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  • Image processing for correlated and multimodal imaging techniques

    19 October 2020 - 8 March 2022

    Elixir node event
    Image processing for correlated and multimodal imaging techniques https://tess.elixir-europe.org/events/image-processing-for-correlated-and-multimodal-imaging-techniques The purpose of this event is to dedicate three days of intense training to an audience with little or basic expertise. The program will first cover a full day of online lectures (19 October 2020), followed by two days of hands-on training (8 & 9 March 2021, Ghent). 2020-10-19 09:00:00 UTC 2022-03-08 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []

  • Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance

    1 January - 31 December 2021

    Bacterial Genomes: Disease Outbreaks and Antimicrobial Resistance https://tess.elixir-europe.org/events/bacterial-genomes-disease-outbreaks-and-antimicrobial-resistance-b178602b-e29f-4ac7-afbf-5deafd52f8dd # Overview * **Duration**: There is no longer a live period for this course, and there will be no live monitoring of the forums, but you can still join and complete the course throughout 2021. * Free * Certificate of achievement available on satisfactory completion * **CPD Approval**: Royal College of Pathologists (9 credits), Royal College of Nursing (9 credits)** ** ### Why join the course? The increase in resistance of harmful bacteria to antibiotics is a major global threat to health. Here we explore bacterial genomes and the use of genome sequencing to identify and track these drug resistant bacteria. Join us to discover how genome research is helping scientists and healthcare professionals track disease outbreaks and prevent the rise of antibiotic resistant ‘superbugs’. ### Who is the course for? This course will be of interest to scientists, healthcare professionals, biomedical researchers and bioinformaticians. The course offers all learners an opportunity to learn about genomes, disease, and antimicrobial resistance. You require no previous knowledge of genome science to complete the course. ### What do people say about this course? "_I would definitely point students to this resource. Text, videos, and figures were all very well done._" Pablo Tsukayama, Assistant Professor of Microbiology "_A highlight of the course was the introduction to whole genome sequencing – new information for me._" Christine Laws, Medical Doctor “_Exchanging genetic information quickly throughout the world is clearly going to revolutionise the ability to combat disease._” Prue van der Hoorn, Artist # Programme and start dates ### What topics will you cover? * Diseases caused by bacteria * What bacterial genomes look like * Genome sequencing technology * Mechanisms of transmission and resistance * Genomic epidemiology – tracking the spread of bacterial pathogens * Antimicrobial resistance ### What will you achieve? By the end of the course, you'll be able to... * Explain why some bacteria are pathogenic * Explore the structure of bacterial genomes * Describe the uses of different genome sequencing technologies * Investigate how genome data are used to track the spread of bacterial disease * Discuss the role of genome sequencing in stopping the spread of antimicrobial resistance # Educators ## **Lead Educators** **[Dr Adam Reid][1]** I am a senior staff scientist at the Wellcome Sanger Institute near Cambridge in the United Kingdom. I'm interested in using genomics and bioinformatics to better understand infectious diseases. **[Dr Josie Bryant][2]** I am a Henry Wellcome Postdoctoral Fellow in the University of Cambridge, Department of Medicine. I am working on bacterial genomics and evolution with a focus on within-patient microbial diversity ### Dr Francesca Short I am a scientist at the Wellcome Sanger Institute. I am interested in using functional genomics techniques to understand infections caused by the bacterium _Klebsiella pneumoniae_. ## **Programme Lead Educator** **[Professor Nicholas Thomson][3]** I am a Group Leader at the Wellcome Sanger Institute. I provide scientific oversight for this course. I am interested in bacterial evolution and the spread of infectious disease. ### The course also features interviews with distinguished scientists, including: * **[Mathew Beale][4]** - Wellcome Sanger Institute * **[Daryl Domman][5]** - Wellcome Sanger Institute * **[Gal Horesh][6]** - Wellcome Sanger Institute * **[Catherine Ludden][7]** - London School of Hygiene and Tropical Medicine * **[Tapoka Mkandawire][8]** - Wellcome Sanger Institute * **[Julian Parkhill][9]** - Wellcome Sanger Institute * **Lindsay Pike** - Wellcome Sanger Institute * **[Michael Quail][10]** - Wellcome Sanger Institute * **[Susannah J. Salter][11]** - Wellcome Sanger Institute * **[Estee Torok][12]** - Addenbrooke’s Hospital and University of Cambridge [1]: http://www.sanger.ac.uk/people/directory/reid-adam-james [2]: https://www.infectiousdisease.cam.ac.uk/directory/josie-bryant [3]: http://www.sanger.ac.uk/people/directory/thomson-nicholas-robert [4]: http://www.sanger.ac.uk/people/directory/beale-mathew [5]: http://www.sanger.ac.uk/people/directory/domman-daryl [6]: http://www.sanger.ac.uk/people/directory/horesh-gal [7]: https://www.lshtm.ac.uk/aboutus/people/ludden.catherine [8]: http://www.sanger.ac.uk/people/directory/mkandawire-tapoka-t [9]: http://www.sanger.ac.uk/people/directory/parkhill-julian [10]: http://www.sanger.ac.uk/people/directory/quail-michael-andrew [11]: http://www.sanger.ac.uk/people/directory/salter-susannah-j [12]: https://www.infectiousdisease.cam.ac.uk/directory/et317@medschl.cam.ac.uk # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible # CDP Approval 2021-01-01 09:00:00 UTC 2021-12-31 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] bacterialgenomesAMRHDRUK

  • What is Genetic Counselling?

    25 January - 19 April 2021

    What is Genetic Counselling? https://tess.elixir-europe.org/events/what-is-genetic-counselling-fe2fc46a-63e5-4681-b66f-575aac9b49b7 # Overview * **Duration:** 6 weeks live, 2 hours per week * **Free** * **Certificate of achievement** available on satisfactory completion * **Start Date:** The course is run ‘live’ for 6 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period. ### Why join the course? Who are genetic counsellors? Who has genetic counselling and what does a genetic counsellor do? On this course, you will find the answers to these questions whilst learning about the role of genetic counselling in healthcare and the genomic era. You will discover why people seek genetic counselling and how it compares in different contexts and countries. You will explore the main skills and knowledge needed of a genetic counsellor, as well as their key responsibilities to patients. You will also discuss the ethical issues of genetic counselling, and its varied opportunities and challenges for the future. ### Who is the course for? This course is designed for healthcare professionals, clinicians, biomedical research scientists, and anyone curious about genetic counselling. Although not required, a basic knowledge of genetics, genetic testing technologies, and inheritance patterns would help support your learning on this course. ### What do people say about this course? _"What a great course. Perfect introduction to genetic counseling. This has given me a very real insight into the work that is carried out prior to my role in a genetic testing laboratory. Also overwhelming to think of the hours that go into the counselling sessions, ensuring patients are prepared, informed and able to make their own decisions." - Previous Participant_ _"Thank you very much for such an informative, enjoyable and though-provoking course. I have learnt a lot during these six weeks and I definitely know more now than I did prior to starting! I am glad to say that this has increased my interest in Genetic counselling as a profession and am very likely going to pursue it as a career." - Previous Participant_ _"Thank you Anna and Jonathan for a very interesting course, I have enjoyed the role play as it allowed me to be in the GC and clients shoes, and discussing my thoughts/comments with my fellow learners, and learning about the difference in other countries that was shared. Kept me gripped learning something new." _- _Previous Participant_ _"It has been a great and interesting time in the last six weeks. Understanding the personal feelings/ views of patients (autonomy, empathy, patience, etc), professional ways of communication in GC, ethics of GC, with the professional know how of the Genetic Counsellors; the different contexts of Genetic Services in different countries,and also sharing the view of my co-learners, has been a great experience._ _These will greatly assist in the discharge of my duties to the the patients as I come across them whether at my duty post or elsewhere."_ - Previous Participant # Programme ### What topics will you cover? * Why people would see a genetic counsellor * Some of a genetic counsellor’s key tasks * A genetic counsellor’s key skills and knowledge: counselling skills, medical and scientific knowledge * Ethical issues in genetic counselling * What the future might hold for genetic counsellors ### What will you achieve? By the end of the course, you'll be able to... * Identify why people have genetic counselling and the different contexts in which people receive genetic counselling * Describe the different skills and knowledges needed by genetic counsellors * Compare genetic counselling in different contexts and different countries * Reflect on some ethical issues that arise in genetic counselling * Discuss the role of genetic counselling in healthcare as we enter the ‘genomic era'. ### What software or tools do you need? No specific software, hardware or other resources are required to complete the course. # Educators ## Lead Educators ### Anna Middleton I am the Chair of the Association of Genetic Nurses and Counsellors in the UK and ROI (2018/19) and Head of Society and Ethics Research at the Wellcome Genome Campus, Connecting Science, Cambridge, UK ### Jonathan Roberts I am a pre-registration genetic counsellor at Addenbrooke’s Hospital, Cambridge. I am also a Staff Scientists at the Wellcome Genome Campus. I conduct my research within the Society and Ethics Research group. # What's Included Wellcome Genome Campus Advanced Courses and Scientific Conferences are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get: * Unlimited access to this course * Includes any articles, videos, peer reviews and quizzes * Tests to validate your learning * A PDF Certificate of Achievement to prove your success when you’re eligible 2021-01-25 09:00:00 UTC 2021-04-19 23:59:59 UTC Wellcome Genome Campus - Advanced Courses [] advancedcourses@wellcomegenomecampus.org [] [] workshops_and_courses [] geneticcounsellingHDRUK

  • [ONLINE] Fortran for Scientific Computing @ HLRS

    12 - 16 April 2021

    [ONLINE] Fortran for Scientific Computing @ HLRS https://tess.elixir-europe.org/events/online-fortran-for-scientific-computing-hlrs Overview This course will be provided as ONLINE course (using Zoom).   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/1113/ 2021-04-12 06:30:00 UTC 2021-04-16 13:30:00 UTC [] [] [] workshops_and_courses [] []

  • LIPID MAPS Spring School

    12 - 16 April 2021

    Cardiff, United Kingdom

    LIPID MAPS Spring School https://tess.elixir-europe.org/events/lipid-maps-spring-school This Spring School will focus on theoretical and practical aspects of lipidomics, using state-of-the-art approaches. There will be a major focus on the underlying biology and biochemistry of lipids, including their roles in health and disease. There will be 20+ sessions over 5 days, topics include neutral lipids, fatty acids, eicosanoids, sphingolipids, sterols and bile acids. An introduction to MS-based lipidomics will cover all aspects from sample preparation, storage, chromatography, instrumentation, and identification using databases including LIPID MAPS. There will be a dedicated session on novel technologies, such as iKnife, REIMS, imaging, and new standards for quantitation. This will be alongside practical tutorials on software and informatics tools for lipidomics. An introduction into data integration using biostatistics and systems biology, to include lipid 2021-04-12 09:00:00 UTC 2021-04-16 17:00:00 UTC Cardiff University Park Plaza Cardiff, Greyfriars Road, Cardiff, United Kingdom Park Plaza Cardiff, Greyfriars Road Cardiff United Kingdom CF10 3AL [] [] Early Career Researcher [] [] lipidomics

  • Bioinformatics carpentry utilizing Galaxy

    12 - 16 April 2021

    Bioinformatics carpentry utilizing Galaxy https://tess.elixir-europe.org/events/bioinformatics-carpentry-utilizing-galaxy Educators: de.STAIR Partners Date: April 12-16, 2021, 09:00 - 12:00 (MEZ) Location: Online Training Content: The upcoming training course is divided into five consecutive days, centered on bioinformatic questioning and utilizing Galaxy. Each training course is divided into an interactive lecture followed by a hands-on session. Each day will start with an optional discussion about the previous hands-on. We aim to convey the following topics. Monday, April 12th - Introduction to Galaxy Tutor: Steffen C. Lott In the first lesson, we will dive into the Galaxy platform to master data handling focused on bioinformatics. Here, we get to know the benefits of using Galaxy, the FAIR principles, version control, batch processing, and workflow design. Additionally, sharing data and working with Galaxy histories will also be part of this session. Tuesday, April 13th - Data formatting Tutor: David Brauer Galaxy and its integrated tools offer a flexible way for analyzing complex and diverse data. While autonomously generated data, such as RNA-seq data, are "usually ready-to-go", manually formatted data, like spreadsheets and other text documents, are more challenging to integrate. This course aims to give you an overview of the data formatting tools in Galaxy. We will showcase simple operations like transposing rows and columns and further introduce more complex data operations using regular expressions and UNIX utilities like "sed" and "awk". Wednesday, April 14th - Transcriptomics Tutor: Markus Wolfien This session will introduce the RNA-Seq data analysis capabilities of the Galaxy framework for scientific data analyses. We will compare current RNA-Seq technologies to meet specific research questions and show initial data exploration as well as quality control of NGS datasets. Further, concepts of genome alignment and data visualization will be introduced. Thursday, April 15th - Machine learning Tutor: Maximilian Hillemanns Machine Learning (ML) has become an indispensable part of today's data processing techniques. Nowadays, researchers are using Support Vector Machines (SVMs), Random Forests (RFs), and Convolutional Neural Networks (CNNs) to analyze their data. This session provides an introduction to different ML technologies and their applications using Galaxy. Together we will address the following questions: How can I use ML, and is it suitable to analyze my data, and what can ML tell me about my data (or not)? Friday, April 16th - Workflow Generator Tutor: Konstantin Riege This course showcases the setup of the de.STAIR Galaxy flavor, which enables you to set up a customized Galaxy instance on your own system. This Galaxy instance comprises our established workflow generator plugin, which leverages on a new concept of Galaxy Atoms that combines interactive tours and alternative tools. With this technology, we can build personalized, reusable Galaxy workflows in a guided and self-educated fashion. Here, we do also recap learning goals from previous training sessions. Prerequisites: This workshop is intended for students and researchers with a background in life sciences and a functional web browser. Keywords: Galaxy, Machine Learning, Docker, Galaxy Flavors, Interactive Tours, Transcriptomics, Data formatting Tools: Galaxy (https://usegalaxy.eu) 2021-04-12 09:00:00 UTC 2021-04-16 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []

  • KNIME Analytics Platform for Data Scientists (Life Science): Advanced - Online

    12 - 16 April 2021

    KNIME Analytics Platform for Data Scientists (Life Science): Advanced - Online https://tess.elixir-europe.org/events/knime-analytics-platform-for-data-scientists-life-science-advanced-online Educators: NN Date: April 12, 13, 14, 15: 5 - 6:15 PM UTC +2 (Berlin) April 16, 2021: 5 PM - 5:15 PM UTC +2 (Berlin) Location: Online Contents: This course builds on the [L1-LS] KNIME Analytics Platform for Data Scientists (Life Science): Basics by introducing advanced data science concepts using Life Science examples. Learn all about flow variables, different workflow controls such as loops, switches, and error handling. Find out how to automatically find the best parameter settings for your machine learning model, get a taste for ensemble models, parameter optimization, and cross validation and see how Date/Time integrations work. This is an instructor-led course consisting of four, 75-minutes online sessions run by one of our KNIME data scientists. Each session has an exercise for you to complete at home and together, we will go through the solution at the start of the following session. The course concludes with a 15-minute wrap up session. Course Content: • Session 1: Flow Variables • Session 2: Workflow Control - Loops, Switch and Try Catch • Session 3: Advanced Machine Learning - Ensemble Models, Parameter Optimization, and Cross Validation • Session 4: Integrated Deployment & Date/Time Data The course fee is 50€ + VAT. Learning goals: Usage of KNIME in Life Science, Data Manipulation, Visualization, Exploration, Similarity Search Prerequisites: You should be an advanced KNIME user and ideally have already built some workflows. This course doesn’t provide an introduction to KNIME Analytics Platform - it focuses on more advanced data science concepts. You need your own laptop, ideally pre-installed with the latest version of KNIME Analytics Platform, which you can download at knime.com/downloads. Keywords: Data Science, Life Science, KNIME, Exploration Tools: KNIME 2021-04-12 09:00:00 UTC 2021-04-16 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []

  • Galaxy and Jupyter for RNA-Seq and complex data analyses

    12 - 17 April 2021

    Galaxy and Jupyter for RNA-Seq and complex data analyses https://tess.elixir-europe.org/events/galaxy-and-jupiter-for-rna-seq-and-complex-data-analyses 2021-04-12 09:00:00 UTC 2021-04-17 00:00:00 UTC [] Steffen C. Lott, David Brauer, Markus Wolfien, Maximilian Hillemanns, Konstantin Riege [] [] [] [] []

  • Core Statistics (ONLINE LIVE TRAINING)

    13 - 27 April 2021

    Cambridge, United Kingdom

    Elixir node event
    Core Statistics (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/core-statistics-online-live-training-372cc372-3912-4b4b-841e-95abaa36090a PLEASE NOTE that this course will be taught live online, with tutors available to help you throughout if have any questions. All resources and lectures will be recorded and uploaded to the course VLE page so that you will be able to access that information even if technical or time zone restrictions means that you aren't able to join us for all of the live sessions. This [award winning](https://www.cambridge.org/core/cambridge-technology-enabled-learning-prize-2020) virtually delivered course is intended to provide a strong foundation in practical statistics and data analysis using the R or Python software environments. The underlying philosophy of the course is to treat statistics as a practical skill rather than as a theoretical subject and as such the course focuses on methods for addressing real-life issues in the biological sciences. There are three core goals for this course: # Use R or Python confidently for statistics and data analysis # Be able to analyse datasets using standard statistical techniques # Know which tests are and are not appropriate Both R and Python are free software environments that are suitable for statistical and data analysis. In this course, we explore classical statistical analysis techniques starting with simple hypothesis testing and building up to linear models and power analyses. The focus of the course is on practical implementation of these techniques and developing robust statistical analysis skills rather than on the underlying statistical theory. After the course you should feel confident to be able to select and implement common statistical techniques using R or Python and moreover know when, and when not, to apply these techniques. 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=3816286&course-title=Core%20Statistics).'' 2021-04-13 08:30:00 UTC 2021-04-27 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individualsThis course is included as part of several DTP and MPhil programmesas well as other departmental training within the University of Cambridge (potentially under a different name) so participants who have attended statistics training elsewhere should check before applying. workshops_and_courses [] HDRUK

  • OpenMS Developer Meeting 2021

    15 - 16 April 2021

    OpenMS Developer Meeting 2021 https://tess.elixir-europe.org/events/openms-developer-meeting-2021 Educators: Julianus Pfeuffer (CIBI), Timo Sachsenberg (CIBI) Date: 15-16 April 2021 Location: Online Contents: The OpenMS developer meeting brings bioinformaticians working in computational mass spectrometry together to shape the future development of OpenMS. It is targeted to core developers, new developers, and potential future contributors. Short talks, developer tutorials, and code sprints will be intertwined. Participants will have the opportunity to design custom tools and workflows together with instructors. External users are welcome to bring their own ideas and will receive detailed feedback as well as help getting started in OpenMS development. Progress will be tracked on our GitHub page with a resume of each day. Prerequisites: Target audience: This developer retreat is targeted to core, new and potential future developers of the OpenMS library and its tools. Software requirements: For the retreat we require a working installation of any supported compiler, cmake, git, doxygen and OpenMS’ contrib libraries. Basic knowledge in C++ is highly beneficial. Learning goals: - Developing algorithms and tools with the OpenMS library - Working with OpenMS, its build system, and its datastructures - Documenting code with Doxygen - Deeper insights into new and established algorithms of the library - Learning the GitHub workflow of OpenMS - Designing and implementing tools or kernel classes in OpenMS Keywords: LC-MS-based proteomics and metabolomics, OpenMS, C++, algorithms for mass spectrometry, software engineering/design Tools: OpenMS, git, cmake, C++ gcc / clang toolchain 2021-04-15 09:00:00 UTC 2021-04-16 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []

  • [ONLINE] HIP 101 Workshop @ ENCCS/CSC

    16 April 2021

    [ONLINE] HIP 101 Workshop @ ENCCS/CSC https://tess.elixir-europe.org/events/online-hip-101-workshop-enccs-csc With the upcoming LUMI supercomputer (https://www.lumi-supercomputer.eu/) arriving this year in Finland, as well as the Dardel supercomputer (https://www.pdc.kth.se/hpc-services/computing-systems/dardel) arriving this and next year to PDC in Stockholm, ENCCS and CSC are providing a series of training events for future users of these new systems. The main partitions of both LUMI and Dardel will be based on AMD GPUs – users should thus be ready to port their applications to this new architecture. This training event will be about porting CUDA applications to HIP. It will provide an extensive dive into the Hipify tools and showcase many examples. CSC’s Puhti system with Nvidia GPUs will be used for the hands-on part of the training and we will work on a number of different examples in hands-on sessions. This event is open to people affiliated with Swedish universities and industries who want to start using Dardel and LUMI and who have codes that need to be ported to the AMD architecture. Training accounts will be provided for accessing Puhti supercomputer The deadline for the registration is April 9th. Learning Outcome After this course the participants will know how to use the AMD Hipify tools to convert CUDA codes to HIP. They will be familiar with the AMD architecture, issues that could arise from the code conversion and the differences between CUDA and HIP. Prerequisites In order to take the course, the participant should be familiar with GPU concepts and CUDA. Any experience with GPUs is welcome. Examples and exercises will be available in different programming languages, including Fortran and C. Agenda (Times are in CET) Time Topic 09:00–10:00 Introduction to AMD architecture, HIP, and Hipify tools 10:00–10:15 Break 10:15-10:45 Deep dive to Hipify tools and examples 10:45-11:30 Lunch 11:30-12:10 Hands-on sessions 12:10-12:20 Break 12:20-13:00 Hands-on sessions Registration Registration will open soon. Contact For any questions send an email to Thor Wikfeldt at ENCCS (kjartan.thor.wikfeldt@it.uu.se) or Georgios Markomanolis at CSC (georgios.markomanolis@csc.fi). Original event page: https://enccs.se/events/2021/04/hip101-workshop/ https://events.prace-ri.eu/event/1187/ 2021-04-16 07:00:00 UTC 2021-04-16 11:00:00 UTC [] [] [] workshops_and_courses [] []

  • [ONLINE] Introduction to OpenACC @ BSC

    16 April 2021

    [ONLINE] Introduction to OpenACC @ BSC https://tess.elixir-europe.org/events/introduction-to-openacc-bsc-a4bc8c7d-e1a2-4dc6-b19c-114e45fc8727 All PATC Courses at BSC do not charge fees.   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. 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. Further information: In the context of virtual meetings, the Organiser may facilitate live webstreaming and audio recording. You have the option to opt out of inclusion in recordings by contacting our Education&Training team. CONTACT US for further details about MSc, PhD, Post Doc studies, exchanges and collaboration in education and training with BSC. For further details about Postgraduate Studies in UPC - Barcelona School of Informatics (FiB), visit the website Sponsors: BSC and PRACE 6IP project are funding the PATC @ BSC training events. If you want to learn more about PRACE Project, visit the website.   9:15 - 10:00 Introduction to OpenACC on x86 CPU and GPU Antonio J. Peña 10:00 - 11:00 Hands-on: Introduction Marc Jordà 11:00 - 11:30 Break   11:30 - 12:30 Profiling and Parallelizing with the OpenACC Toolkit Simón García de Gonzalo / Orestis Korakitis 12:30 - 13:30 Hands-on: Profiling and Parallelizing Marc Jordà 13:30 - 14:30 Lunch break   14:30 - 15:30 Expressing Data Locality and Optimizations with OpenACC Simon García de Gonzalo / Orestis Korakitis 15:30 - 16:30 Hands-on: Data Locality and Optimizations Marc Jordà 16:30 - 17:00 Break   17:00 - 18:00 Advanced OpenACC Techniques: Interoperability, MPI, and Pipelining Simon García de Gonzalo / Orestis Korakitis 18:00 - 19:00 Hands-on: Advanced Techniques Marc Jordà https://events.prace-ri.eu/event/1157/ 2021-04-16 07:00:00 UTC 2021-04-16 15:00:00 UTC [] [] [] workshops_and_courses [] []

  • ELIXIR and Galaxy Project

    16 - 17 April 2021

    ELIXIR and Galaxy Project https://tess.elixir-europe.org/events/elixir-and-galaxy-project 2021-04-16 09:00:00 UTC 2021-04-17 00:00:00 UTC [] Martin Čech [] [] [] [] []

  • [ONLINE] Parallelization with MPI @ VSC Vienna

    19 - 22 April 2021

    [ONLINE] Parallelization with MPI @ VSC Vienna https://tess.elixir-europe.org/events/online-parallelization-with-mpi-vsc-vienna This course will be delivered as an ONLINE COURSE (using Zoom) for remote participation. REGISTRATION is strictly NECESSARY since the details to access the online course will be provided to the registered and accepted attendees only. Registration follows the "first come – first served" principle. For the online course we can take a maximum of 40 persons. Additional registrations will be added to a waiting list. Furthermore, accepted participants will be contacted a few days before the course and asked to do a short PRE-ASSIGNMENT that has to be completed before the course starts. For doing the HANDS-ON LABS all you need is a C/C++ or Fortran compiler and a recent MPI library. Participants can choose between using their own laptops or any system they have access to that provides these, it's even possible to do the exercises in Google Colab. Alternatively, participants can ask for a training user account at the VSC for the duration of the course. Overview On clusters and distributed memory architectures, parallel programming with the Message Passing Interface (MPI) is the dominating programming model. This 4 half-days course teaches parallel programming with MPI starting from a beginners level. Hands-on sessions (in C and Fortran) will allow users to immediately test and understand the basic constructs of the Message Passing Interface (MPI). Content Levels: Beginners = 8:00h (50%) + Intermediate = 6:00h (37%) + Advanced = 2:00h (13%) This course is a PRACE training event. It is organized by the VSC Research Center, TU Wien, in cooperation with the High-Performance Computing-Center Stuttgart (HLRS). Agenda & Content 1st day – 19 April 2021 08:15   Join online 08:30       Welcome (talk) 08:35       MPI overview (talk+demo) 10:00   Breakout-Rooms - meet your exercise group 10:15       Process model and language bindings (talk+demo+practical) 11:30   Break 11:40       Messages and point-to-point communication (talk+practical) 13:00   End of first day 2nd day – 20 April 2021 08:15   Join online 08:30       Ping pong benchmark - solution and results (talk+discussion) 08:40       Nonblocking communication (talk+demo+practical) 10:00   Break 10:15       Collective communication (talk+demo+practical) 11:30   Break 11:45       Optimizing MPI communication - a real world example (talk+discussion) 12:00       Short Tour: other MPI topics (talk) 12:30       Fortran and MPI - only for Fortran participants (talk) 13:00   End of second day 3rd day – 21 April 2021 08:15   Join online 08:30       Groups & Communicators (talk+practical) 09:30   Break 09:45       Virtual topologies (talk+practical) 11:30   Break 11:45       Derived datatypes (talk+demo+practical) 13:00   End of third day 4th day – 22 April 2021 08:15   Join online 08:30       One-sided Communication (talk+practical) 10:00   Break 10:15       Shared Memory One-sided Communication (talk+practical) 11:30   Break 11:45       Short Tour: MPI I/O (talk) 12:15       Best practice, Summary, Q&A (talk+discussion) 13:00   End of fourth day (course) https://events.prace-ri.eu/event/1171/ 2021-04-19 06:45:00 UTC 2021-04-22 11:00:00 UTC [] [] [] workshops_and_courses [] []

  • Introduction to working with UNIX and bash (ONLINE LIVE TRAINING)

    19 April 2021

    Cambridge, United Kingdom

    Elixir node event
    Introduction to working with UNIX and bash (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/introduction-to-working-with-unix-and-bash-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. Using the Linux operating system and the bash command line interface, we will demonstrate the basic structure of the UNIX operating system and how we can interact with it using a basic set of commands. Applying this, we will learn how to navigate the filesystem, manipulate text-based data and structure simple pipelines out of these commands. Building on the techniques learnt so far, we will then construct bash scripts combining the commands and structures already learnt into more complex, reusable tools. We will look at how we can apply these scripts to common problems faced in UNIX environments such as: communicating with remote servers; managing custom software installations and integrating these tools into our simple pipelines. This course is targeted at participants with no prior experience working with UNIX-like systems (OSX, Linux) or command line interfaces. 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 Interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=3843256&course-title=Introduction%20to%20working%20with%20Unix%20and%20bash).'' 2021-04-19 08:30:00 UTC 2021-04-19 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR 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

  • Tools for reproducible research workshop (ONLINE)

    19 - 24 April 2021

    Elixir node event
    Tools for reproducible research workshop (ONLINE) https://tess.elixir-europe.org/events/tools-for-reproducible-research-workshop-online-35cf2694-bd65-4f04-9e60-9b66f27e33e5 #training #url: https://www.scilifelab.se/event/tools-for-reproducible-research-online-2 2021-04-19 09:00:00 UTC 2021-04-24 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] #trainingtraining

  • Introductory statistics in GraphPad Prism 9

    19 - 26 April 2021

    Elixir node event
    Introductory statistics in GraphPad Prism 9 https://tess.elixir-europe.org/events/introductory-statistics-in-graphpad-prism-9 The following topics will be covered: How to use Prism 9 for simple statistical analyses: t tests, one-way ANOVA and non-parametric counterparts How to use Prism 9 for more advanced statistical analyses: two-way ANOVA  How to use Prism 9 to create graphs Curve fitting in Prism 9 Survival analysis in Prism 9 Participants can use their own data on the training. 2021-04-19 09:00:00 UTC 2021-04-26 00:00:00 UTC VIB Bioinformatics Core [] [] [] [] [] []

  • Plant Transcriptome Analysis using Galaxy

    19 - 24 April 2021

    Plant Transcriptome Analysis using Galaxy https://tess.elixir-europe.org/events/plant-transcriptome-analysis-using-galaxy 2021-04-19 09:00:00 UTC 2021-04-24 00:00:00 UTC [] Instructors [] [] [] [] []

  • Omics integration and Systems Biology (ONLINE)

    19 - 24 April 2021

    Elixir node event
    Omics integration and Systems Biology (ONLINE) https://tess.elixir-europe.org/events/omics-integration-and-systems-biology-online #training #url: https://nbisweden.github.io/workshop_omics_integration/   For questions about this workshop please contact: edu.omics-integration@nbis.se  2021-04-19 09:00:00 UTC 2021-04-24 00:00:00 UTC [] jessica.lindvall@scilifelab.se [] [] [] [] #trainingtraining

  • [ONLINE] Interactive High-Performance Computing with Jupyter @ JSC

    20 - 22 April 2021

    [ONLINE] Interactive High-Performance Computing with Jupyter @ JSC https://tess.elixir-europe.org/events/online-interactive-high-performance-computing-with-jupyter-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: Introduction to Jupyter Parallel computing using Jupyter Coupling and control of simulations Interactive & in-situ visualization Simulation dashboards Prerequisites: Experience in Python Date: 20-22 April 2021, 09:00-13:00 Application Registrations are only considered until 1 April 2021, the maximal number of participants is limited. Applicants will be notified, whether they are accepted for participitation. Instructors: Jens Henrik Göbbert, Alice Grosch, Jülich Supercomputing Centre https://events.prace-ri.eu/event/1162/ 2021-04-20 07:00:00 UTC 2021-04-22 11:00:00 UTC [] [] [] workshops_and_courses [] []

  • Efficient use of the HPE Cray EX Supercomputer ARCHER2 @ EPCC Online

    20 - 22 April 2021

    Efficient use of the HPE Cray EX Supercomputer ARCHER2 @ EPCC Online https://tess.elixir-europe.org/events/efficient-use-of-the-hpe-cray-ex-supercomputer-archer2-epcc-online Overview: This three day workshop will provide attendees with the knowledge required to understand the most optimal way to port, execute and optimize applications for ARCHER2. The workshop is a mixture of lectures and practical hands-on sessions. Example exercises will be provided but attendees are encouraged to bring their own applications. Specific topics that will be covered include: Cray EX System Architecture Compiling and running applications ( Programming Environment, compilers, libraries, Slurm ) Debugging tools Application profiling Optimization of applications for serial performance, parallel execution and efficient use of I/O Prerequisites: Although the first day is of a more introductory nature it is expected that attendees are proficient Linux users, are familiar with HPC system environments in general and have a good understanding of parallel programming in C/Fortran. Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They are also required to abide by the ARCHER2 Training Code of Conduct. This course is open to users of ARCHER2. https://events.prace-ri.eu/event/1194/ 2021-04-20 08:00:00 UTC 2021-04-22 16:30:00 UTC [] [] [] workshops_and_courses [] []

  • [ONLINE] Working effectively with HPC systems @ SNIC

    20 April 2021

    [ONLINE] Working effectively with HPC systems @ SNIC https://tess.elixir-europe.org/events/online-working-effectively-with-hpc-systems In brief The seminar will present useful tools and best practices for working effectively on HPC systems. It is expected to be of interest for a general HPC system user, both at a more familiar (intermediate) or starting (beginner) level. To participate, register down below. Introduction Working efficiently with HPC starts with the tools you use to interact with the HPC system. It is also helpful to understand the general anatomy of HPC systems and storage. Following on from these fundamentals, we will give some recommendations for data organization on the system and examples of various types of file systems (e.g. parallel vs. local) and their individual strengths and weaknesses. We will then discuss the concepts of parallelism, scalability, scheduling and what types of OS and software you can expect of HPC systems. We will go through some important things to consider when building and installing software. Finally, we will look at different ways of running software on HPC systems and ways to monitor your software as it is running, with the aim of ensuring that your jobs are not poorly configured or wasting resources. While the content and the practices are useful for HPC systems in general, we will show examples and tools more specific for the NSC clusters, e.g. Tetralith and Sigma. Schedule The schedule for the day is divided into two main parts, before and after lunch break. The parts include several blocks of ca. 30 minutes including optional breaks. There will be opportunities for questions. Depending on time, the day might end with a longer questions session. The detailed schedule can be found at the NSC event page. 10:00 -12:00 Part I 12:00 -13:00 L u n c h 13:00 -15:00 Part II Topics/blocks Welcome, introductions and practicalities Tools at your end (e.g. terminal, ssh config., file transfer tools, VNC) HPC system anatomy (login and compute nodes, interconnect, storage) Properties and features of storage areas (e.g. quotas, performance, locality, backups, snapshots, scratch) Concept of parallelism (Amdahl’s law), scalability, scheduling and practical advice for good performance Software on an HPC system (OS, modules, python envs., concept of build envs., containers with Singularity) Ideas and strategies for organizing your workflow (data and file management, traceability and reproducibility) Interacting with the Slurm queueing system (requesting resources interactively or in batch) Practical example (preparing, submitting, monitoring and evaluating job efficiency) Materials The course materials, presentations, as well as detailed schedule etc., will be made available at the corresponding NSC event page. In future, refer to NSC past events. Organizers Weine Olovsson and Hamish Struthers will present, Peter Kjellström and Torben Rasmussen will also help out during the sessions, all at NSC, LiU, Sweden. https://events.prace-ri.eu/event/1026/ 2021-04-20 08:00:00 UTC 2021-04-20 13:00:00 UTC [] [] [] workshops_and_courses [] []

  • Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2021

    20 - 22 April 2021

    Tools for Systems biology modeling and data exchange: COPASI, CellNetAnalyzer, SABIO-RK, FAIRDOMHub/SEEK 2021 https://tess.elixir-europe.org/events/tools-for-systems-biology-modeling-and-data-exchange-copasi-cellnetanalyzer-sabio-rk-fairdomhub-seek-2021 Educators: Axel von Kamp, Steffen Klamt, Sven Thiele (MPI Magdeburg), Frank T. Bergmann, Ursula Kummer (Heidelberg University), Wolfgang Müller, Maja Rey, Andreas Weidemann, Ulrike Wittig (HITS) (de.NBI-SysBio) Date: 20. - 22 April 2021 Location: online Contents: Key concepts of stoichiometric and kinetic modeling of biochemical networks: - stoichiometric matrix and stoichiometric networks - steady state flux distributions - principles of constraint-based modeling - metabolic flux analysis and flux optimization (flux balance analysis) - metabolic pathway analysis with elementary flux modes - metabolic network design via minimal cut sets - simulation of dynamic (kinetic) models - sensitivity analysis - carrying out parameter estimation tasks - model exchange using SBML Data and model management: - manual/programmatic access to reaction kinetics data from SABIO-RK - storage and exchange of data and models using FAIRDOMHub/SEEK - modeling specific functionalities in FAIRDOMHub/SEEK Learning goals: During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer. The second day continues with kinetic modeling techniques which will be illustrated and exercised with COPASI. The third day SABIO-RK is used as a resource for kinetic data and FAIRDOM Hub/SEEK is introduced as a data and model management platform fitted to the needs of systems biologists. The hands on exercises throughout the three days will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks. Prerequisites: Some knowledge of mathematical modeling will be advantageous. The participants should bring their own laptop with MATLAB installed (if you do not have MATLAB please let us know during registration so we can send you information on how to obtain a trial license). Keywords: CellNetAnalyzer (CNA), COPASI, SBML, FAIR, modeling, kinetic data access, database, data and model management Tools: CellNetAnalyzer, COPASI, Matlab, SABIO-RK, FAIRDOMHub/SEEK 2021-04-20 09:00:00 UTC 2021-04-22 17:00:00 UTC de.NBI [] [] [] workshops_and_courses [] []

  • Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING)

    21 - 23 April 2021

    Cambridge, United Kingdom

    Elixir node event
    Analysis of bulk RNA-seq data (ONLINE LIVE TRAINING) https://tess.elixir-europe.org/events/analysis-of-bulk-rna-seq-data-online-live-training-840d7bcc-8372-428a-9cde-a308c3b5d98b PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout. 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. 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=3748821&course-title=Analysis%20of%20bulk%20RNA-seq%20data).'' 2021-04-21 08:30:00 UTC 2021-04-23 16:30:00 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 [] HDRUK

  • Data Management Planning workshop for Life Science Projects - Bergen

    21 - 22 April 2021

    Elixir node event
    Data Management Planning workshop for Life Science Projects - Bergen https://tess.elixir-europe.org/events/data-management-planning-workshop-for-life-science-projects-bergen We are pleased to announce the Data Management planning workshop for Life Scientists in Bergen by [ELIXIR Norway](https://www.elixir-norway.org/), [Digital Life Norway](https://digitallifenorway.org/) and the [UiB University Library Research Data team](https://www.uib.no/ub/110811/forskingsdata-og-datahandtering). The intended audience are researchers (PhD candidates, Post Doctoral Fellows, Researchers, Associate Professors and Professors) that are planning to submit a grant application for a research project. Maximum number of participants: 40. Looking forward to see you at the workshop, [Kjersti Hasle Enerstvedt](https://www.uib.no/en/persons/Kjersti.Hasle.Enerstvedt) (UiB University Library Research Data team), [Jenny Ostrop](https://www.uib.no/en/persons/Jenny.Ostrop) (UiB University Library Research Data team),  [Tore Linde](https://www.uib.no/en/persons/Tore.Andre.Linde) (SAFE/UiB IT divison),  [Siri Kallhovd](https://www.uib.no/en/persons/Siri.Kallhovd) (UiB/Metacenter/ELIXIR-Norway), [Korbinian Bösl](https://www.uib.no/en/persons/Korbinian.Boesl) (UiB/ELIXIR-Norway/Centre for Digital Life Norway) and others (TBA) ### 21.04.2021 0900 - 0915 Introduction 0915 - 0945 Requirements from institutions & funding bodies UiB H2020/ERC Research Council Norway 0945 - 1015 Information on national and local storage infrastructures UiB Storage resources NeLS/StoreBioInfo SAFE NIRD TSD 1015 - 1030 Short break 1030 - 1230 Relevant deposition repositories/ data archives domain specific archives (ELIXIR/EMBL-EBI, NCBI) UiB Open Research Data/Dataverse NO NIRD archive NSD B2SHARE ### 22.04.2021 0900 - 1000 Key legal requirements for research in the GDPR and Health research act Personal Data Act Health Research Act 1000 - 1015 Short break 1015 - 1045 Licensing of data, biological material and software 1045 - 1300 Hands on training and assistance to generate a data management plan ### Requirements: Join us online and bring your research project if you have one. You will get the opportunity to set up a data management plan for your project with help of the [Data Stewardship Wizard](https://elixir-no.ds-wizard.org/) tool using a structured and detailed questionnaire with references to relevant resources. Register [here](https://nettskjema.no/a/195116) before 18th of April 2021 [This event on digitallifenorway.org](https://www.digitallifenorway.org/services/data-management/events/-data-management-planning-workshop-for-life-scienc.html) 2021-04-21 09:00:00 UTC 2021-04-22 13:00:00 UTC Korbinian Bösl Data management University of Bergen korbinian.bosl@uib.no Centre for Digital Life Norway All postgraduatesPhD studentsPost DocsResearchersProfessors 40 workshops_and_courses first_come_first_served Data management planningDMPData management plan

  • Plant genomics: chloroplast genome assembly using Galaxy Australia

    21 - 22 April 2021

    Plant genomics: chloroplast genome assembly using Galaxy Australia https://tess.elixir-europe.org/events/workshop-plant-genomics-chloroplast-genome-assembly-using-galaxy-australia It is becoming increasingly practical to use large genomic data sets to answer research questions in plant biology, but it can be difficult to know where to start. In this workshop, you will perform a genome assembly using chloroplast sequencing data and the Galaxy Australia web platform. You'll have the opportunity to try out the workflows on the same or other data, using the free Galaxy platform and its tools. Galaxy is an online platform for biological research that allows people to use computational data analysis tools and workflows without the need for programming experience. The material covered in this workshop is freely available through the Galaxy Training Network. The workshop will be held via Zoom and involve a combination of presentations by the lead trainer and smaller breakout groups supported by experienced facilitators. **Lead trainer:** Dr Anna Syme, Bioinformatician, Australian BioCommons, Melbourne Bioinformatics, University of Melbourne. Anna has a long history as a research scientist and has recently worked at the Royal Botanic Gardens Victoria. Her work on the Bioplatforms Australia project, Genomics for Australian Plants, and her current Australian BioCommons role sees her contributing to workforce transition of researchers working with genomic data. **Learning objectives** By the end of the workshop you should be able to: - Assemble a chloroplast genome from a test dataset of Oxford Nanopore long sequencing reads - Polish the assembly with short Illumina sequencing reads - View the assembly in a genome browser and an assembly graph viewer - Describe how common tools can be combined to produce a workflow for genome assembly **Who the workshop is for** This workshop is suitable for Australian researchers with an interest in using Galaxy Australia for genome assembly. The workshop requires some prior knowledge of genome assembly and the basics of using Galaxy Australia. If you are new to these topics we recommend that you work through the following tutorials in advance: - [A short introduction to Galaxy] (https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html) - [Introduction to Genome Assembly] (https://training.galaxyproject.org/training-material/topics/assembly/tutorials/general-introduction/tutorial.html) Additional tutorials on genome assembly can be found on the Galaxy Training Network. **Date/Time:** 21 April 1:00pm - 4:00pm AEST **How to join** The workshop is free but places are strictly limited and registration requires an Australian institutional email address. [Register here] (https://plant-genomics-galaxy.eventbrite.com.au/) The workshop is presented by the Australian Biocommons and Melbourne Bioinformatics with the assistance of a network of Facilitators from around Australia. This event is part of a series of bioinformatics training events in partnership with Galaxy Australia. If you'd like to hear when registrations open for other events, please subscribe to Australian Biocommons. 2021-04-21 09:00:00 UTC 2021-04-22 00:00:00 UTC Australian BioCommons Australia, Australia Australia Australia [] Anna Syme [] [] 30 workshops_and_courses first_come_first_served []

  • Intermediate statistics: data analysis in practice - streamed

    21 - 22 April 2021

    Streamed from Lausanne, Switzerland

    Elixir node event
    Intermediate statistics: data analysis in practice - streamed https://tess.elixir-europe.org/events/intermediate-statistics-data-analysis-in-practice This course is now full with a waiting list. This course will be streamed only for the registered participants. Registered participants will receive specific information directly from the respective course’s organizers. 2021-04-21 09:00:00 UTC 2021-04-22 00:00:00 UTC SIB, Streamed from Lausanne, Switzerland SIB Streamed from Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []

  • Analyzing data in an HPC environment using R @SNIC

    22 April 2021

    Analyzing data in an HPC environment using R @SNIC https://tess.elixir-europe.org/events/analyzing-data-in-an-hpc-environment-using-r Speakers: Henric Zazzi Do you use R for analysing large amounts of data? Join us at this free SNIC-PRACE course on speeding up the performance of R code by parallelizing it! Why run your R code in parallel? R is a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering. But default R is not executed in parallel and consequently - for huge datasets or for extensive calculations - the analysis of your data can be quite slow. In this course, which is being organised by PDC in its role as a SNIC PRACE training centre, you will learn what parallelization means, and how to make your R code faster using parallelization. We will also teach you how to run these codes on Tegner, which is a high-performance computing (HPC) cluster at PDC. For registration to this event please visit the PDC webpage: https://www.pdc.kth.se/about/events/analyzing-data-in-an-hpc-environment-using-r-1.1057170 https://events.prace-ri.eu/event/1190/ 2021-04-22 07:00:00 UTC 2021-04-22 14:00:00 UTC [] [] [] workshops_and_courses [] []

  • QM/MM simulation with GROMACS + CP2K @ EPCC Online

    22 - 23 April 2021

    QM/MM simulation with GROMACS + CP2K @ EPCC Online https://tess.elixir-europe.org/events/qm-mm-simulation-with-gromacs-cp2k-epcc-online Dmitry Morozov (Chemistry, University of Jyväskylä), Emiliano Ippoliti (Computational Biomedicine, Forschungszentrum Jülich), Holly Judge (EPCC, University of Edinburgh) 22 - 23 April 2021 9:30-15:00 CEST (8:30-14:00 BST) Online This course is organised and funded by BioExcel - the Centre of Excellence for Computational Biomolecular Research (http://bioexcel.eu) and PRACE, and delivered in collaboration with ARCHER2 - the UK national supercomputing service (https://www.archer2.ac.uk/).       Learning outcomes This course will equip participants to perform hybrid QM/MM simulations using the molecular dynamics code GROMACS in combination with the quantum chemistry package CP2K through an interface developed by one of the instructors from the BioExcel Centre of Excellence (www.bioexcel.eu). Prerequisites Participants should be familiar with using GROMACS to perform molecular dynamics simulations. A background in computational quantum chemistry is not strictly required since an introduction of key aspects will be provided, but previous familiarity is beneficial. You should be familiar with connecting to a remote machine using ssh and will benefit from experience using an HPC facility as you will execute hands-on practicals on the UK supercomputer ARCHER2. Description Most classical molecular mechanics (MM) force fields are not sufficiently flexible to model processes in which chemical bonds are broken or formed. Instead, some level of quantum mechanical (QM) description is needed to gain detailed mechanistic insights into reaction mechanisms, e.g. the catalytic action of enzymes, and to compute photochemical properties such as absorption and emission spectra of fluorescent proteins. However biochemical systems (including solvent) are too large to be solved in their entirety at ab initio QM level or efficiently even with a high-quality density functional theory (DFT) approximation. To overcome the cost of a QM description on the one hand versus the limitations of a MM treatment on the other hand, methods have been developed that treat a small critical region of interest at QM level while retaining the computationally cheaper MM force field for the majority of the system. Despite the simplicity of the QM/MM concept, its application is currently restricted to a relatively small group of specialised expert users often using in-house codes. To unlock the power of QM/MM simulations for the wider biomolecular simulation community, the BioExcel Centre of Excellence has developed an interface between the molecular dynamics code GROMACS, which is widely used in the biomolecular simulation community, and the quantum chemistry package CP2K, which supports calculations under periodic boundary conditions with DFT methods. This course explains key aspects relating to the use of QM/MM for biomolecular simulation with these two codes and equips participants with the ability to start using GROMACS and CP2K for this purpose in their own research. Participants are provided with the opportunity to gain hands-on practical experience running several example calculations on ARCHER2, the UK national supercomputing service. Topics that will be covered are: Introduction to QM/MM a brief overview of: Relevant computational quantum chemistry QM-MM coupling Functionals, basis sets, pseudopotentials, and dispersion How to use GROMACS+CP2K to perform biomolecular QM/MM simulations, including: Umbrella sampling Energy minimisation Large phytochrome protein system setup Calculation of photochemical properties CP2K parameter choice guidance, including: Checking convergence Modifying functional and basis set Performance Schedule (all times CEST) Day 1 9:30 Welcome 9:45 Lecture: Introduction to QM/MM I: computational quantum chemistry 10:15 Q&A 10:30 Break 10:45 GROMACS+CP2K Practical 1 12:00 Lunch 13:00 Lecture: Introduction to QM/MM II: QM-MM coupling 13:30 Q&A 13:45 Break 14:00 GROMACS+CP2K Practical 2 15:00 Wrap up Day 2 9:30 Lecture: Introduction to QM/MM III: functionals, pseudopotentials, dispersion corrections 10:00 Q&A 10:15 Break 10:30 Lecture & practical: CP2K parameter choice guidance 12:00 Lunch 13:00 GROMACS+CP2K Practical 3 14:30 Q&A 15:00 Wrap up Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They are also required to abide by the ARCHER2 Training Code of Conduct. Registration We expect high demand for this course and places are limited to 30, so we urge potential participants to register only if they meet the prerequisites and expect to be able to take part. Recordings will be made available after the course on the BioExcel YouTube channel (https://www.youtube.com/c/bioexcelcoe). Training materials such as practicals/tutorials will appear on the BioExcel Github (https://github.com/bioexcel), however these will require installation of a custom version of GROMACS (https://gitlab.com/aracsmd/gromacs/-/tree/2021.1-plumed-qmmm) that links with CP2K (this will be provided on ARCHER2). https://events.prace-ri.eu/event/1204/ 2021-04-22 07:30:00 UTC 2021-04-23 13:00:00 UTC [] [] [] workshops_and_courses [] []

  • Building a bioinformatics platform: Lessons learned from immuneML

    22 - 23 April 2021

    Building a bioinformatics platform: Lessons learned from immuneML https://tess.elixir-europe.org/events/building-a-bioinformatics-platform-lessons-learned-from-immuneml 2021-04-22 09:00:00 UTC 2021-04-23 00:00:00 UTC [] Lonneke Scheffer, Milena Pavolović [] [] [] [] []

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