virtual Hinxton United Kingdom CB10 1SD [] Scientific Conferences [] [] [] [] HDRUK
  • RNA-Seq Analysis Using Galaxy

    13 - 14 October 2020

    RNA-Seq Analysis Using Galaxy https://tess.elixir-europe.org/events/rna-seq-analysis-using-galaxy-c3d51ca3-b539-4b53-8305-5d073259153d 2020-10-13 09:00:00 UTC 2020-10-14 00:00:00 UTC [] QCIF [] [] [] [] []
  • RNA-Seq Analysis Using Galaxy

    13 October 2020

    Australia

    RNA-Seq Analysis Using Galaxy https://tess.elixir-europe.org/events/rna-seq-analysis-using-galaxy-04e78ac1-40c5-492d-8cc2-1dc8557c7e77 2020-10-13 10:00:00 UTC 2020-10-13 18:00:00 UTC QCIF Australia Australia Bioinformatics QCIF [] [] [] [] bioinformaticsRNA-SeqGalaxy
  • [ONLINE] Parallel Programming Workshop @ BSC

    13 - 22 October 2020

    [ONLINE] Parallel Programming Workshop @ BSC https://tess.elixir-europe.org/events/online-parallel-programming-workshop-bsc The registration to this course is now open. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course Convener: Xavier Martorell Sessions will be in October 13th-16th and 19th-22nd from 2pm to 5.30pm and delivered via Zoom. Level: Intermediate: For trainees with some theoretical and practical knowledge, some programming experience. Advanced: For trainees able to work independently and requiring guidance for solving complex problems. Attendants can bring their own applications and work with them during the course for parallelization and analysis. Prerequisites: Fortran, C or C++ programming. All examples in the course will be done in C Objectives: The objectives of this course are to understand the fundamental concepts supporting message-passing and shared memory programming models. The course covers the two widely used programming models: MPI for the distributed-memory environments, and OpenMP for the shared-memory architectures. The course also presents the main tools developed at BSC to get information and analyze the execution of parallel applications, Paraver and Extrae. It also presents the Parallware Assistant tool, which is able to automatically parallelize a large number of program structures, and provide hints to the programmer with respect to how to change the code to improve parallelization. It deals with debugging alternatives, including the use of GDB and Totalview. The use of OpenMP in conjunction with MPI to better exploit the shared-memory capabilities of current compute nodes in clustered architectures is also considered. Paraver will be used along the course as the tool to understand the behavior and performance of parallelized codes. The course is taught using formal lectures and practical/programming sessions to reinforce the key concepts and set up the compilation/execution environment. Attendants can bring their own applications and work with them during the course for parallelization and analysis. Learning Outcomes: The students who finish this course will be able to develop benchmarks and applications with the MPI, OpenMP and mixed MPI/OpenMP programming models, as well as analyze their execution and tune their behaviour in parallel architectures. Agenda:  all times are 2pm to 5.30pm with two breaks of 15' Tuesday 13/10/2020 1. Introduction to parallel architectures, algorithms design and performance parameters 2. Introduction to the MPI programming model 3. Practical: How to compile and run MPI applications Wednesday 14/10/2020 1. MPI: Point-to-point communication, collective communication 2. Practical: Simple matrix computations 3. MPI: Blocking and non-blocking communications 4. Practical: matrix computations with non-blocking communication Thursday 15/10/2020 1. Introduction to Paraver: tool to analyze and understand performance 2. Practical: Trace generation and trace analysis Friday 16/10/2020 1. MPI: Collectives, Communicators, Topologies 2. Practical: Heat equation example Monday 19/10/2020 1. OpenMP Fundamentals: the fork-join model (lecture) 2. OpenMP Fundamentals: the fork-join model (hands-on) 3. OpenMP Fundamentals: the data environment (lecture) 4. OpenMP Fundamentals: the data environment (hands-on) Tuesday 20/10/2020 1. OpenMP Work-sharing: distributing work among threads (lecture)  2. OpenMP Work-sharing: distributing work among threads (hands-on)  3. OpenMP Work-sharing: loop distribution (lecture)  4. OpenMP Work-sharing: loop distribution (hands-on)  Wednesday 21/10/2020 1. OpenMP Tasking model: basics (lecture)    The task construct    The taskwait 2. OpenMP Tasking model: basics (hands-on) 3. OpenMP Tasking model: intermediate (lecture) 4. OpenMP Tasking model: intermediate (hands-on) Thursday 22/10/2020 1. Hybrid MPI+OpenMP    Standard (threading level, synchronous/asynchronous MPI)    TAMPI 2. Practical: Heat, nbody End of Course https://events.prace-ri.eu/event/1041/ 2020-10-13 12:00:00 UTC 2020-10-22 15:30:00 UTC [] [] [] workshops_and_courses [] []
  • PDBe tools in GitHub

    13 October 2020

    Elixir node event
    PDBe tools in GitHub https://tess.elixir-europe.org/events/pdbe-tools-in-github This webinar will show you how to access some of the software packages created at PDBe, used to generate the data displayed on our website. This will include a walkthrough of our GitHub repositories, highlighting the types of packages available, how to access them and some examples of how they can be used. 2020-10-13 15:30:00 UTC 2020-10-13 16:30:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • Exploring biological sequences

    14 - 16 October 2020

    Cambridge, United Kingdom

    Elixir node event
    Exploring biological sequences https://tess.elixir-europe.org/events/exploring-biological-sequences-29445985-7c94-447f-b262-fc5d6208cfd0 We are currently developing the course programme for 2020, and as further information about the course becomes available we will update this page. 2020-10-14 09:00:00 UTC 2020-10-16 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Charlotte Pearton [] [] [] [] HDRUK
  • 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
  • ELIXIR Webinar: Bioschemas - Improving interoperability of life science resources

    14 October 2020

    ELIXIR Webinar: Bioschemas - Improving interoperability of life science resources https://tess.elixir-europe.org/events/elixir-webinar-bioschemas-improving-interoperability-of-life-science-resources This ELIXIR webinar will present the Bioschemas initiative that uses the schema.org markup to improve the discoverability of life science data and other resources. Bioschemas develops schema.org specifications for content relevant to life science research (dataset, gene, protein and many more) and encourages consistent use of the specifications to ease the consumption of the contained markup across many sites. This structured information then makes it easier to discover, collate, and analyse distributed data. The webinar will be presented by Alasdair Gray (Heriot-Watt University, Edinburgh, UK, ELIXIR UK), Chair of the Bioschemas Leadership team. More information will be available closer to the event. 2020-10-14 14:00:00 UTC 2020-10-14 14:00:00 UTC [] [] [] [] [] []
  • A guide to UniProt for students

    14 October 2020

    Elixir node event
    A guide to UniProt for students https://tess.elixir-europe.org/events/a-guide-to-uniprot-for-students-00d9f686-8be0-4763-b5b2-6798dbe9568a UniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. This webinar will guide you through searching, exploring and analysing data with UniProt using case studies typically useful for students or early researchers beginning to use bioinformatics resources in their studies/research. 2020-10-14 15:30:00 UTC 2020-10-14 16:30:00 UTC [] Anna Swan [] [] [] [] HDRUK
  • Extracting biological information from gene lists (ONLINE LIVE TRAINING)

    15 October 2020

    Cambridge, United Kingdom

    Elixir node event
    Extracting biological information from gene lists (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/extracting-biological-information-from-gene-lists-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 will be teaching the course live online in conjunction with the presenters. Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting biological themes which turn up in the lists. This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication. Course materials are available [here](https://www.bioinformatics.babraham.ac.uk/training.html#fagl). 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=3566444&course-title=Extracting%20biological%20information%20from%20gene%20lists).'' 2020-10-15 08:30:00 UTC 2020-10-15 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Biology Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] HDRUK
  • Using MOFA for integration of omics data, online

    15 - 16 October 2020

    Gent, Belgium

    Elixir node event
    Using MOFA for integration of omics data, online https://tess.elixir-europe.org/events/using-mofa-for-integration-of-omics-data-autumn-session Participants can analyze their own data in the course. What kind of preprocessing of the data is required for MOFA? How to train MOFA on a multi-omic data set? How to interpret the MOFA factors by their loadings, using gene set enrichment or sample ordination? How to use MOFA for downstream analyses including regression, classification or clustering? How to impute missing values with MOFA? How to select the number of factors and compare different MOFA fits? 2020-10-15 09:00:00 UTC 2020-10-16 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []
  • Initiation à l’utilisation de Galaxy

    15 - 16 October 2020

    Initiation à l’utilisation de Galaxy https://tess.elixir-europe.org/events/initiation-a-l-utilisation-de-galaxy-af5debd2-17c2-4fbc-b66d-9814357d25f2 2020-10-15 09:00:00 UTC 2020-10-16 00:00:00 UTC [] Véronique Martin [] [] [] [] []

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