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  • [POSTPONED] Basic Parallel Programming with MPI and OpenMP @SURFsara

    2 - 3 June 2020

    [POSTPONED] Basic Parallel Programming with MPI and OpenMP @SURFsara https://tess.elixir-europe.org/events/basic-parallel-programming-with-mpi-and-openmp-surfsara NOTE: this is the basic part of a 4-day course at SURFsara. If you wish to attend the full course, you should also register for the advanced part separately. Please check here the advanced part.   This 2-day basic course is focused on providing an introduction to parallel programming using the most widely used approaches: Message Passing Interface (MPI) and Open Multi-Processing (OpenMP). You will start exploring the benefits (and limitations) of parallel programming, and then you will explore the possibilities that task and data parallelism offer to develop multi-core and multi-node programs. Each session includes hands-on exercises to facilitate the understanding of the different constructs.   As a participant, you have already some familiarity with C or Fortran programming, and in these two days you will be able to start the development of your own parallel application. Moreover, right after this short course you will have the opportunity to continue exploring advanced topics on parallel programming and everyday use of MPI/OpenMP. For this you'll need to register for the advanced course too. https://events.prace-ri.eu/event/1004/ 2020-06-02 07:00:00 UTC 2020-06-03 15:35:00 UTC [] [] [] workshops_and_courses [] []
  • Statistical Analysis of Biological Data in R

    2 June 2020

    United Kingdom

    Statistical Analysis of Biological Data in R https://tess.elixir-europe.org/events/statistical-analysis-of-biological-data-in-r-8763da73-bed8-4cf7-8b11-dc61e09e7d32 This course provides a refresher on the foundations of statistical analysis. 2020-06-02 08:30:00 UTC 2020-06-02 16:00:00 UTC Bartolome House, Seminar Room EG03, United Kingdom Bartolome House, Seminar Room EG03 United Kingdom S10 2HQ [] bioinformatics-core@sheffield.ac.uk [] [] workshops_and_courses [] []
  • Mass spectrometry data processing - postponed

    2 - 3 June 2020

    Gent, Belgium

    Elixir node event
    Mass spectrometry data processing - postponed https://tess.elixir-europe.org/events/mass-spectrometry-data-processing-f80a1c34-fcd4-40bf-83df-1ba4b05dd38e Obtain a good understanding of the origins and properties of mass spec data Obtain an understanding of the processing of mass spec data, aimed at identifying and quantifying peptides and proteins Gain sufficient understanding of the software tools and database used, and of the issues and caveats involved, to critically analyse and assess results from mass spectrometry based proteomics experiments 2020-06-02 09:00:00 UTC 2020-06-03 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []
  • Cryo-EM sample preparation and data collection (POSTPONED)

    2 - 4 June 2020

    Elixir node event
    Cryo-EM sample preparation and data collection (POSTPONED) https://tess.elixir-europe.org/events/cryo-em-sample-preparation-and-data-collection-4921cece-9b6d-460f-a1b2-1bce618fb3d6 2020-06-02 09:00:00 UTC 2020-06-04 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • WEBINAR: Introduction to containers

    2 June 2020

    Online, Australia

    WEBINAR: Introduction to containers https://tess.elixir-europe.org/events/webinar-introduction-to-containers 2020-06-02 13:00:00 UTC 2020-06-02 14:00:00 UTC Australian BioCommons Online, Australia Online Australia Bioinformatics Australian Biocommons [] [] [] [] bioinformaticslife sciences
  • Protein Function Prediction with Machine Learning and Interactive Analytics

    3 - 4 June 2020

    Cambridge, United Kingdom

    Elixir node event
    Protein Function Prediction with Machine Learning and Interactive Analytics https://tess.elixir-europe.org/events/protein-function-prediction-with-machine-learning-and-interactive-analytics-cfca40cd-e960-416b-a96a-6a04d7e52bba This workshop explores how to conduct functional annotation of proteins through machine learning (ML) approaches. 2020-06-03 09:00:00 UTC 2020-06-04 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • Protein function prediction with machine learning and interactive analytics (Cancelled)

    3 - 4 June 2020

    Cambridge, United Kingdom

    Elixir node event
    Protein function prediction with machine learning and interactive analytics (Cancelled) https://tess.elixir-europe.org/events/protein-function-prediction-with-machine-learning-and-interactive-analytics-cancelled EMBL-EBI has taken the difficult decision to pause our programme of external courses and conferences. As a result, we are cancelling this course and apologise for the inconvenience. 2020-06-03 09:00:00 UTC 2020-06-04 17:00:00 UTC European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) Cambridge United Kingdom CB10 1SD [] Meredith Willmott [] [] [] [] HDRUK
  • Introduction to high-performance computing (sciCORE cluster) - streamed

    3 June 2020

    Streamed from Basel, Switzerland

    Elixir node event
    Introduction to high-performance computing (sciCORE cluster) - streamed https://tess.elixir-europe.org/events/introduction-to-high-performance-computing-scicore-cluster-17743d87-92b4-473f-9591-384d43fe776d This course will be streamed only for the registered participants. Registered participants will receive specific information directly from the respective course’s organizers. 2020-06-03 09:00:00 UTC 2020-06-03 00:00:00 UTC SIB, Streamed from Basel, Switzerland SIB Streamed from Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • First steps with R in Life Sciences - streamed

    3 - 4 June 2020

    Streamed from Lausanne, Switzerland

    Elixir node event
    First steps with R in Life Sciences - streamed https://tess.elixir-europe.org/events/first-steps-with-r-in-life-sciences-4ddd6df7-e4ed-4f77-a73f-8540aae27887 This course will be streamed, and accessible only for the registered participants. The course is now full with a waiting list. Application is now closed. There will be other sessions next year. Thank you for your understanding. 2020-06-03 09:00:00 UTC 2020-06-04 00:00:00 UTC SIB, Streamed from Lausanne, Switzerland SIB Streamed from Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • [POSTPONED] MPI and OpenMP in Scientific Software Development @SURFsara

    4 - 5 June 2020

    [POSTPONED] MPI and OpenMP in Scientific Software Development @SURFsara https://tess.elixir-europe.org/events/advanced-parallel-programming-with-mpi-and-openmp-surfsara NOTE: this is the advanced part of a 4-day course at SURFsara. If you wish to attend the full course, you should also register for the basic part separately. Please check here the basic part.   This 2-day advanced course describes different everyday challenges that developers of parallel code have to face in everyday work, and provides working solutions for them. Here you will see how to deal with parallel profiling and explore the knobs and dials that make your code exploit the best possible performance, just like domain decomposition techniques and parallel I/O. Each of these sessions includes hands-on exercises to facilitate the understanding of the different constructs. Moreover, you will also obtain some insight on useful parallel libraries and routines for scientific code development, like ParMETIS and PETSc.   As a participant for these two days, you already have basic knowledge on parallel programming with MPI and OpenMP using the C or Fortran programming languages, which are covered in our basic course. If you are not very familiar with these basic concepts, please register for the basic course and then you can also register for this advanced part! https://events.prace-ri.eu/event/1005/ 2020-06-04 07:00:00 UTC 2020-06-05 15:35:00 UTC [] [] [] workshops_and_courses [] []
  • Data Carpentry - ONLINE

    4 - 5 June 2020

    United Kingdom

    Data Carpentry - ONLINE https://tess.elixir-europe.org/events/data-carpentry-online-03216c87-bcbe-428e-ba6b-ad69d32ccd2e Data Carpentry trains researchers in the core data skills for efficient, shareable, and reproducible research practices. We run accessible, inclusive training workshops; teach openly available, high-quality, domain-tailored lessons; and foster an active, inclusive, diverse instructor community that promotes and models reproducible research as a community norm. 2020-06-04 09:00:00 UTC 2020-06-05 00:00:00 UTC ONLINE, United Kingdom ONLINE United Kingdom University of Edinburgh [] [] workshops_and_courses [] []
  • Course Data analysis for Metabolomics

    4 - 5 June 2020

    Wageningen, Netherlands

    Elixir node event
    Course Data analysis for Metabolomics https://tess.elixir-europe.org/events/course-data-analysis-for-metabolomics Metabolomics experiments based on mass spectrometry (MS) or nuclear magnetic resonance (NMR) produce large and complex data sets. This course will introduce approaches to process and analyse data and design high-quality experiments. Through hands-on workshops and lectures highlighting the different… The post Course Data analysis for Metabolomics appeared first on Dutch Techcentre for Life Sciences. 2020-06-04 09:00:00 UTC 2020-06-05 00:00:00 UTC Wageningen, Netherlands, Wageningen, Netherlands Wageningen, Netherlands Wageningen Netherlands [] [] [] workshops_and_courses [] []
  • GWAS and Genomic selection analysis using Galaxy - POSTPONED

    5 - 6 June 2020

    GWAS and Genomic selection analysis using Galaxy - POSTPONED https://tess.elixir-europe.org/events/gwas-and-genomic-selection-analysis-using-galaxy 2020-06-05 09:00:00 UTC 2020-06-06 00:00:00 UTC [] Organisers [] [] [] [] []
  • Reproducible and Transparent Analysis with Galaxy

    6 - 10 June 2020

    Reproducible and Transparent Analysis with Galaxy https://tess.elixir-europe.org/events/reproducible-and-transparent-analysis-with-galaxy 2020-06-06 09:00:00 UTC 2020-06-10 00:00:00 UTC [] Anton Nekrutenko [] [] [] [] []
  • Reproducible and Transparent Analysis of SARS/Cov-2 intra-host variants and differential gene expression of infected tissues using Galaxy

    6 - 10 June 2020

    Reproducible and Transparent Analysis of SARS/Cov-2 intra-host variants and differential gene expression of infected tissues using Galaxy https://tess.elixir-europe.org/events/reproducible-and-transparent-analysis-with-galaxy-9fb10ad1-7197-4f0c-9d70-49dfd966f5f4 2020-06-06 09:00:00 UTC 2020-06-10 00:00:00 UTC [] Anton Nekrutenko, Marius van den Beek [] [] [] [] []
  • RaukR, Advanced R for Bioinformatics, Summer course (NBIS course)

    7 - 19 June 2020

    Visby, Sweden

    Elixir node event
    RaukR, Advanced R for Bioinformatics, Summer course (NBIS course) https://tess.elixir-europe.org/events/raukr-advanced-r-for-bioinformatics-summer-course-nbis-course #training #url: https://www.scilifelab.se/events/raukr-advanced-r-for-bioinformatics-summer-course-2/  Important dates  Application deadline: April 3rd, 2020 Notification of acceptance/decline: April 17th, 2020 email: raukr@nbis.se course leaders: Marcin Kierzcak and Sebastian DiLorenzo 2020-06-07 09:00:00 UTC 2020-06-19 00:00:00 UTC Visby, Sweden Visby Sweden [] jessica.lindvall@scilifelab.se [] [] [] [] #trainingtraining
  • RaukR, Advanced R for Bioinformatics, Summer course (CANCELLED)

    7 - 18 June 2020

    Elixir node event
    RaukR, Advanced R for Bioinformatics, Summer course (CANCELLED) https://tess.elixir-europe.org/events/raukr-advanced-r-for-bioinformatics-summer-course-53c91aeb-5cb1-4a8c-8a91-03076abd6403 2020-06-07 09:00:00 UTC 2020-06-18 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • [POSTPONED] High-performance computing with Python @ JSC

    8 - 10 June 2020

    [POSTPONED] High-performance computing with Python @ JSC https://tess.elixir-europe.org/events/high-performance-computing-with-python-jsc-8f572b9d-fe3d-4357-a015-1be3342e47a8 This course was postponed to autumn 2020. The exact date will be fixed later. Python is increasingly used in high-performance computing projects. It can be used either as a high-level interface to existing HPC applications and libraries, as embedded interpreter, or directly. This course combines lectures and hands-on sessions. We will show how Python can be used on parallel architectures and how to optimize critical parts of the kernel using various tools. The following topics will be covered: Interactive parallel programming with IPython Profiling and optimization High-performance NumPy Just-in-time compilation with numba Distributed-memory parallel programming with Python and MPI Bindings to other programming languages and HPC libraries Interfaces to GPUs This course is aimed at scientists who wish to explore the productivity gains made possible by Python for HPC. Prerequisites: Good working knowledge of Python and NumPy Application Registrations are only considered until 7 May 2020 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, Dr. Olav Zimmermann, JSC Contact For any questions concerning the course please send an e-mail to j.meinke@fz-juelich.de https://events.prace-ri.eu/event/982/ 2020-06-08 07:00:00 UTC 2020-06-10 14:30:00 UTC [] [] [] workshops_and_courses [] []
  • [ONLINE] HPC code optimisation workshop @ LRZ

    8 - 10 June 2020

    [ONLINE] HPC code optimisation workshop @ LRZ https://tess.elixir-europe.org/events/hpc-code-optimisation-workshop-lrz-8793a2fd-4991-4524-97f3-e424f669005a          This course will be delivered as an ONLINE COURSE for remote participation because of the COVID-19 measures enforced by most European governments. REGISTRATION is strictly NECESSARY since the details to access the online course will be provided to the registered and accepted attendees only. The AGENDA is still subject to be adopted to online training. Please mind that the time has been changed to 10:00-12:00 & 13:00-16:00 CEST.   Contents In the ever-growing complexity of computer architectures, code optimization has become the main route to keep pace with hardware advancements and effectively make use of current and upcoming High Performance Computing systems. Have you ever asked yourself: Where does the performance of my application lay? What is the maximum speed-up achievable on the architecture I am using? Is my implementation matching the HPC objectives? In this workshop, we will answer these questions and provide a unique opportunity to learn techniques, methods and solutions on how to improve code, how to enable the new hardware features and how to use the roofline model to visualize the potential benefits of an optimization process. We will begin with a description of the latest micro-processor architectures and how the developers can efficiently use modern HPC hardware, in particular the vector units via SIMD programming and AVX-512 optimization and the memory hierarchy. The attendees are then conducted along the optimization process by means of hands-on exercises and learn how to enable vectorization using simple pragmas and more effective techniques, like changing data layout and alignment. The work is guided by the hints from the Intel® compiler reports, and using Intel® Advisor. Besides Intel® Advisor, the participants will also be guided to the use of Intel® VTune™ Amplifier, Intel® Application Performance Snapshot and LIKWID as tools for investigating and improving the performance of a HPC application. We further cover the Intel® Math Kernel Library (MKL), in order to show how to gain performance through the use of libraries. We provide an N-body code, to support the described optimization solutions with practical hands-on. You can ask Intel in the Q&A session about how to optimise your code. Please provide a description of your code in the registration form. Learning Goals Through a sequence of simple, guided examples of code modernization, the attendees will develop awareness on features of multi and many-core architecture which are crucial for writing modern, portable and efficient applications. A special focus will be dedicated to scalar and vector optimizations for the latest Intel® Xeon® Scalable processor, code-named Skylake, utilized in the SuperMUC-NG machine at LRZ. The workshop interleaves frontal and practical sessions. Here is a preliminary outline: Day 1 Introduction to systems and software Code modernization approach Scalar optimization Compiler autovectorization Data layout from AoS to SoA Memory access optimization SDLT (Intel® SIMD Layout Templates) / Explicit vectorization / Skylake optimization Day 2 Introduction to roofline model Intel® Advisor analysis Intel® Math Kernel Library (MKL) and other libraries Day 3 Introduction to Intel® VTune™ Amplifier Introduction to Intel® Application Performance Snapshot (APS) LIKWID ( “Like I Knew What I’m Doing.”)  Performance Tools Q&A Session Please use your own laptop or PC (with X11 support and an ssh client installed) for the hands-on sessions. For GUI applications we require the installation of vncviewer (https://www.realvnc.com/en/connect/download/viewer/ )”. The workshop is a PRACE training event organized by LRZ in cooperation with Intel and RRZE. About the Lecturers Fabio Baruffa is a senior software application engineer at Intel. He provides customer support in the high-performance computing (HPC) area and artificial intelligence software solutions at large scale. He collaborates with several research institutes in Europe to develop prototypes of quantum computing algorithm simulations running on current HPC systems. Prior at Intel, he has been working as HPC application specialist and developer in the largest supercomputing centers in Europe, mainly the Leibniz Supercomputing Center and the Max-Plank Computing and Data Facility in Munich, as well as Cineca in Italy. He has been involved in software development, analysis of scientific code and optimization for HPC systems. He holds a PhD in Physics from University of Regensburg for his research in spintronics devices and quantum computing. Gennady Fedorov is a Technical Consulting Engineer supporting technical and Intel Performance Libraries ( IPP, MKL and DAAL) within the Intel Architecture, Graphics and Software Group at Intel in Russia. His focus areas are Image Processing, Crypto, Compressing techniques, High Performance Computing and Artificial Intelligence. Thomas Gruber (né Röhl) collected experience with all kinds of clustering approaches during his apprenticeship at the Erlangen Regional Computing Center (RRZE), the IT service provider for the Friedrich-Alexander-University Erlangen-Nuernberg (FAU). Afterwards, he studied Computer Science at RWTH Aachen University with emphasis on parallel programming and operating system kernel development. At the same time, he worked as a research assistant for the HPC group of the RWTH IT center. After receiving his M. Sc. degree, he went back to RRZE to work for the HPC group. Thomas Gruber leads the development of the performance tool suite LIKWID, which comprises easy-to-use tools for hardware performance monitoring, affinity control and micro-benchmarking. He also works on projects involving monitoring and analysis of hardware performance data. Carla Guillen works as a researcher in the application support group at the LRZ. She obtained her PhD in computer science at the Technische Universitaet Muenchen in 2015. She joined the LRZ in 2009, and has been working in the fields of system-wide performance monitoring and energy optimization of large scale clusters. Gerald Mathias works in the application support for the HPC systems at LRZ since 2015 and leads the Biolab@LRZ. After his PhD in Computational Biopyhsics at the LMU Munich he joined the chair of Theoretical Chemistry at the RUB in Bochum afterwards as a postdoc. He is experienced in the development and optimization of highly parallel ab initio and force field based molecular dynamics codes, both in Fortran and C. Michael Steyer is a Technical Consulting Engineer supporting technical and High Performance Computing segments within the Intel Architecture, Graphics and Software Group at Intel in Germany. His focus areas are High Performance Computing and Artificial Intelligence. Igor Vorobtsov has more than 11 years of experience in the areas of C/C++ and Fortran compilers, application tuning and developer support. Igor got a Master of Science degree in Applied Mathematics. Since joining Intel in 2008, Igor has worked as a Technical Consulting Engineer supporting software developers throughout EMEA region. Igor has a broad array of application experience, including enterprise applications and high performance computing environments. https://events.prace-ri.eu/event/1003/ 2020-06-08 08:00:00 UTC 2020-06-10 14:00:00 UTC [] [] [] workshops_and_courses [] []
  • Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT)

    8 June - 9 August 2020

    Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT) https://tess.elixir-europe.org/events/bacterial-genomes-comparative-genomics-using-artemis-comparison-tool-act-34117159-0fd6-4263-8a2c-9882b99f2572 # 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 2020-06-08 09:00:00 UTC 2020-08-09 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] comparativegenomicsHDRUK
  • FlowSOM for handling cytometry data - postponed

    8 June 2020

    Zwijnaarde, Belgium

    Elixir node event
    FlowSOM for handling cytometry data - postponed https://tess.elixir-europe.org/events/flowsom-for-handling-cytometry-data-11ea1188-9c4e-498f-9f5f-af44bcddad4a Participants will learn how to handle cytometry data in R, including quality control, visualization, clustering and comparison of samples. This will be demonstrated on an example dataset, but participants are welcome to bring some of their own fcs files to explore in addition. 2020-06-08 09:00:00 UTC 2020-06-08 00:00:00 UTC VIB Bioinformatics Core Bio-Accelerator Meeting Center Ghent, Zwijnaarde, Belgium Bio-Accelerator Meeting Center Ghent Zwijnaarde Belgium 9052 [] [] [] [] [] []
  • ELIXIR All Hands 2020

    8 - 10 June 2020

    Amsterdam, Netherlands

    ELIXIR All Hands 2020 https://tess.elixir-europe.org/events/elixir-all-hands-2020 Timeline 27 April 2020 Agenda for the virtual All Hands meeting is published. 4 May 2020 Registration and poster submission opens for the virtual All Hands meeting. 1 June 2020 Registration for meeting, workshops and mini symposia and poster submission closes. The sixth ELIXIR All Hands meeting will take place virtually 8 -10 June 2020. The meeting brings together members of the ELIXIR community from across the ELIXIR Nodes, and collaborators from partner organisations, in order to review ELIXIR’s achievements and activities so far and discuss plans for the future. We welcome attendance from participants from ELIXIR Nodes and invited guests. Registration Registration to the virtual All Hands is now open. The registration link is at the top of this page when you are logged in. If you are not logged in then log in to view the link. Those who already registered to the face-to-face meeting will not need to register again, but have been sent a confirmation of attendance to the virtual meeting. Additionally, participants currently on the reserve list will be asked to register. If you need to cancel your registration, please contact allhands@elixir-europe.org. Posters Participants of the meeting are invited to present a poster to enable all researchers with an interest to contact you and ask questions. Submitted posters will be made accessible via the ELIXIR Gateway on the F1000Research platform and we will advertise the online poster area at various times across the virtual ELIXIR All Hands 2020 meeting. We will also be awarding prizes to each of the top three posters, as selected by our Poster Prize Committee. In order to be eligible, and for your work to be seen by as many people as possible, we ask that you submit your abstract to EasyChair by Monday 1 June 2020. The link for submissions is at the top of this page when you are logged in. If you are not logged in then log in to view the links. Code of Conduct The ELIXIR Code of Conduct has been created to ensure that people at ELIXIR events can interact with each other in a respectful and safe environment. It provides ways you can voice your concern if you believe there has been a breach to this Code of Conduct. The ELIXIR Code of Conduct will be in place at this event. Note: The virtual All Hands meeting ends on Wednesday 10 Jun 2020 at 16:00 BST. There are two project meetings taking place virtually on 11 June: the CONVERGE AGM and the Federated Human Data Strategic Implementation Study meeting. Both of these meetings are restricted to named project partners. 2020-06-08 09:00:00 UTC 2020-06-10 16:00:00 UTC Eye Filmmuseum, Amsterdam, Netherlands Eye Filmmuseum Amsterdam Netherlands 1031 KT [] [] [] meetings_and_conferences [] []
  • Analyse Next Generation Sequencing (NGS) data

    8 June 2020

    Leiden, Netherlands

    Elixir node event
    Analyse Next Generation Sequencing (NGS) data https://tess.elixir-europe.org/events/analyse-next-generation-sequencing-ngs-data Deze tweedaagse workshop geeft toepasbare up to date informatie over NGS. Verschillende platforms, de werking van sequencers en nucleïnezuur isolatie komen uitvoerig aan bod. De analyse van NGS data bij DNA en RNA sequencing wordt geïntroduceerd. Verschillende toepassingen zoals genoom… The post Analyse Next Generation Sequencing (NGS) data appeared first on Dutch Techcentre for Life Sciences. 2020-06-08 09:00:00 UTC 2020-06-08 00:00:00 UTC Leiden, Netherlands, Leiden, Netherlands Leiden, Netherlands Leiden Netherlands [] [] [] workshops_and_courses [] []
  • Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT)

    8 June - 9 August 2020

    Bacterial Genomes: Comparative Genomics using Artemis Comparison Tool (ACT) https://tess.elixir-europe.org/events/bacterial-genomes-comparative-genomics-using-artemis-comparison-tool-act-78fb77a6-ce29-4ed5-a32b-56b7f46a5d8e # 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 2020-06-08 09:00:00 UTC 2020-08-09 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] comparativegenomicsHDRUK
  • [ONLINE] Parallel Programming with OpenMP and MPI @ VSC Belgium & SURFsara

    9 - 12 June 2020

    [ONLINE] Parallel Programming with OpenMP and MPI @ VSC Belgium & SURFsara https://tess.elixir-europe.org/events/online-parallel-programming-with-openmp-and-mpi-vsc-belgium-surfsara Overview The Flemish Supercomputing Center (VSC, Belgium) and SURFsara (The Netherlands) are organizing this online course on parallel programming using OpenMP and MPI. The materials of this course have been developed by Dr. Rolf Rabenseifner (HLRS, Stuttgart). Course format The training sessions will be provided online using the Blackboard Collaborate system. More information on how to access the system for the training sessions and how to follow the course will be provided soon. Course level Basic content: 40 % Intermediate content: 40 % Advanced content: 20 % After every day there will be a round of "Questions and Answers". Indicative timetable Tue 9th of June   09:00    Welcome and presentation 09:10    Introduction to parallel computing 10:00    An overview of OpenMP: execution model 10:30    Coffee break 10:45    Worksharing directives 12:30    Lunch break 13:30    Data environment and combined constructs 15:00    Coffee break 15:15    Optimization and pitfalls 16:00    Summary / Questions and Answers    16:30    End of first day   Wed 10th of June 09:00   MPI Overview 10:30   Coffee break 10:45   MPI Process Model 11:30   Messages and Point-to-Point Communication 12:30   Lunch break 13:30   Messages and Point-to-Point Communication (cont.) 14:00   Non-Blocking Communication 15:00   Coffee break 15:15   Error handling and new Fortran module 16:00   Summary / Questions and Answers    16:30   End of second day   Thu 11th of June 09:00   Collective Communication 10:30   Coffee break 10:45   Groups & Communicators 12:30   Lunch break 13:30   Virtual Topologies 15:00   Coffee break 15:15   Derived Datatypes 16:00   Summary / Questions and Answers 16:30   End of third day   Fri 12th of June 09:00   One-sided Communication 10:30   Coffee break 10:45   Shared Memory 12:30   Lunch break 13:30   MPI + Threads 14:15   Parallel I/O 15:00   Coffee break 15:15   Best practices 16:00   Summary / Questions and Answers   16:25   Closing  16:30   End of fourth day https://events.prace-ri.eu/event/1028/ 2020-06-09 07:00:00 UTC 2020-06-12 14:30:00 UTC [] [] [] workshops_and_courses [] []
  • First steps in Python, and more!

    9 - 11 June 2020

    Basel, Switzerland

    Elixir node event
    First steps in Python, and more! https://tess.elixir-europe.org/events/first-steps-in-python-and-more Overview Python is an open-source and general-purpose scripting language which runs on all major operating systems. 2020-06-09 09:00:00 UTC 2020-06-11 00:00:00 UTC SIB, Basel, Switzerland SIB Basel Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Recombinant Protein Expression, postponed

    9 June 2020

    Elixir node event
    Recombinant Protein Expression, postponed https://tess.elixir-europe.org/events/recombinant-protein-expression The training will start with an introduction on the available recombinant protein expression systems, with their advantages and limitations, from which to choose for your favorite protein. Also, high-throughput protein expression, expression in plant cells, antibody and nanobody expression and a difficult-to-express protein case will be discussed. A next session will focus on strategy design to optimize protein purification and how to address quality assurance of the purified proteins. For clinical use of a protein-based biological stability and production yields are critical issues that come on top of the desired therapeutic efficacy. Why and how to deal with these critical aspects will be addressed as well during the training. Furthermore, also the key steps that are required for optimal protein formulation will be reviewed. We plan to end the day with a keynote talk from a pharma industry speaker illustrating the issues that need to be considered when engineering recombinant proteins for clinical applications. 2020-06-09 09:00:00 UTC 2020-06-09 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []
  • Analyzing flow cytometry data using FlowJo - postponed

    9 June 2020

    Ghent, Belgium

    Elixir node event
    Analyzing flow cytometry data using FlowJo - postponed https://tess.elixir-europe.org/events/analyzing-flow-cytometry-data-using-flowjo-c46f238c-d46d-45cd-ac64-df9421f741b6 Learn researchers how to analyze flow cytometry data in an efficient way using FlowJo v10,the world’s nr.1 analysis software tool for flow cytometry data. This training will make you familiar with all the basic and advanced features of FlowJo v10. In the end you will be able to analyze and visualize your flow data and learn how to get the statistics out of it 2020-06-09 09:00:00 UTC 2020-06-09 00:00:00 UTC VIB Bioinformatics Core Clemenspoort Gent, Ghent, Belgium Clemenspoort Gent Ghent Belgium 9000 [] [] [] [] [] []
  • Using MOFA for integration of omics data - postponed

    9 June 2020

    Gent, Belgium

    Elixir node event
    Using MOFA for integration of omics data - postponed https://tess.elixir-europe.org/events/using-mofa-for-integration-of-omics-data-f849603e-3ab6-453b-b6d4-6d22f3666d6e Participants can bring their own data to 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? 2020-06-09 09:00:00 UTC 2020-06-09 00:00:00 UTC VIB Bioinformatics Core iGent, Gent, Belgium iGent Gent Belgium 9052 [] [] [] [] [] []
  • Genome Assembly Using Galaxy

    9 - 10 June 2020

    Genome Assembly Using Galaxy https://tess.elixir-europe.org/events/genome-assembly-using-galaxy-566d571d-4b1b-4412-848d-6eec1ae4baef 2020-06-09 09:00:00 UTC 2020-06-10 00:00:00 UTC [] QCIF [] [] [] [] []

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