255 events found
  • Introduction to RNA-seq data analysis

    27 - 29 March 2019

    Cambridge, United Kingdom

    Elixir node event
    Introduction to RNA-seq data analysis https://tess.elixir-europe.org/events/introduction-to-rna-seq-data-analysis-5ad59a77-0bc1-444d-b42c-8f9d499d2ef4 The aim of this course is to familiarize the participants with the primary analysis of RNA-seq data. This course starts with a brief introduction to RNA-seq and discusses quality control issues. Next, we will present the alignment step, quantification of expression and differential expression analysis. For downstream analysis we will focus on tools available through the Bioconductor project for manipulating and analysing bulk RNA-seq. The training room is located on the first floor and there is currently no level access. 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=2673403&course-title=Introduction%20to%20RNA-seq%20data%20analysis).'' 2019-03-27 09:30:00 UTC 2019-03-29 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR RNA-Seq Data mining Transcriptomics Data visualisation Functional genomics Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] []
  • Fortran for Scientific Computing @ HLRS

    1 - 5 April 2019

    Fortran for Scientific Computing @ HLRS https://tess.elixir-europe.org/events/fortran-for-scientific-computing-hlrs-1eea0cf9-97bc-4560-aff3-896bc194648b Overview This course is dedicated to scientists and students to learn (sequential) programming with Fortran of scientific applications. The course teaches newest Fortran standards. Hands-on sessions will allow users to immediately test and understand the language constructs. This workshop provides scientific training in Computational Science, and in addition, the scientific exchange of the participants among themselves. Only the last three days of this course are sponsored by the PATC project. For further information and registration please visit the HLRS course page. https://events.prace-ri.eu/event/808/ 2019-04-01 06:30:00 UTC 2019-04-05 13:30:00 UTC [] [] [] workshops_and_courses [] []
  • GPU Programming with CUDA @ JSC

    1 - 3 April 2019

    GPU Programming with CUDA @ JSC https://tess.elixir-europe.org/events/gpu-programming-with-cuda-jsc-5b4c9199-55c1-44b6-b1df-7b7f28804105 GPU-accelerated computing drives current scientific research. Writing fast numeric algorithms for GPUs offers high application performance by offloading compute-intensive portions of the code to an NVIDIA GPU. The course will cover basic aspects of GPU architectures and programming. Focus is on the usage of the parallel programming language CUDA-C which allows maximum control of NVIDIA GPU hardware. Examples of increasing complexity will be used to demonstrate optimization and tuning of scientific applications. Topics covered will include: Introduction to GPU/Parallel computing Programming model CUDA GPU libraries like CuBLAS and CuFFT Tools for debugging and profiling Performance optimizations Prerequisites: Some knowledge about Linux, e.g. make, command line editor, Linux shell, experience in C/C++ Application Registrations are only considered until 28 February 2018 due to available space, the maximal number of participants is limited. Applicants will be notified, whether they are accepted for participitation. Instructors: Dr. Jan Meinke, Jochen Kreutz, Dr. Andreas Herten, JSC; Jiri Kraus, NVIDIA Contact For any questions concerning the course please send an e-mail to j.meinke@fz-juelich.de https://events.prace-ri.eu/event/823/ 2019-04-01 07:00:00 UTC 2019-04-03 14:30:00 UTC [] [] [] workshops_and_courses [] []
  • Performance portability for GPU application using high-level programming approaches @ MdlS /Idris

    1 - 2 April 2019

    Performance portability for GPU application using high-level programming approaches @ MdlS /Idris https://tess.elixir-europe.org/events/performance-portability-for-gpu-application-using-high-level-programming-approaches-mdls-idris-e05a2681-bd72-4aea-9ea1-7fa210925446 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 Ouessant (http://www.idris.fr/ouessant/), equipped with Nvidia Pascal GPUs. Prerequisites: Some basic knowledge of the CUDA programming model and of C++. https://events.prace-ri.eu/event/818/ 2019-04-01 07:30:00 UTC 2019-04-02 15:00:00 UTC [] [] [] workshops_and_courses [] []
  • Signalling Networks: From Data to Modelling

    1 - 5 April 2019

    Norwich, United Kingdom

    Signalling Networks: From Data to Modelling https://tess.elixir-europe.org/events/signalling-networks-from-data-to-modelling-505fd9f3-a493-46f7-8f3f-1c942e09c0ed Signalling pathways and networks are very important to regulate and control cellular processes, cell fate, and their malfunctions often lead to diseases, such as cancer or diabetes. This course provides an introductory overview about the most useful resources and tools to investigate signalling pathways and network, and also to introduce basic approaches to model signalling events. Hands-on trainings will give a wide overview on tools and concepts related to signalling networks. In this course you will learn how to use Cytoscape, where to find the most reliable signalling data, how to reconstruct, analyze and visualize a network. You will also learn how to develop your own models, mostly with logic modeling, what other modeling approaches exist, and how you can apply a model for your own research work. 2019-04-01 09:00:00 UTC 2019-04-05 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ [] training@earlham.ac.uk [] [] workshops_and_courses [] []
  • Introduction to Next Generation Sequencing

    1 - 5 April 2019

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Next Generation Sequencing https://tess.elixir-europe.org/events/introduction-to-next-generation-sequencing-ddd5fbf5-5c90-47ab-91f8-7928f76d4005 This course will provide an introduction to the technology, data analysis, tools and resources for next generation sequencing (NGS) data. The content is intended to provide a broad overview of the subject areas, and to highlight key resources, approaches and methodologies. Topics will be delivered using a mixture of lectures, practical sessions and open discussions. Practical work during the course will use small, example data-sets and there will not be scope to analyse personal data. 2019-04-01 09:00:00 UTC 2019-04-05 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 2, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 2 Cambridge United Kingdom CB10 1SD [] EMBL-EBI Training Team [] [] [] [] []
  • Regulatory Oxylipins

    1 - 4 April 2019

    Gent, Belgium

    Elixir node event
    Regulatory Oxylipins https://tess.elixir-europe.org/events/regulatory-oxylipins Oxylipins, from plants and other organisms, form a constantly growing group of signalling molecules that comprise oxygenated fatty acids and their metabolites. The most renowned regulatory oxylipins are undoubtedly the jasmonates, which, following their discovery in the 1960s, became recognized as regulators of defence, floral organ development and fertility, as growth inhibitors and modulators of senescence, and as elicitors of specialized metabolism in numerous plant species. As such, the jasmonates currently belong to an elite group of heavily investigated phytohormones. Over the last decade, the understanding of biosynthesis, metabolism, and action of regulatory oxylipins has greatly advanced. The ROXY2019 meeting wishes to bring together the international community and leading researchers in the field. Thereby it aims to provide a timely and exciting forum to present and discuss the recent advances and expertise on the study of these molecules that are so crucial for plant growth, development, metabolism, and interaction with the environment. There will be seven plenary sessions that, through combining lectures from invited speakers and short talks on selected abstracts and posters, will highlight the various aspects involved in Regulatory Oxylipin research. These sessions cover the following major themes: Regulatory oxylipins in emerging model systems and non-plant systems, Biochemistry and structural biology, Control of growth and defence, Control of Metabolism, Reproduction, Jasmonate signalling mechanisms and Long-distance signalling, Ecology. We look forward to your contributions to make this an exciting conference. See you in Gent! The organizers Alain Goossens and Ted Farmer Poster information Format: A0 (841 x 1189 mm / 33.1 x 46.8 in), portrait orientation 2019-04-01 09:00:00 UTC 2019-04-04 17:00:00 UTC VIB Conferences Ghent University - Aula, 9, Voldersstraat, Gent, Belgium Ghent University - Aula, 9, Voldersstraat Gent Oost-Vlaanderen Belgium 9000 [] [] [] meetings_and_conferences [] []
  • Regulatory Oxylipins

    1 - 4 April 2019

    Gent, Belgium

    Elixir node event
    Regulatory Oxylipins https://tess.elixir-europe.org/events/regulatory-oxylipins-661da9dc-2159-4a34-8809-7851dfbe0b8a Oxylipins, from plants and other organisms, form a constantly growing group of signalling molecules that comprise oxygenated fatty acids and their metabolites. The most renowned regulatory oxylipins are undoubtedly the jasmonates, which, following their discovery in the 1960s, became recognized as regulators of defence, floral organ development and fertility, as growth inhibitors and modulators of senescence, and as elicitors of specialized metabolism in numerous plant species. As such, the jasmonates currently belong to an elite group of heavily investigated phytohormones. Over the last decade, the understanding of biosynthesis, metabolism, and action of regulatory oxylipins has greatly advanced. The ROXY2019 meeting wishes to bring together the international community and leading researchers in the field. Thereby it aims to provide a timely and exciting forum to present and discuss the recent advances and expertise on the study of these molecules that are so crucial for plant growth, development, metabolism, and interaction with the environment. There will be seven plenary sessions that, through combining lectures from invited speakers and short talks on selected abstracts and posters, will highlight the various aspects involved in Regulatory Oxylipin research. These sessions cover the following major themes: Regulatory oxylipins in emerging model systems and non-plant systems, Biochemistry and structural biology, Control of growth and defence, Control of Metabolism, Reproduction, Jasmonate signalling mechanisms and Long-distance signalling, Ecology. We look forward to your contributions to make this an exciting conference. See you in Gent! The organizers Alain Goossens and Ted Farmer Poster information Format: A0 (841 x 1189 mm / 33.1 x 46.8 in), portrait orientation 2019-04-01 09:00:00 UTC 2019-04-04 17:00:00 UTC VIB Conferences - Alain Goossens & Ted Farmer Ghent University - Aula, 9, Voldersstraat, Gent, Belgium Ghent University - Aula, 9, Voldersstraat Gent Oost-Vlaanderen Belgium 9000 [] conferences@vib.be Faculty of ScienceJournal of Experimental BotanyPCP (Plant & Cell Physiology)The Plant CellThe Plant Journal [] [] [] Regulatory OxylipinsBiochemistrystructural biologyMetabolismreproductionJasmonate signallingEcology
  • Metabolomics with the Q Exactive

    1 - 3 April 2019

    Birmingham, United Kingdom

    Elixir node event
    Metabolomics with the Q Exactive https://tess.elixir-europe.org/events/metabolomics-with-the-q-exactive This 3-day course will introduce you to using the Q Exactive mass spectrometer in your metabolomics investigations. The course will be led by experts in the field of metabolomics and include lectures, laboratory sessions and computer workshops to provide a detailed overview of the metabolomics pipeline applying the Q Exactive mass spectrometer. 2019-04-01 09:00:00 UTC 2019-04-03 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Introduction to Next Generation Sequencing

    1 - 5 April 2019

    Cambridge, United Kingdom

    Elixir node event
    Introduction to Next Generation Sequencing https://tess.elixir-europe.org/events/introduction-to-next-generation-sequencing-fefd0a92-9254-4c73-b6d9-c4dac54afba0 This course will provide an introduction to the technology, data analysis, tools and resources for next generation sequencing (NGS) data. 2019-04-01 09:45:00 UTC 2019-04-05 09:45:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 1, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 1 Cambridge United Kingdom CB10 1SD [] EMBL-EBI Training Team [] [] [] [] []
  • Livestock Genomics

    1 - 5 April 2019

    Cambridge, United Kingdom

    Elixir node event
    Livestock Genomics https://tess.elixir-europe.org/events/livestock-genomics This course will introduce participants to methods and approaches for analysing genomic data from common livestock species. 2019-04-01 10:00:00 UTC 2019-04-05 18:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 2, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 2 Cambridge United Kingdom CB10 1SD [] Marina Pujol [] [] [] [] []
  • First steps with R in Life Sciences

    2 - 3 April 2019

    Lausanne, Switzerland

    Elixir node event
    First steps with R in Life Sciences https://tess.elixir-europe.org/events/first-steps-with-r-in-life-sciences-be891d7c-9d78-4af4-a585-a82bfdbe1eb7 Overview R is a complete, flexible and open source system for statistical analysis and graphics, which has become a tool of choice for biologists and biomedical scientists who need to analyse and visualise large amounts of data. 2019-04-02 09:00:00 UTC 2019-04-03 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Introduction to OpenACC @ BSC

    4 - 5 April 2019

    Introduction to OpenACC @ BSC https://tess.elixir-europe.org/events/introduction-to-openacc-bsc-6b5fe755-572a-40b7-b62e-65213011ef43 The registration to this course will open in January. All PATC Courses at BSC do not charge fees. PLEASE BRING YOUR OWN LAPTOP. Local Web Page: This is an expansion of the topic "OpenACC and other approaches to GPU computing" covered on this year's and last year's editions of the Introduction to CUDA Programming. This course will provide very good introduction to the PUMPS Summer School run jointly with NVIDIA -  also  at Campus Nord, Barcelona. For further information visit the school website. Convener: Antonio Peña, Computer Sciences Senior Researcher, Accelerators and Communications for High Performance Computing, BSC Objectives:  As an NVIDIA GPU Center of Excellence, BSC and UPC are deeply involved in research and outreach activities around GPU Computing. OpenACC is a high-level, directive-based programming model for GPU computing. It is a very convenient language to leverage the GPU power with minimal code modifications, being the preferred option for non computer scientists. This course will cover the necessary topics to get started with GPU programming in OpenACC, as well as some advanced topics. The target audiences of the course are students who want to develop exciting applications for these processors, as well as those who want to develop programming tools and future implementations for these processors. Level:  BEGINNERS: for trainees from different background or very little knowledge. Agenda: DAY 1 Session 1 / 9:00am – 1:00 pm (2h lectures, 2 h practical) 9:00 - 10:00 Introduction to OpenACC on x86 CPU and GPU 10:00 - 11:00 Hands-on: Introduction 11:00 - 11:30 Break 11:30 - 12:30 Profiling and Parallelizing with the OpenACC Toolkit 12:30 - 13:30 Hands-on: Profiling and Parallelizing 13:30 - 15:00 Lunch break Session 2 / 2:00pm – 5:00 pm (2 h practical) 15:00 - 17:00 Hands-on: Open Labs   DAY 2 Session 3 / 9:00am – 1:00 pm (2h lectures, 2 h practical) 9:00 - 10:00 Expressing Data Locality and Optimizations with OpenACC 10:00 - 11:00 Hands-on: Data Locality and Optimizations 11:00 - 11:30 Break 11:30 - 12:30 Advanced OpenACC Techniques: Interoperability, MPI, and Pipelining 12:30 - 13:30 Hands-on: Advanced Techniques 13:30 - 15:00 Lunch break Session 4 / 2:00pm – 5:00 pm (2 h practical) 15:00 - 17:00 Hands-on: Open Labs End of Course   https://events.prace-ri.eu/event/769/ 2019-04-04 07:00:00 UTC 2019-04-05 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Metabolite identification with the Q Exactive and LTQ Orbitrap Elite

    4 - 5 April 2019

    Birmingham, United Kingdom

    Elixir node event
    Metabolite identification with the Q Exactive and LTQ Orbitrap Elite https://tess.elixir-europe.org/events/metabolite-identification-with-the-q-exactive-and-ltq-orbitrap This 2-day course will provide a hands-on approach to teach the attendees about the latest techniques and tools available to perform metabolite identification in non-targeted metabolomics studies. The course will be led by experts working within the fields of metabolomics and chemical analysis and will include a significant proportion of hands-on experience of using mass spectrometers, software tools and databases. A maximum of four people will be working on each mass spectrometer in a session. We will apply these tools on the Q Exactive and LTQ-Orbitrap family of mass spectrometers. 2019-04-04 09:00:00 UTC 2019-04-05 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Introduction to CUDA Programming @ BSC

    8 - 11 April 2019

    Introduction to CUDA Programming @ BSC https://tess.elixir-europe.org/events/introduction-to-cuda-programming-bsc-865fc5e1-a20d-4615-a4ea-a964fcd15bf5 The registration to this course will open in Jaunary. All PATC Courses at BSC do not charge fees. PLEASE BRING YOUR OWN LAPTOP. Local Web Page: This course will provide very good introduction to the PUMPS Summer School run jointly with NVIDIA -also  at Campus Nord, Barcelona. For further information visit the school website  as this school has attendee selection process. You may also be interested in our Introduction to OpenACC course. Convener:  Antonio Peña, Computer Sciences Senior Researcher, Accelerators and Communications for High Performance Computing, BSC Objectives:  The aim of this course is to provide students with knowledge and hands-on experience in developing applications software for processors with massively parallel computing resources. In general, we refer to a processor as massively parallel if it has the ability to complete more than 64 arithmetic operations per clock cycle. Many commercial offerings from NVIDIA, AMD, and Intel already offer such levels of concurrency. Effectively programming these processors will require in-depth knowledge about parallel programming principles, as well as the parallelism models, communication models, and resource limitations of these processors. Agenda: DAY 1 Session 1 / 9:00am – 1:00 pm (3:30 h lectures) L1 9:00-10:45 The GPU hardware: Many-core Nvidia developments 10:45-11:15 Coffee break L2 11:15-13:00 CUDA Programming: Threads, blocks, kernels, grids 13:00-14:00 Lunch break   Session 2 / 2:00pm – 6:00 pm (3:30 h lectures) L3 14:00-15:45 CUDA Tools: Compiling, debugging, profiling, occupancy calculator 15:45-16:15 Coffee break L4 16:15-18:00 CUDA Examples(1): VectorAdd, Stencil, ReverseArray   DAY 2 Session 3 / 9:00am – 1:00 pm (3:30 h lectures) L5   9:00-10:45 CUDA Examples (2): Matrices Multiply. Assorted optimizations 10:45-11:15 Coffee break L6 11:15-13:00 CUDA Examples (3): Dynamic parallelism, Hyper-Q, unified memory 13:00-14:00 Lunch break   Session 4 / 2:00pm – 6:00 pm (3:30 h practical) H1 14:00-15:45 Hands-on Lab 1 15:45-16:15 Coffee break H2 16:15-18:00 Hands-on Lab 2   DAY 3 Session 5 / 9:00am – 1:00 pm (3:30 h lectures) L7 9:00-10:45 Inside Pascal: Multiprocessors, stacked memory, NV-link 10:45-11:15 Coffee break L8 11:15-13:00 OpenACC and other approaches to GPU computing 13:00-14:00 Lunch break   Session 6 / 2:00pm – 6:00 pm (3:30 h practical) H3 14:00-15:45 Hands-on Lab 3 15:45-16:15 Coffee break H4 16:15-18:00 Hands-on Lab 4   DAY 4 Session 7 / 9:00am – 1:00 pm (3:30 h practical) H5 9:00-10:45 Hands-on Lab 5 10:45-11:15 Coffee break H6 11:15-13:00 Hands-on Lab 6 13:00-14:00 Lunch break   Session 8 / 2:00pm – 6:00 pm (3:30 h practical) H7 14:00-15:45 Hands-on Lab 7  15:45-16:15 Coffee break H8 16:15-18:00 Free Hands-on Lab End of Course The target audiences of the course are students who want to develop exciting applications for these processors, as well as those who want to develop programming tools and future implementations for these processors. Level: INTERMEDIATE: for trainees with some theoretical and practical knowledge; those who finished the beginners course ADVANCED: for trainees able to work independently and requiring guidance for solving complex problems Prerequisites: Basics of C programming and concepts of parallel processing will help, but are not critical to follow the lectures. https://events.prace-ri.eu/event/768/ 2019-04-08 07:00:00 UTC 2019-04-11 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Advanced RNA-Seq Analysis

    8 - 12 April 2019

    Cambridge, United Kingdom

    Elixir node event
    Advanced RNA-Seq Analysis https://tess.elixir-europe.org/events/advanced-rna-seq-analysis-9f0e84cd-6615-4989-9a83-f501afeb2753 The aim of this course is to familiarise the participants with advanced data analysis methodologies and provide hands-on training on the latest analytical approaches. Lectures will give insight into how biological knowledge can be generated from RNA-seq experiments and illustrate different ways of analyzing such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq data under the guidance of the lecturers and teaching assistants. 2019-04-08 09:00:00 UTC 2019-04-12 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 2, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 2 Cambridge United Kingdom CB10 1SD [] Frank O’Donnell [] [] [] [] []
  • RNA-Sequence Analysis

    8 - 12 April 2019

    Cambridge, United Kingdom

    Elixir node event
    RNA-Sequence Analysis https://tess.elixir-europe.org/events/rna-sequence-analysis This course will familiarise participants with advanced data analysis methodologies in the field of transcriptomics and to provide practical training in the latest analytical approaches. 2019-04-08 09:00:00 UTC 2019-04-12 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 2, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 2 Cambridge United Kingdom CB10 1SD [] Frank O’Donnell [] [] [] [] []
  • Intermediate stats: data analysis in practice

    8 - 9 April 2019

    Lausanne, Switzerland

    Elixir node event
    Intermediate stats: data analysis in practice https://tess.elixir-europe.org/events/intermediate-stats-data-analysis-in-practice-c75a1c84-c1c3-4f2d-ae68-1d6b39e2a6c3 Overview Do you feel unable to statistically analyse data, despite having already followed an introduction course on statistics ? If yes, this course was created for you. 2019-04-08 09:00:00 UTC 2019-04-09 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Interactive High-Performance Computing @ JSC

    9 - 10 April 2019

    Interactive High-Performance Computing @ JSC https://tess.elixir-europe.org/events/interactive-high-performance-computing-jsc Interactive exploration and analysis of large amounts of data from scientific simulations, in-situ visualization and application control are convincing scenarios for explorative sciences. Based on the open source software Jupyter or JupyterLab, a way has been available for some time now that combines interactive with reproducible computing while at the same time meeting the challenges of support for the wide range of different software workflows. Even on supercomputers, the method enables the creation of documents that combine live code with narrative text, mathematical equations, visualizations, interactive controls, and other extensive output. However, a number of challenges must be mastered in order to make existing workflows ready for interactive high-performance computing. With so many possibilities, it's easy to lose sight of the big picture. This course provides a detailed introduction to interactive high-performance computing. The following topics are covered: Opportunities and challenges of interactive HPC Functionality and interaction of the necessary components Introduction to the most important libraries Coupling and control of simulations Visualizing results interactively   Prerequisites: Experience in Python Application Registrations are only considered until 15 March 2018 due to available space, the maximal number of participants is limited. Applicants will be notified, whether they are accepted for participitation. Instructors: Jens Henrik Göbbert, Alice Grosch, JSC Contact For any questions concerning the course please send an e-mail to j.goebbert@fz-juelich.de https://events.prace-ri.eu/event/826/ 2019-04-09 07:00:00 UTC 2019-04-10 14:30:00 UTC [] [] [] workshops_and_courses [] []
  • Using the Ensembl Genome Browser

    10 April 2019

    Cambridge, United Kingdom

    Elixir node event
    Using the Ensembl Genome Browser https://tess.elixir-europe.org/events/using-the-ensembl-genome-browser-2d9e2b70-9d6f-48e2-828c-f60c49897a26 The [Ensembl Project](http://www.ensembl.org) provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences. This workshop offers a comprehensive practical introduction to the use of the Ensembl genome browser as well as essential background information. This course will focus on the vertebrate genomes in Ensembl, however much of what will be covered is also applicable to the non-vertebrates (plants, bacteria, fungi, metazoa and protists) in Ensembl Genomes. The training room is located on the first floor and there is currently no level access. 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=2827337&course-title=Using%20the%20Ensembl%20Genome%20Browser).'' 2019-04-10 08:30:00 UTC 2019-04-10 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Gene transcripts Gene structure 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 [] []
  • Ensembl REST API workshop

    11 April 2019

    Cambridge, United Kingdom

    Elixir node event
    Ensembl REST API workshop https://tess.elixir-europe.org/events/ensembl-rest-api-workshop-17fe72fb-bf8f-4699-a745-29bd19426eca The [Ensembl project](http://www.ensembl.org/) provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl [REST APIs](http://rest.ensembl.org/), including understanding the major endpoints and how to write scripts to call them. The training room is located on the first floor and there is currently no level access. 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 by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2027436&course-title=Ensembl%20REST%20API%20Workshop).'' 2019-04-11 08:30:00 UTC 2019-04-11 14:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Bioinformatics University of Cambridge Bioinformatics Training [] Bioinformaticians and wet-lab biologists who can programGraduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] []
  • Introduction to RNA-seq

    11 April 2019

    Sheffield, United Kingdom

    Introduction to RNA-seq https://tess.elixir-europe.org/events/introduction-to-rna-seq-03705bbf-08b1-4e5d-b3ff-d48069b094b4 High-throughput RNA-sequencing is now the standard technique for quantifying transcript abundance in a biological sample of interest. In this course we will describe the processes that take place once you submit a library for RNA sequencing, and what data you should expect to receive from the Bioinformatics Core. We will describe the steps involved to go from sequencing library to a list of genes that show statistically significant differences between your biological conditions of interest. Practical sessions will use the user-friendly Galaxy interface (https://usegalaxy.org/) to demonstrate tasks such as alignment, quality control and assessing differential expression. We will also showcase some web sites you can use for enrichment and pathways analysis. 2019-04-11 08:30:00 UTC 2019-04-11 16:00:00 UTC The Diamond, Workroom 1, Sheffield, United Kingdom The Diamond, Workroom 1 Sheffield United Kingdom S3 7RD [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • ELIXIR Board meeting (Bergen)

    15 - 16 April 2019

    Bergen, Norway

    ELIXIR Board meeting (Bergen) https://tess.elixir-europe.org/events/elixir-board-meeting-bergen The ELIXIR Board meeting takes place in Bergen, Norway on 15 - 16 April 2019. This meeting is only open to the ELIXIR Board and Observers. Agenda items, location and venue will be confirmed to members in the near future.  Any inquiries about ELIXIR Board meetings event should be sent to info@elixir-europe.org. 2019-04-15 09:00:00 UTC 2019-04-16 00:00:00 UTC Bergen, Norway Bergen Norway [] [] [] meetings_and_conferences [] []
  • Workshop on Mathematical and Statistical Aspects of Molecular Biology

    25 - 26 April 2019

    Cambridge, United Kingdom

    Elixir node event
    Workshop on Mathematical and Statistical Aspects of Molecular Biology https://tess.elixir-europe.org/events/workshop-on-mathematical-and-statistical-aspects-of-molecular-biology MASAMB workshop (Mathematical and Statistical Aspects of Molecular Biology) 30 years edition (1989-2019) 2019-04-25 10:00:00 UTC 2019-04-26 15:00:00 UTC EMBL-EBI - Kendrew Lecture Theatre, Cambridge, United Kingdom EMBL-EBI - Kendrew Lecture Theatre Cambridge United Kingdom CB10 1SD [] [] [] [] [] []
  • NGS - Genome variant analysis

    29 - 30 April 2019

    Bern, Switzerland

    Elixir node event
    NGS - Genome variant analysis https://tess.elixir-europe.org/events/ngs-genome-variant-analysis-61e3f31b-dcd2-48bf-b446-9a115382b002 Overview Among other genomic applications, Whole genome sequencing “WGS”, Whole Exome Sequencing “WES” and RNA sequencing are used for the detection of genomic variants. 2019-04-29 09:00:00 UTC 2019-04-30 00:00:00 UTC SIB, Bern, Switzerland SIB Bern Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • ChIP-seq and ATAC-seq analysis

    2 - 3 May 2019

    Cambridge, United Kingdom

    Elixir node event
    ChIP-seq and ATAC-seq analysis https://tess.elixir-europe.org/events/chip-seq-and-atac-seq-analysis The primary aim of this course is to familiarise participants with the analysis of ChIP-seq and ATAC-seq data and provide hands-on training on the latest analytical approaches. The course starts with an introduction to ChIP-seq experiments for the detection of genome-wide DNA binding sites of transcription factors and other proteins. We first show data quality control and basic analytical steps such as alignment, peak calling and motif analysis, followed by practical examples on how to work with biological replicates and fundamental quality metrics for ChIP-seq datasets. On the second day, we then focus on the analysis of differential binding, comparing between different samples. We will also give an introduction to ATAC-seq data analysis for the detection of regions of open chromatin. 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=2836139&course-title=ChIP-seq%20and%20ATAC-seq%20analysis).'' 2019-05-02 08:30:00 UTC 2019-05-03 16:00:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR ChIP-seq Data mining Data visualisation Functional genomics Epigenomics Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] []
  • Using MOFA for integration of omics data

    3 May 2019

    Leuven, Belgium

    Elixir node event
    Using MOFA for integration of omics data https://tess.elixir-europe.org/events/using-mofa-for-integration-of-omics-data 2019-05-03 09:30:00 UTC 2019-05-03 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Course: Genome Annotation

    6 - 9 May 2019

    Elixir node event
    Course: Genome Annotation https://tess.elixir-europe.org/events/course-genome-annotation More information will follow 2019-05-06 09:00:00 UTC 2019-05-09 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] []
  • ELIXIR Bioinformatics Suppliers Forum 2019

    7 May 2019

    United Kingdom

    ELIXIR Bioinformatics Suppliers Forum 2019 https://tess.elixir-europe.org/events/elixir-bioinformatics-suppliers-forum-2019 The ELIXIR Bioinformatics Suppliers Forum (EBSF) is a one day event for suppliers of bioinformatics services, solutions and resources. Suppliers can learn about ELIXIR services with a focus on compute and exchange technical information relating to their products through presentations or demonstrations. The Forum will be highly interactive with opportunities for informal networking as well as structured discussions and presentations. We anticipate this inaugural event will set the stage for a regular series of  meetings for bioinformatics suppliers and become an annual constant in the bioinformatics ecosystem. Aims: Give companies the chance to present technical advances in their field, and receive input on those from ELIXIR Provide a forum for knowledge exchange and collaboration in the pre-competitive space Create networking opportunities with bioinformatics opinion leaders, academic experts in ELIXIR and other industry members Provide a forum to articulate scientific and technical challenges with experts in the field and potentially develop  innovative solutions for e.g. analytics, infrastructure and AI exploitation Location Wellcome Collection, 183 Euston Road, London NW1 2BE Contacts For all logistical inquiries, please contact: Melissa Balzano (melissa.balzano@elixir-europe.org)  For all documentation inquiries, please contact: Katharina Lauer (katharina.lauer@elixir-europe.org)    2019-05-07 09:00:00 UTC 2019-05-07 09:00:00 UTC 183 Euston Road, United Kingdom 183 Euston Road United Kingdom NW1 2BE [] [] [] meetings_and_conferences [] []
  • First Steps in Parallelization with OpenMP

    8 May 2019

    Basel, Switzerland

    Elixir node event
    First Steps in Parallelization with OpenMP https://tess.elixir-europe.org/events/first-steps-in-parallelization-with-openmp-1bbfd630-8e6e-424b-93c3-692f1df61027 Overview We currently live in the era of multicore computers, where almost every computing machine has many CPUs. In order to benefit from this computational power we need to devise programs explicitly written for parallel machines. 2019-05-08 09:00:00 UTC 2019-05-08 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
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