255 events found
  • Flow Cytometry

    26 February 2019

    Norwich, United Kingdom

    Flow Cytometry https://tess.elixir-europe.org/events/flow-cytometry Improve theoretical knowledge in flow cytometry to assist with planning and running your own experiment Learning Outcomes: Gain an understanding of how fluorochromes behave and considerations when planning a multicolour panel experiment Understand the importance of controls and how compensation works Understand how a cytometer works Gain confidence to diagnose problems and how to remedy them Develop knowledge of what CS&T and accudrop beads do Have broadened understanding of important considerations for single cell sorting Have the opportunity to discuss your experimental planning with experienced cytometrists Depending on applicants’ interests, there may be time to cover additional topics of common interest, for example cell sorting experiments, so please highlight these in your application. 2019-02-26 09:00:00 UTC 2019-02-26 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ [] training@earlham.ac.uk [] [] workshops_and_courses [] Introduction flow cytometry
  • Bioinformatics Resources for Protein Biology

    26 - 28 February 2019

    Cambridge, United Kingdom

    Elixir node event
    Bioinformatics Resources for Protein Biology https://tess.elixir-europe.org/events/bioinformatics-resources-for-protein-biology-ec67c4eb-5298-41b3-82d1-2bc034c0d4ef This three day workshop will introduce you to data resources and tools developed by EMBL-EBI that can help you in your protein studies. 2019-02-26 09:00:00 UTC 2019-02-28 17:30:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 1, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 1 Cambridge United Kingdom CB10 1SD [] Marina Pujol [] [] [] [] []
  • Systems Workshop: Programming MareNostrum 4 @ BSC

    27 - 28 February 2019

    Systems Workshop: Programming MareNostrum 4 @ BSC https://tess.elixir-europe.org/events/systems-workshop-programming-marenostrum-4-bsc-93bcf81b-5b06-49e7-b43a-2905ce9ecab8 The registration to this course is now open. Please, bring your own laptop.  All the PATC courses at BSC are free of charge. Course convener: David Vicente Lecturers: David Vicente, Javier Bartolomé, Carlos Tripiana, Oscar Hernandez, Rubén Ramos, Félix Ramos, Pablo Ródenas, Jorge Rodríguez, Marta Renato, Cristian Morales Objectives: The objective of this course is to present to potential users the new configuration of MareNostrum and a introduction on how to use the new system (batch system, compilers, hardware, MPI, etc).Also It will provide an introduction about RES and PRACE infrastructures and how to get access to the supercomputing resources available. Learning Outcomes: The students who finish this course will know the internal architecture of the new MareNostrum, how it works, the ways to get access to this infrastructure and also some information about optimization techniques for its architecture. Level: INTERMEDIATE -for trainees with some theoretical and practical knowledge; those who finished the beginners course. Prerequisites:  Any potential user of a HPC infrastructure will be welcome Agenda: DAY 1 (Feb. 27) 9am - 5pm Session 1 / 9:00am – 1:00 pm  (2:45 h lectures, 45’ practical) 09:00h - 09:30h Introduction to BSC, PRACE PATC and this training (David Vicente) 09:30h - 10:30h MareNostrum 4 – the view from System administration group (Javier Bartolomé) 10:30h – 11:00h COFFEE BREAK 11:00h - 11:30h Deep Learning and Big data tools on MN4 (Carlos Tripiana) 11:30h - 12:15h How to use MN4 – Basics: Batch system, file systems, compilers, modules, DT, DL, BSC commands (Oscar Hernandez, Rubén Ramos, Félix Ramos) 12:15h - 13:00h Hands-on I (Oscar Hernandez, Rubén Ramos, Félix Ramos) 13:00h - 14:30h LUNCH (not hosted)   Session 2 / 2:30pm – 5:15 pm (3:30 h practical) 14:30h - 15:15h How to use MN4 – HPC architectures and parallelism (Jorge Rodriguez, Pablo Ródenas) 15:15h - 16:00h How to use MN4 – Parallel programming: MPI, MPI IO, MKL, GREASY (Pablo Ródenas, Jorge Rodríguez) 16:00h - 16:15h COFFEE BREAK 16:15h - 16:45h Hands-on II (Pablo Ródenas, Jorge Rodriguez) 16:45h - 17:15h Optional: MareNostrum 4 visit (In the chapel) 17:15h - Adjourn   DAY 2 (Feb. 28) 9:00am – 1:00 pm  Session 3 / 9:00am – 1:00 pm  (2 h lectures, 1:30 h practical) 09:00h - 09:30h Optional: Doubts + Continue previous hands-on + Tunning your app (David Vicente, Jorge Rodríguez) 09:30h - 10:00h How can I get resources from you? (RES Marta Renato) 10:00h - 10:30h How can I get Resources from you? – (PRACE Cristian Morales) 10:30h - 11:00h COFFEE BREAK 11:00h - 11:30h Debugging on MareNostrum, from GDB to DDT (Pablo Ródenas, Oscar Hernandez) 11:30h - 12:30h Hands-on III – Debugging your application (Pablo Ródenas, Oscar Hernandez) 12:30h - 13:00h Wrap-up : Can we help you in your porting ? How ? when ? (David Vicente) 13:00h - Adjourn   END of COURSE   END of COURSE https://events.prace-ri.eu/event/763/ 2019-02-27 08:00:00 UTC 2019-02-28 12:00:00 UTC [] [] [] workshops_and_courses [] []
  • NGS - Quality control, Alignment, Visualisation

    27 February - 1 March 2019

    Bern, Switzerland

    Elixir node event
    NGS - Quality control, Alignment, Visualisation https://tess.elixir-europe.org/events/ngs-quality-control-alignment-visualisation-d26251dc-323a-4f69-a39c-f893e90527eb Overview Usage of NGS is increasing in several biological fields due to a very rapid decrease in cost. However, it often results in hundreds of Gbs of data making the downstream analysis very challenging and requires bioinformatics skills. 2019-02-27 09:00:00 UTC 2019-03-01 00:00:00 UTC SIB, Bern, Switzerland SIB Bern Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • An Introduction to Solving Biological Problems with Python

    27 - 28 February 2019

    Cambridge, United Kingdom

    Elixir node event
    An Introduction to Solving Biological Problems with Python https://tess.elixir-europe.org/events/an-introduction-to-solving-biological-problems-with-python-b0c5de54-d51d-4c41-821a-267a854773f3 This course provides a practical introduction to the writing of Python programs for the complete novice. Participants are lead through the core aspects of Python illustrated by a series of example programs. Upon completion of the course, attentive participants will be able to write simple Python programs and customize more complex code to fit their needs. Course materials are available [here](http://pycam.github.io). Please note that the content of this course has recently been updated. This course now mostly focuses on core concepts including Python syntax, data structures and reading/writing files. Concepts and strategies for working more effectively with Python are now the focus of a new 2-days course, [Data Science in Python](http://training.csx.cam.ac.uk/bioinformatics/course/bioinfo-dspyt/). The training room is located on the first floor and there is currently no level access. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2823201&course-title=An%20Introduction%20to%20Solving%20Biological%20Problems%20with%20Python).'' 2019-02-27 09:30:00 UTC 2019-02-28 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Biology Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] []
  • Introduction to Metabolomics for the Environmental Scientist

    28 February - 1 March 2019

    Birmingham, United Kingdom

    Elixir node event
    Introduction to Metabolomics for the Environmental Scientist https://tess.elixir-europe.org/events/introduction-to-metabolomics-for-the-environmental-scientist This 2-day NERC-funded Advanced Training Short Course will provide environmental scientists with an overview of the metabolomics pipeline. The course is intended for environmental scientist with little or no previous experience of metabolomics and who are interested to discover how this relatively new and powerful approach could be integrated into their research. Experts working in the NERC Metabolomics facility-NBAF-Birmingham will teach the course. 2019-02-28 09:00:00 UTC 2019-03-01 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • ELIXIR Heads of Nodes Teleconference

    28 February 2019

    ELIXIR Heads of Nodes Teleconference https://tess.elixir-europe.org/events/elixir-heads-of-nodes-teleconference The ELIXIR Heads of Nodes Teleconference is scheduled to take place on Thu, 28 February 2019 from 10:00 - 13:00 UK time. This meeting is for the ELIXIR Heads of Nodes and Platform ExCos. 2019-02-28 10:00:00 UTC 2019-02-28 10:00:00 UTC [] [] [] meetings_and_conferences [] []
  • Extracting biological information from gene lists

    1 March 2019

    Cambridge, United Kingdom

    Elixir node event
    Extracting biological information from gene lists https://tess.elixir-europe.org/events/extracting-biological-information-from-gene-lists Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting biological themes which turn up in the lists. This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication. Course materials are available [here](https://www.bioinformatics.babraham.ac.uk/training.html#fagl). The training room is located on the first floor and there is currently no level access. Please note that if you are not eligible for a University of Cambridge [Raven](http://www.ucs.cam.ac.uk/docs/faq/raven/n5) account you will need to book or register your interest by linking [here](http://bioinfotraining.bio.cam.ac.uk/booking-form/?event-id=2672953&course-title=Extracting%20biological%20information%20from%20gene%20lists).'' 2019-03-01 09:30:00 UTC 2019-03-01 17:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR Biology Bioinformatics University of Cambridge Bioinformatics Training [] Graduate studentsPostdocs and Staff members from the University of CambridgeInstitutions and other external Institutions or individuals workshops_and_courses [] []
  • Python for Life Scientists

    4 - 6 March 2019

    Bern, Switzerland

    Elixir node event
    Python for Life Scientists https://tess.elixir-europe.org/events/python-for-life-scientists-78a0a484-9179-42c1-8ff3-7da98c61d215 Overview Python is an open-source and general-purpose scripting language which runs on all major operating systems. 2019-03-04 09:00:00 UTC 2019-03-06 00:00:00 UTC SIB, Bern, Switzerland SIB Bern Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Data Carpentry

    5 - 6 March 2019

    Norwich, United Kingdom

    Data Carpentry https://tess.elixir-europe.org/events/data-carpentry-workshop-5b2d17cb-f74b-4613-be3a-9cf0e744f1ab Data Carpentry workshops are for any researcher who has data they want to analyse, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills, and tools for working more effectively with data. We will cover data organisation in spreadsheets, data cleaning, SQL, the command line, and R for data analysis and visualisation using examples from biology. Participants should bring their laptops and plan to actively participate. By the end of the workshop, learners should be able to more effectively manage and analyse data and apply the tools and approaches directly to their ongoing research. Data Carpentry's aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. 2019-03-05 09:00:00 UTC 2019-03-06 17:00:00 UTC Earlham Institute Earlham Institute (EI), Colney Lane, Norwich, United Kingdom Earlham Institute (EI), Colney Lane Norwich Norfolk United Kingdom NR4 7UZ [] training@earlham.ac.uk [] [] workshops_and_courses [] []
  • ELIXIR Innovation and SME Forum: Genomics and Associated Data in National Healthcare Initiatives

    5 - 6 March 2019

    Sweden

    ELIXIR Innovation and SME Forum: Genomics and Associated Data in National Healthcare Initiatives https://tess.elixir-europe.org/events/elixir-innovation-and-sme-forum This free ELIXIR Innovation and SME Forum with a focus on Genomics and Associated Data in National Healthcare Initiatives in Stockholm is open to researchers working in the personalised medicine sector, large and small companies that develop services for healthcare systems or are users of genomics and/or associated data, as well as people involved in national healthcare initiatives and anyone else who is interested in learning more about data-driven innovation in the healthcare sector. It aims to inform about ELIXIR resources and create a space to network for industry and academia. In this lunch-to-lunch event, attendees will be immersed in a world of data-driven innovation, illustrated through talks. With a mix of high-level keynote speakers and interactive sessions, this event will allow you to discuss and interact with other companies and ELIXIR partners. A specific session with Flash Talks, will give new companies the chance to introduce their work to a broad audience.   ELIXIR Beacon Workshop  The Human Data Community is working with the Global Alliance for Genomics and Health to provide a simple way to make data discoverable through “Beacons” (https://beacon-project.io/ ). You can query the lightweight metadata provided by a data resource (a 'beacon') to ask questions like 'Does this dataset have genomes with this allele at that position?' and get a 'Yes' or 'No' answer. This workshop will show examples of current Beacon users and give you hands on experience on how to light a “Beacon” in your company/research institute.     Testimonials "ELIXIR is a very interesting initiative for companies like HPE because the members are top notch in their environment. It helps us to get an idea about the user requirements on one side and on the other to better understand their challenges. After the ELIXIR event we have already two companies that have a huge demand in faster, but affordable compute platforms. So, we met and discussed next steps of engagement. They have a problem and we have the tools to support them". Andreas Hausmann, HPE Aruba "I really enjoyed the ELIXIR Innovation and SME Forum in Frankfurt! What if IT would be an enabler for innovation and open your mind on new questions!" Catherine Sirven, Bayer Crop Sciences 2019-03-05 12:00:00 UTC 2019-03-06 13:00:00 UTC SciLifeLab, Sweden SciLifeLab Sweden [] [] [] meetings_and_conferences [] []
  • Parallel Programming with MPI and OpenMP @SURFsara

    6 - 8 March 2019

    Parallel Programming with MPI and OpenMP @SURFsara https://tess.elixir-europe.org/events/parallel-programming-with-mpi-and-openmp-surfsara-eeb96613-54d8-4840-afd9-9523550d25ce The 3-days MPI/OpenMP course aims at giving people with some programming experience an introduction into the parallel programming models MPI and OpenMP. It starts on beginners level but also includes advanced features of the current standards. Hands-on sessions (in C and Fortran) will allow users to immediately test and understand the constructs of the Message Passing Interface (MPI) and the shared memory directives of OpenMP. The program will start with OpenMP on the first day, an introduction to MPI on the second day, and the advanced features in MPI-2.0 and MPI-3.0 standard on the third day. https://events.prace-ri.eu/event/828/ 2019-03-06 08:00:00 UTC 2019-03-08 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • High Performance Parallel IO and post-processing @ MdlS

    11 - 13 March 2019

    High Performance Parallel IO and post-processing @ MdlS https://tess.elixir-europe.org/events/high-performance-parallel-io-and-post-processing-mdls The increase in computational power goes hand in hand with an increase in the size of the data to be managed, both on the input and on the output sides. IO can easily become a bottleneck for large scale architectures. Understanding of parallel file system mechanisms and parallel IO concepts enables users to efficiently use existing high level libraries like HDF5. With the increasing performance gap between compute and storage, even the best use of IO bandwidth might not be enough and data reduction based on in-situ or in-transit post-processing becomes a requirement for large-scale codes. More and more libraries able to handle this become available. This course proposes an introduction to FlowVR, a technology developed at Inria dedicated to in-situ and in-transit post-processing. To handle the multiplication of libraries, this course will also introduce the Parallel Data Interface (PDI), a solution to couple simulation codes with libraries for I/O and post-processing based on simple annotations. PDI improves code quality with a) annotations independent of the library used, b) a choice of IO strategy at runtime in YAML and c) negligible overhead to access the full power of the underlying libraries. Agenda: Day 1: HDF5, pHDF5 and general parallel IO concepts (2x3h, including hands-on) Day 2: Lustre file system (1h30) Day 2: FlowVR (1h30 + 3h including hands-on) Day 3: Parallel Data Interface (3h including hands-on) Day 3: Diving deeper into HDF5, FlowVR or PDI, your choice ! (3h) Instructors: M. Haefele (Maison de la Simulation, CNRS), Thomas Leibovici (TGCC, CEA), Bruno Raffin (INRIA), Julien Bigot (Maison de la Simulation, CEA) Learning outcomes: After this course, participants should understand the trade-offs implied by using a parallel file-system, and know how to efficiently use parallel IO libraries. Participants will also have a basic understanding and practise of FlowVR and PDI. Prerequisites: Knowledge of C or Fortran programming languages, parallel programming with MPI   https://events.prace-ri.eu/event/814/ 2019-03-11 08:30:00 UTC 2019-03-13 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to Metabolomics for the Clinical Scientist

    11 March 2019

    Birmingham, United Kingdom

    Elixir node event
    Introduction to Metabolomics for the Clinical Scientist https://tess.elixir-europe.org/events/introduction-to-metabolomics-for-the-clinical-scientist The 1-day course in partnership with the Phenome Centre Birmingham will provide clinicians with an overview of the metabolomics pipeline highlighting the benefits of this technique to the medical field and an introduction to the Phenome Centre Birmingham and the MRC-NIHR National Phenome Centre. The course will provide a suitable introduction to metabolomics prior to taking additional training courses at either the Birmingham Metabolomics Training Centre or the Imperial International Phenome Training Centre. 2019-03-11 09:00:00 UTC 2019-03-11 00:00:00 UTC Birmingham Metabolomics Training Centre, Birmingham, United Kingdom Birmingham Metabolomics Training Centre Birmingham United Kingdom B15 2TT [] [] [] [] [] []
  • Bioweek: Containers, clouds, clusters -combining CSC services in biosciences

    11 - 12 March 2019

    Elixir node event
    Bioweek: Containers, clouds, clusters -combining CSC services in biosciences https://tess.elixir-europe.org/events/bioweek-containers-clouds-clusters-combining-csc-services-in-biosciences CSC provides several alternative platforms for doing bioscience related computing. This course provides overview of these services so that after the course the students know how to choose a right platform combination for their analysis. No previous knowledge is required - the course is suitable for everybody! 2019-03-11 09:00:00 UTC 2019-03-12 17:00:00 UTC CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. [] [] [] workshops_and_courses [] []
  • Enrichment Analysis

    11 March 2019

    Lausanne, Switzerland

    Elixir node event
    Enrichment Analysis https://tess.elixir-europe.org/events/enrichment-analysis-d90d0524-d2ea-4f91-a840-3a7c69068a99 Overview Several statistical methods are available to determine whether a set of genes shows statistically significant differences between two classes (two biological states, two phenotype states, two experimental conditions, etc). 2019-03-11 09:00:00 UTC 2019-03-11 00:00:00 UTC SIB, Lausanne, Switzerland SIB Lausanne Switzerland [] training@sib.swiss [] Graduate studentsIndustryAcademicsPhDPhD students workshops_and_courses [] []
  • Data Visualisation

    11 - 15 March 2019

    Cambridge, United Kingdom

    Elixir node event
    Data Visualisation https://tess.elixir-europe.org/events/data-visualisation-983aee0c-32a8-49a9-8a15-10e7255f28c2 This workshop will give insights and practical experience in data visualisation for exploring biological data. 2019-03-11 12:00:00 UTC 2019-03-15 12:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 2, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 2 Cambridge United Kingdom CB10 1SD [] Frank O’Donnell [] [] [] [] []
  • Data Visualisation for Biology: a practical workshop on design, techniques and tools

    11 - 15 March 2019

    Cambridge, United Kingdom

    Elixir node event
    Data Visualisation for Biology: a practical workshop on design, techniques and tools https://tess.elixir-europe.org/events/data-visualisation-for-biology-a-practical-workshop-on-design-techniques-and-tools-99314d2e-9271-4824-b071-5b8a0ff48973 This workshop will give insights and practical experience in data visualisation for exploring biological data. 2019-03-11 12:00:00 UTC 2019-03-15 12:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 2, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 2 Cambridge United Kingdom CB10 1SD [] Frank O’Donnell [] [] [] [] []
  • Introduction for Simulation Environments for Life Sciences @ BSC

    14 - 15 March 2019

    Introduction for Simulation Environments for Life Sciences @ BSC https://tess.elixir-europe.org/events/introduction-for-simulation-environments-for-life-sciences-bsc The registration to this course will open in January. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Objectives: The course will make the attendants familiar with simulation technologies used in Life Sciences and their specific adaptation to HPC environment Course convener: Josep Gelpi Detailed outline: Introduction to biomolecular simulation Coarse-grained and atomistic simulation strategies Automated setup for simulation HPC specifics: Large scale parallelization, use of GPU’s Storage and strategies for large scale trajectory analysis Learning Outcomes: Setup, execute, and analyze standard simulations in HPC environment Level: (All courses are designed for specialists with at least 1st cycle degree or similar background experience) INTERMEDIATE: for trainees with some theoretical and practical knowledge. Course Program Outline: TBA     https://events.prace-ri.eu/event/764/ 2019-03-14 08:00:00 UTC 2019-03-15 17:00:00 UTC [] [] [] workshops_and_courses [] []
  • Bioweek: Single cell RNA-seq data analysis using Chipster

    14 - 15 March 2019

    Elixir node event
    Bioweek: Single cell RNA-seq data analysis using Chipster https://tess.elixir-europe.org/events/bioweek-single-cell-rna-seq-data-analysis-using-chipster-ac65eb29-66e9-4d0f-b0ba-2b52dbdd795a This introductory course covers single cell RNA-seq data analysis methods, tools and file formats. The free and user-friendly Chipster software is used in the exercises, and the course is thus suitable for everybody. 2019-03-14 09:00:00 UTC 2019-03-15 16:00:00 UTC CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. [] [] [] workshops_and_courses [] []
  • Advanced Topics in High Performance Computing @ LRZ

    18 - 21 March 2019

    Advanced Topics in High Performance Computing @ LRZ https://tess.elixir-europe.org/events/advanced-topics-in-high-performance-computing-lrz-cfe82cd6-32b5-4187-b72a-b90b2c55c36d In this add-on course to the parallel programming course special topics are treated in more depth, in particular performance analysis, I/O and PGAS concepts. It is provided in collaboration of Erlangen Regional Computing Centre (RRZE) and LRZ within KONWIHR. The course is a PRACE Training event. Each day is comprised of approximately 5 hours of lectures and 2 hours of hands-on sessions. Tentative schedule: Day 1 (09:00-17:00) Processor-Specific Optimization (Eitzinger) Day 2 (09:00-17:00) 09:00-12:30 Parallel I/O with MPI IO (N.N.) 13:30-14:30 SuperMUC Tour (Weinberg) 14:30-17:00 Tuning I/O on LRZ's HPC systems / I/O Profiling: Darshan tool (Mendez) Day 3 (09:00-17:00) 09:00-12:30 Scientific Data Libraries: HDF5 / Scalable I/O library: SIONlib (Mendez) 13:30 - 17:00 Advanced OpenMP Programming (Weinberg) Day 4 (09:00-17:00) PGAS programming with coarray Fortran and Unified Parallel C (Bader) https://events.prace-ri.eu/event/822/ 2019-03-18 08:00:00 UTC 2019-03-21 16:00:00 UTC [] [] [] workshops_and_courses [] []
  • Gatersleben Research Conference: Applied Bioinformatics for Crops

    18 - 21 March 2019

    Gatersleben Research Conference: Applied Bioinformatics for Crops https://tess.elixir-europe.org/events/gatersleben-research-conference-applied-bioinformatics-for-crops 2019-03-18 09:00:00 UTC 2019-03-21 00:00:00 UTC [] Björn Grüning [] [] [] [] []
  • Spring School in Computational Chemistry 2019 @ CSC

    19 - 22 March 2019

    Spring School in Computational Chemistry 2019 @ CSC https://tess.elixir-europe.org/events/spring-school-in-computational-chemistry-2019-csc Description The Spring School provides a comprehensive, tutorial-style, hands-on, introductory and intermediate-level treatment to the essential ingredients for molecular modeling and computational chemistry using modern supercomputers. The School program is being prepared, but the main content will be similar to last years and consists of: Classical molecular dynamics, intro + hands on (1 day) Electronic structure theory, intro  + hands on (1 day) Machine learning in chemistry, intro + hands on Special topics: e.g. on Visualization, Enchanced Sampling Techniques, etc. The school is a must for graduate students in the field, providing an overview on "what can be calculated and how should it be done", without forgetting the important aspect of network building. Note: the School has been overbooked in one week after registration was opened. We are investigating the possibility to accommodate more participants, but it is likely that new registrations will go to waiting list. Learning outcome The learning outcome is to gain an overview of the two main methods in computational chemistry — molecular dynamics and electronic structure calculations — in connection with related HPC software packages and other useful skills in the trade. The workshop is also suited for an intensive crash course (the first two days) in computational modelling and is expected to be useful for students and researchers also in physics, materials sciences and biosciences. The following "Special topics" then build on this foundation. Prerequisites Working knowledge and some work experience from some branch of computational chemistry will be useful. Basic linux skills for hands-on exercises and elementary Python for Machine Learning hands-on. More detailed description of pre-requisites and links for self study. Programme See tentative timetable on the left menu, browse 2018 materials or comments from participants in 2018. Lecturers:  Dr. Mikael Johansson, University of Helsinki, Finland Dr. Luca Monticelli, IBCP (CNRS), Lyon, France Dr. Michael Patzschke, Helmholtz-Zentrum Dresden-Rossendorf, Germany to be continued Dr. Martti Louhivuori, CSC - IT Center for Science, Finland Dr. Atte Sillanpää, CSC - IT Center for Science, Finland Dr. Nino Runeberg, CSC- IT Center for Science, Finland Language:  EnglishPrice:         Free of charge https://events.prace-ri.eu/event/786/ 2019-03-19 07:00:00 UTC 2019-03-22 13:00:00 UTC [] [] [] workshops_and_courses [] []
  • Exploring Human Genetic Variation

    19 - 20 March 2019

    Cambridge, United Kingdom

    Elixir node event
    Exploring Human Genetic Variation https://tess.elixir-europe.org/events/exploring-human-genetic-variation-e6a33d21-d6e3-4586-85e5-9b2be06f1752 This two-day workshop will data resources and bioinformatics tools available at EMBL-EBI and the Sanger Institute that will aid understanding of human genetic variation. 2019-03-19 09:00:00 UTC 2019-03-20 17:15:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 2, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 2 Cambridge United Kingdom CB10 1SD [] Charlotte Pearton [] [] [] [] []
  • Petaflop System Administration; Marenostrum 4 @ BSC

    20 - 21 March 2019

    Petaflop System Administration; Marenostrum 4 @ BSC https://tess.elixir-europe.org/events/petaflop-system-administration-marenostrum-4-bsc-6ce6f94e-a95e-432c-9e44-f7ceec5653c8 The registration to this course will open in January. Please, bring your own laptop. All the PATC courses at BSC are free of charge. Course Convener: Javier Bartolome, Systems Group Manager, Operations - System Administration, BSC Objectives: Explain the different components that MareNostrum 4 is composed, which were the design decisions taken and why. Explain how the system administration is taken in this Petaflop system. Learning Outcomes: The students will learn how MareNostrum 4 is organized and how it works. This can have some insights and ideas about how to manage clusters of thousands of nodes in a HPC or no-HPC environment. Level: INTERMEDIATE, for trainees with some theoretical and practical knowledge; those who finished the beginners course. Prerequisites: Experience on Linux system administration is required. Lecturer: Javier Bartolome, Systems Group Manager, Operations - System Administration, BSC Agenda: Day 1 (March, 20) Session 1 / 9:00am – 1:00 pm  (3:30 h lectures) 9h-9:20h Introduction & outline of the course 9:20h-9:40h MareNostrum4 Overview 9:40h-10:40h Storage in MareNostrum4 10:40h-11h COFFE BREAK 11h-11:30h Networks on MareNostrum4 11:30h -13h Clustering Software 13h-14h LUNCH BREAK   Session 2 / 2:00pm – 6:00 pm (3:30 h practical) 14h-15:30h Practice on clustering software 15:30h-15:45h COFFE BREAK 15:45-16:30h Monitoring MareNostrum4 16:30h-17h MareNostrum4 Facility 17h-18h Visit to MareNostrum4 18h Adjourn   Day 2 (March, 21) 9am – 12:30pm Session 3 / 9:00am – 12:30 pm  (3 h lectures) 9h-10h MareNostrum4 Schedule system 10h-11h PRACE Project and Services 11h-11:15h COFFEE BREAK 11:15h-12h MareNostrum4 software stack 12h-12:30h Questions/Wrap-up   End Of Course https://events.prace-ri.eu/event/765/ 2019-03-20 08:00:00 UTC 2019-03-21 12:00:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction into Galaxy and how to design your own analysis workflow

    20 - 23 March 2019

    Introduction into Galaxy and how to design your own analysis workflow https://tess.elixir-europe.org/events/introduction-into-galaxy-and-how-to-design-your-own-analysis-workflow 2019-03-20 09:00:00 UTC 2019-03-23 00:00:00 UTC [] Anne Fiebig [] [] [] [] []
  • Revolutionizing Next-Generation Sequencing (3rd edition)

    25 - 26 March 2019

    Antwerpen, Belgium

    Revolutionizing Next-Generation Sequencing (3rd edition) https://tess.elixir-europe.org/events/revolutionizing-next-generation-sequencing-3rd-edition After two successful editions (Jan 2015, Leuven and March 2017, Antwerp), VIB is proud to present the third edition of this Tools & Technologies conference. VIB believes that the revolutionary discoveries enabled by NGS are not yet at its zenith and that the technology can go much further. During this 3rd edition VIB will bring together over 30 top scientists and technology developers form both industry and academia. They will discuss emerging tools and approaches in several sessions such as: • Long reads, Genome Structure and Mapping • Epigenomics • Metagenomics • Spatial transcriptomics • Population Scale and Clinical Sequencing • Single Cell Sequencing • Emerging technologies In addition to a great scientific and technology program, the conference will provide ample opportunities to network during the breaks, poster sessions and the conference dinner. Also young scientists are encouraged to showcase their own work to the international research community by oral or poster presentation! Information for poster submissions: The format for your poster should be: A0 (841 x 1189 mm / 33.1 x 46.8 in), portrait orientation Deadlines: • Early Bird: 11/02/2019 • Late Registration: 11/03/2019 • Abstract deadline: 21/01/2019 2019-03-25 08:00:00 UTC 2019-03-26 18:00:00 UTC VIB Conferences BluePoint Antwerpen, 9, Filip Williotstraat, Antwerpen, Belgium BluePoint Antwerpen, 9, Filip Williotstraat Antwerpen Antwerpen Belgium 2600 Mapping Population genomics Population genetics Sequencing Transcriptomics Metagenomic sequencing Metagenomics Epigenetics Epigenomics Genotyping experiment Genotype and phenotype Genomics [] Evy Vierstraete +32 9 244 66 11 conferences@vib.be BioradBiokeLexogenAnalisBio-techneBGI [] 350 meetings_and_conferences [] Genome Structure Genome MappingEpigenomicsMetagenomicsSpatial transcriptomicsPopulation Scale clinical sequencingSequencingSingle Cell Sequencing
  • Introduction to Proteomics

    25 March 2019

    Elixir node event
    Introduction to Proteomics https://tess.elixir-europe.org/events/introduction-to-proteomics Proteomics is a systems biology approach to study the entire protein complement of a cell, tissue, or organism. This large-scale study of proteins is increasingly popular in post genomics era and has found its widespread applications in fields including drug discovery, cardiovascular research, and nutrition research, just to name a few. This course will provide both theoretical and practical training at the introductory level. Participants will learn the principles of current methodologies and apply bioinformatics tools for data analysis. 2019-03-25 09:00:00 UTC 2019-03-25 17:00:00 UTC CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. CSC Training Facilities located in the premises of CSC at Keilaranta 14, Espoo, Finland. [] [] [] workshops_and_courses [] []
  • Antibody based technologies

    26 - 27 March 2019

    Elixir node event
    Antibody based technologies https://tess.elixir-europe.org/events/antibody-based-technologies 2019-03-26 09:00:00 UTC 2019-03-27 00:00:00 UTC [] [] [] workshops_and_courses [] []
  • Introduction to RNA-Seq and Functional Interpretation

    26 - 29 March 2019

    Cambridge, United Kingdom

    Elixir node event
    Introduction to RNA-Seq and Functional Interpretation https://tess.elixir-europe.org/events/introduction-to-rna-seq-and-functional-interpretation This course will provide an introduction to the technology, data analysis, tools and resources used in RNA sequencing and transcriptomics. 2019-03-26 12:00:00 UTC 2019-03-29 14:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 1, Cambridge, United Kingdom European Bioinformatics Institute (EMBL-EBI) - Training Room 1 Cambridge United Kingdom CB10 1SD [] Johanna Langrish [] [] [] [] []
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