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235 events found

  • Myths and Realities of Personalised Medicine: the Genetic Revolution

    06 Mar - 10 Apr 2017

    Myths and Realities of Personalised Medicine: the Genetic Revolution https://tess.elixir-europe.org/events/myths-and-realities-of-personalised-medicine-the-genetic-revolution-67b14d5d-eab9-42c1-9533-36bb9a5537a7 Learn about personalised medicine and the impact that our enhanced understanding of genetics has on modern medicine and society. 2017-03-06 09:00:00 UTC 2017-04-10 00:00:00 UTC UNSW Sydney
  • Employability outside academia

    13 Mar - 22 May 2017

    Utrecht, Netherlands

    Employability outside academia https://tess.elixir-europe.org/events/employability-outside-academia PCDI’s course to enhance your employability in non-academic careers. Employability Outside Academia is a course that supports PhD students and postdocs in their preparation to make the transition to industry and/or non-profit organisations. It helps them finding out what position… The post Employability outside academia appeared first on Dutch Techcentre for Life Sciences. 2017-03-13 09:00:00 UTC 2017-05-22 00:00:00 UTC Utrecht, Netherlands, Utrecht, Netherlands Utrecht, Netherlands Utrecht Netherlands
  • Clinical Bioinformatics: Unlocking Genomics in Healthcare

    13 Mar - 17 Apr 2017

    Clinical Bioinformatics: Unlocking Genomics in Healthcare https://tess.elixir-europe.org/events/clinical-bioinformatics-unlocking-genomics-in-healthcare-38ee7385-b996-4950-b0a0-f2cf84ab87fb Learn about the role of clinical bioinformaticians in healthcare and how their work is helping to realise the genomics revolution. 2017-03-13 09:00:00 UTC 2017-04-17 00:00:00 UTC The University of Manchester
  • 25th VI-HPS Tuning Workshop @ RWTH Aachen University

    27 - 31 Mar 2017

    25th VI-HPS Tuning Workshop @ RWTH Aachen University https://tess.elixir-europe.org/events/25th-vi-hps-tuning-workshop-rwth-aachen-university Goals This workshop organized by JSC through the VI-HPS for the German PRACE Advanced Training Centre  will: give an overview of the VI-HPS programming tools suite explain the functionality of individual tools, and how to use them effectively offer hands-on experience and expert assistance using the tools For details see: http://www.vi-hps.org/training/tws/tw25.html Programme Overview Presentations and hands-on sessions are planned on the following topics: Setting up, welcome and introduction Score-P instrumentation and measurement Scalasca automated trace analysis Vampir interactive trace analysis TAU performance system Extra-P automated performance modeling Paraver/Extrae/Dimemas trace analysis and performance prediction MAQAO performance analysis & optimisation MUST runtime error detection for MPI ARCHER runtime error detection for OpenMP ... and potentially others A brief overview of the capabilities of these and associated tools is provided in the VI-HPS Tools Guide. The workshop will be held in English and run from 09:00 to not later than 18:00 each day, with breaks for lunch and refreshments. For participants from public research institutions in PRACE countries, the course fee is sponsored through the PRACE PATC program. All participants are responsible for their own travel and accommodation. Classroom capacity is limited, therefore priority will be given to applicants with parallel codes already running on the workshop computer system (CLAIX), and those bringing codes from similar x86 cluster systems to work on. Participants are therefore encouraged to prepare their own MPI, OpenMP and hybrid MPI+OpenMP parallel application codes for analysis. Participants are expected to use their own notebook computers to connect to the workshop computer systems via SSH: X11 will also be required for the graphical tools. Hardware and Software Platforms CLAIX2016: NEC x86_64 Linux cluster system:   600+ 'MPI' compute nodes each with two Intel Xeon E5-2650v4 'Broadwell' processors (2.2GHz, 12 cores per processor, 2 hardware threads per core) and 128GB shared memory 8 'SMP' compute nodes each with eight Intel Xeon E7-8860v4 'Broadwell' processors (2.2GHz, 18 cores per processor, 2 hardware threads per core) and 1024GB shared memory software: CentOS 7.2 GNU/Linux, Intel MPI; Intel, GCC and other compilers;   The local HPC system CLAIX is the primary platform for the workshop and will be used for the hands-on exercises. Course accounts will be provided during the workshop. Participants with accounts on the JURECA cluster and JUQUEEN BlueGene/Q at JSC will also be assisted using those systems. Other systems where up-to-date versions of the tools are installed can also be used when preferred, though support may be limited and participants are expected to already possess user accounts. Regardless of whichever systems they intend to use, participants should be familiar with the relevant procedures for compiling and running their parallel applications (via batch queues where appropriate). Accommodation in Aachen A contingent of rooms at various hotels in Aachen have been reserved until 5 March 2017: after that there's no guarantee desired rooms will still be available. Alternatively consult the full accommodation list. The detailed program will be available under VI-HPS training web site.   https://events.prace-ri.eu/event/584/ 2017-03-27 07:00:00 UTC 2017-03-31 16:00:00 UTC
  • R Programming Foundations for Life Scientists, 2 hp

    27 - 31 Mar 2017

    Uppsala

    R Programming Foundations for Life Scientists, 2 hp https://tess.elixir-europe.org/events/r-programming-foundations-for-life-scientists-2-hp-f3c02264-0573-45bf-9d3e-4067bfa91d1d 2017-03-27 09:00:00 UTC 2017-03-31 00:00:00 UTC Uppsala Uppsala
  • Advanced course Bioprocess Design

    27 - 31 Mar 2017

    Delft, Delft

    Advanced course Bioprocess Design https://tess.elixir-europe.org/events/advanced-course-bioprocess-design Course description With recent advances in molecular biology and a growing biomass availability for use as industrial feedstock, the bio-based economy is getting a wider range of inputs. Scaling up the bio(techno)logy innovations and implementation in large-scale factories or biorefineries… The post Advanced course Bioprocess Design appeared first on Dutch Techcentre for Life Sciences. 2017-03-27 09:00:00 UTC 2017-03-31 00:00:00 UTC Delft, Delft, Delft Delft Delft Delft
  • R Programming Foundations for Life Scientists, 2 hp

    27 Mar - 01 Apr 2017

    R Programming Foundations for Life Scientists, 2 hp https://tess.elixir-europe.org/events/r-programming-foundations-for-life-scientists-2-hp-56fa30d4-110b-45eb-a88c-682e65f58c51 Course content The course is addressed to life scientists with little or moderate experience in programming but enthusiastic about learning how to use R to make their work smoother and easier. The course covers fundamental concepts of programming and software design focusing on programming in R. We will go through various aspects of R scripting with some more attention paid to the parts useful for life scientists. After introductory lectures on good programming practices, basic software design theory and a brief overview of R, we will delve into programming. We start by learning how to use R as a simple calculator, what are variable types, how to use data structures, how to implement repeating actions with and without loops, how to take actions based on certain condition. We gradually proceed to loading data, importing data from common file formats, we do some basic matrix algebra; learn how to perform basic statistical tests and how to visualize results. We will also put stress on giving you tools to access help and information on R-related challenges and issues, we will spend some time on learning how to install external packages, how to find bugs and address common installation issues. We also mention some more advanced topics and tell you more about BioConductor that is an invaluable tool for a computational biologist. You will also learn how to document your work and how to generate automatic reports. We try to illustrate all these concepts with some real-life examples and interesting lab tasks. The course will be given by experienced computational biologists from SciLifeLab and Uppsala University. Dr. Marcin Kierczak responsible for the content of the course is an experienced R user/coder, who has previously developed R packages and has experience in teaching programming and R to different audiences. 2017-03-27 09:00:00 UTC 2017-04-01 00:00:00 UTC
  • Flowcytometrie

    27 Mar - 10 Apr 2017

    Rotterdam, Nederland

    Flowcytometrie https://tess.elixir-europe.org/events/flowcytometrie In deze cursus komen zowel theoretische als technische aspecten van de flowcytometrie aan de orde. Tijdens de cursus worden voorbeelden gebruikt uit de medische diagnostiek. 2017-03-27 16:00:00 UTC 2017-04-10 16:00:00 UTC Avans Hogeschool Wytemaweg 80, , Rotterdam, Nederland Wytemaweg 80, Rotterdam Nederland 3015 CN
  • Introduction to high-throughput sequencing data analysis

    28 - 31 Mar 2017

    Cambridge, United Kingdom

    Introduction to high-throughput sequencing data analysis https://tess.elixir-europe.org/events/introduction-to-high-throughput-sequencing-data-analysis This course provides an introduction to high-throughput sequencing (HTS) data analysis methodologies. Lectures will give insight into how biological knowledge can be generated from RNA-seq, ChIP-seq and DNA-seq experiments and illustrate different ways of analyzing such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq, ChIP-seq and DNA-seq data under the guidance of the lecturers and teaching assistants. It is aimed at researchers who are applying or planning to apply HTS technologies and bioinformatics methods in their research. 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=1983575&course-title=Introduction%20to%20high-throughput%20sequencing%20data%20analysis).'' 2017-03-28 08:30:00 UTC 2017-03-31 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • Unix/Linux Tutorial for beginners

    28 - 30 Mar 2017

    Unix/Linux Tutorial for beginners https://tess.elixir-europe.org/events/unix-linux-tutorial-for-beginners NBIS (the Swedish node of Elixir) and Elixir Slovenia are offering an "Introduction to Linux" course targeted at life scientists to extend their skills and knowledge. The course is delivered via classroom training and via an e-learning platform, thus offering the participants the possibility of attending the course either by traveling to Linköping, Umea (Sweden) or Ljubljana (Slovenia), or by connecting remotely via the Elixir Slovenia e-learning platform. The number of remote students is limited to 10. The course will be broad-casted from Sweden, Linköping. NGS technologies generate vast amount of data, usually in the form of very large text files. Trying to handle this data with applications like Word or Excel is difficult or impossible, while using the Linux command line can drastically simplify your work and improve your efficiency. Linux/Unix provides an excellent computing environment for bioinformatics and the command line interpreter (shell) serves as an interface to a large amount of bioinformatics programs. The course provides a basic introduction to Unix/Linux commands for bioinformatics and covers how Unix/Linux commands can be used to manage and inspect your data and results, and how to generate and run bioinformatics pipelines and work-flows using basic shell scripting. Apply here: https://goo.gl/forms/jiyZc4BcTanJvrdl2 2017-03-28 09:00:00 UTC 2017-03-30 17:00:00 UTC Elixir Sweden, Elixir Slovenia
  • Efficient Parallel IO on ARCHER 29-30 Mar 2017 @ EPCC at Durham

    29 - 30 Mar 2017

    Efficient Parallel IO on ARCHER 29-30 Mar 2017 @ EPCC at Durham https://tess.elixir-europe.org/events/efficient-parallel-io-on-archer-29-30-mar-2017-epcc-at-durham Please note:  This course takes place in Durham. One of the greatest challenges to running parallel applications on large numbers of processors is how to handle file IO. Standard IO routines are not designed with parallelism in mind, and IO overheads can grow to dominate the overall runtime. Parallel file systems are optimised for large data transfers, but performance can be far from optimal if every process opens its own file or if all IO is funneled through a single master process. This hands-on course explores a range of issues related to parallel IO. It uses ARCHER and its parallel Lustre file system as a platform for the exercises; however, almost all the IO concepts and performance considerations are applicable to any parallel system. The IO part of the MPI standard gives programmers access to efficient parallel IO in a portable fashion. However, there are a large number of different routines available and some can be difficult to use in practice. Despite its apparent complexity, MPI-IO adopts a very straightforward high-level model. If used correctly, almost all the complexities of aggregating data from multiple processes can be dealt with automatically by the library. The first day of the course will cover the MPI-IO standard, developing IO routines for a regular domain decomposition example. It will also briefly cover higher-level standards such as HDF5 and NetCDF which are built on top of MPI-IO. The second day will concentrate on performance, covering how to configure the parallel file system and tune the MPI-IO library for best performance. Case studies from real codes will be presented. Prerequisites: The course assumes a good understanding of basic MPI programming in Fortran, C or C++. Knowledge of MPI derived datatypes would be useful but not essential. Timetable Wednesday 29 March 09:30 - 10:15 : Parallel IO 10:15 - 11:00 : Practical : Basic IO 11:00 - 11:30 : Break 11:30 - 12:15 : Derived Datatypes for MPI-IO 12:15 - 13:00 : Practical: Derived Datatypes 13:00 - 14:00 : Lunch 14:00 - 14:45 : Basic MPI-IO Routines 14:45 - 15:30 : Practical: Basic MPI-IO 15:30 - 16:00 : Break 16:00 - 16:45 : MPI-IO Features and alternative libraries 16:45 - 17:30 : Practical : Alternative Libraries Thursday 30th March 09:30 - 10:15 : Lustre file system on ARCHER 10:15 - 11:00 : Practical: Lustre configuration 11:00 - 11:30 : Break 11:30 - 12:15 : Parallel IO libraries on ARCHER 12:15 - 13:00 : Practical: tuning parallel IO 13:00 - 14:00 : Lunch 14:00 - 14:45 : Case studies 14:45 - 15:30 : Individual consultancy session https://events.prace-ri.eu/event/591/ 2017-03-29 08:00:00 UTC 2017-03-30 16:30:00 UTC
  • OpenFOAM Programming CFD Training Course

    29 - 30 Mar 2017

    OpenFOAM Programming CFD Training Course https://tess.elixir-europe.org/events/openfoam-programming-cfd-training-course OpenFOAM programming course by CFD Direct Ltd, UK 2017-03-29 09:00:00 UTC 2017-03-30 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.
  • Software Carpentry - Technical University Munich

    29 - 30 Mar 2017

    Freising, Germany

    Software Carpentry - Technical University Munich https://tess.elixir-europe.org/events/software-carpentry-technical-university-munich Find out more at https://konrad.github.io/2017-03-29-munich/ 2017-03-29 09:00:00 UTC 2017-03-30 00:00:00 UTC Software Carpentry Technical University Munich, Freising, Germany Technical University Munich Freising Germany
  • BBMRI-omics: Introduction and Hands-on Application

    30 - 31 Mar 2017

    Utrecht, Netherlands

    BBMRI-omics: Introduction and Hands-on Application https://tess.elixir-europe.org/events/bbmri-omics-introduction-and-hands-on-application During a 2-day program researchers can get acquainted with the data BBMRI-omics has on offer for the research community. On the first day, a series of lectures will introduce the wide spectrum of omics data present within BBMRI (from genomics… The post BBMRI-omics: Introduction and Hands-on Application appeared first on Dutch Techcentre for Life Sciences. 2017-03-30 09:00:00 UTC 2017-03-31 00:00:00 UTC Utrecht, Netherlands, Utrecht, Netherlands Utrecht, Netherlands Utrecht Netherlands
  • BRENDA Workshop 2017

    30 - 31 Mar 2017

    BRENDA Workshop 2017 https://tess.elixir-europe.org/events/brenda-workshop-2017 2017-03-30 09:00:00 UTC 2017-03-31 00:00:00 UTC
  • Introduction to Next Generation Sequencing Bioinformatics Workshop

    31 Mar 2017

    Leuven, Belgium

    Introduction to Next Generation Sequencing Bioinformatics Workshop https://tess.elixir-europe.org/events/introduction-to-next-generation-sequencing-bioinformatics-workshop Introduction to Next Generation Sequencing Bioinformatics Workshop MARCH31, 2017 (08:30-17:00) Lokaal H04.212, ON2, Campus Gasthuisberg, KU Leuven, Leuven Preliminary Program 08:30 – 9:00 - Welcome coffee 09:00 – 09:05 – Welcome by Prof. Joris Vermeesch 09:05 - 10:00 - Overview of NGS sequencing methods and technologies Session lead: Jeroen Van Houdt - Genomics Core Leuven 10:00 - 11:00 – Understanding NGS raw data: Fastq format, quality checking, trimming, adapter clipping Session lead: Koen Herten - Genomics Core Leuven 11:00 – 11:30 – Coffee break 11:30 – 12:30 – Read mapping and alignment: SAM format, alignment tools, visualization on IGV Session lead: Koen Herten - Genomics Core Leuven 12:30 – 13:30 – Lunch 13:30 – 15:00 – Variant calling: tools, GATK, quality scores, baserecalibration, VCF files Session lead: Erika Souche & Luc Dehaspe - Genomics Core Leuven 15:00 – 15:30 – Coffee break 15:30 – 17:00 – RNA-Seq data: Differential expression principles, counting, DE table interpretation Session lead: Alvaro Cortés Calabuig – Genomics Core Leuven Places are limited and are assigned on a first-come first-serve policy. The workshop is free of charge for students and members of academic institutions in Belgium. The cost for members of non-academic institutions (VIB, IMEC, pharma, etc.) is 100€. Sandwiches will be offered at lunch time. Late cancellations are subject to an administrative fee of 50€. Participants are required to bring their own laptops. For inquiries, please send an email to alvaro.cortes@uzleuven.be. 2017-03-31 08:30:00 UTC 2017-03-31 17:00:00 UTC Genomics Core KU Leuven/UZ Leuven Herestraat 49, Rooml H04.212, ON2, Campus Gasthuisberg, KU Leuven, Leuven, Leuven, Belgium Herestraat 49, Rooml H04.212, ON2, Campus Gasthuisberg, KU Leuven, Leuven Leuven Vlaams-Brabant Belgium 3000
  • Using Next Generation Sequencing Data Analysis for the Clinic - CASyM winter school of Systems Medicine

    31 Mar 2017

    Using Next Generation Sequencing Data Analysis for the Clinic - CASyM winter school of Systems Medicine https://tess.elixir-europe.org/events/using-next-generation-sequencing-data-analysis-for-the-clinic-casym-winter-school-of-systems-medicine 2017-03-31 09:00:00 UTC 2017-03-31 00:00:00 UTC
  • Prep course for Biopython

    31 Mar 2017

    Leuven, Belgium

    Prep course for Biopython https://tess.elixir-europe.org/events/prep-course-for-biopython This training is an introduction to the Biopython training. This training is intended for people who have no experience with Linux and will teach them all knowledge of Linux command line that is required to successfully follow the Biopython training. If you want to follow  the Biopython training​ and you have no experience with Linux command line, you have to follow this introduction.  2017-03-31 09:30:00 UTC 2017-03-31 17:00:00 UTC VIB Bioinformatics Core O&N4 room 06.239 Gasthuisberg, Leuven, Belgium O&N4 room 06.239 Gasthuisberg Leuven Belgium 3000
  • Making Babies in the 21st Century

    03 Apr - 15 May 2017

    Making Babies in the 21st Century https://tess.elixir-europe.org/events/making-babies-in-the-21st-century-5c124c1d-d0fe-45a4-80f3-f9c5ec673330 Explores the new reproductive technologies, the opportunities they provide, and the profound social challenges they pose. 2017-04-03 00:00:00 UTC 2017-05-15 00:00:00 UTC UCL (University College London)
  • Metagenomics Data Analysis Workshop @ CSC

    3 - 6 Apr 2017

    Espoo, Finland

    Metagenomics Data Analysis Workshop @ CSC https://tess.elixir-europe.org/events/metagenomics-data-analysis-workshop-csc Description Metagenomics investigates the composition and function of microbial communities in different environments based on direct isolation of genetic material. It has been accelerated by the advances in high-throughput sequencing technologies, and the increasing data sizes require efficient analysis methods and advanced computing approaches. This international workshop covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the workshop has also an optional day on community analysis of amplicon sequencing data. Finally, international databases and standards for storing the data are introduced. The workshop consists of lectures and hands-on exercises. User-friendly analysis platforms META-pipe and Chipster are used in the exercises, so no programming skills are required, and the workshop is thus suitable for everybody. META-pipe has been developed by ELIXIR-Norway, and it offers tools for pre-processing (Prinseq, FastQC), assembly (MetaRay/Ray, Mira), taxonomic classification (LC-classifier), gene prediction (Glimmer/MGA), functional analysis (Blast, Priam, InterProScan) and visualization (Metarep). META-pipe analysis jobs use a Spark cluster in the cloud for computation. Chipster offers over 360 analysis tools for different kinds of high-thoughput data. For community analysis of amplicon sequencing data it has tools for pre-processing (Prinseq, Trimmomatic, FastQC, Mothur), taxonomic classification (Mothur), and statistical analysis for marker gene studies (R packages vegan, rich, biodiversityR, pegas and labdsv).  The workshop is organized in collaboration with the ELIXIR EXCELERATE project. Lecturers Nils Willassen (ELIXIR-Norway) Espen Robertsen (ELIXIR-Norway) Erik Hjerde (ELIXIR-Norway) Aleksandr Agafonov (ELIXIR-Norway) Anu Mikkonen (University of Jyväskylä) Jenni Hultman (University of Helsinki) Petri Auvinen (University of Helsinki) Jarno Tuimala (RS training) Maria Lehtivaara (CSC) Kimmo Mattila (CSC) Eija Korpelainen (CSC) Program Please note that there might be still small changes to the schedule. Day 1, Monday 3.4.2017: OPTIONAL MODULE - Community analysis of amplicon sequencing data 9:00-10:45 LECTURES Who's there? Community analysis by amplicon sequencing (Anu Mikkonen) Short demo: Using QIIME in parallel fashion in HPC environments (Kimmo Mattila) 10:45-11:00 Coffee break 11:00-12:30 HANDS-ON SESSION: Using the Chipster software to analyze 16S rRNA data (Eija Korpelainen, Maria Lehtivaara, Anu Mikkonen) Introduction to Chipster Data preprocessing with Mothur-based tools and FastQC 12:30-13:30 Lunch 13:30-16:30 HANDS-ON SESSION: Using Chipster continues (Eija Korpelainen, Maria Lehtivaara, Anu Mikkonen and Jarno Tuimala) // coffee break included Data preprocessing with Mothur-based tools Taxonomic classification with Mothur-based tools Statistical analysis of marker gene data: Comparing diversity and abundance between groups Visualization Day 2, Tuesday 4.4.2017: Sample preparation, sequencing, quality control, filtering and assembly 9:00-12:30 LECTURES 9:00-10:15 Selecting and preparing samples for metaomics (Anu Mikkonen) Your samples are only as good as your sample preparation routines are, and your results are only as valid as your experimental design is. This talk will discuss, showing plenty of real-life examples, all the things that can go wrong before you even send your DNA samples out for the sequencing. The talk includes lots of practical recommendations on what to do before, or sometimes instead of, metagenomics analysis. 10:15-10:45 Sequencing technologies for metagenomics (Petri Auvinen) 10:45-11:00 Coffee break 11:00-11:30 Metagenomics analysis – an overview (Nils Willassen) 11:30-12:00 META-pipe analysis platform overview (Espen Robertsen, Erik Hjerde) 12:00-12:30 Metagenomics in the cloud (Aleksandr Agafonov) 12:30-13:15 Lunch 13:15-16:30 HANDS-ON EXERCISES: Using the META-pipe platform (Nils Willassen, Espen Robertsen, Erik Hjerde) / / coffee break included Quality control and filtering Assembly Validation Day 3, Wednesday 5.4.2017: Taxonomic and functional analysis 9:00-11:30 LECTURES 9:00-9:30 Taxonomic classification (Nils Willassen) 9:30-10:00 Functional assignment (Espen Robertsen) 10:00-10:15 Coffee break 10:15-10:45 New data resources for marine metagenomics (Nils Willassen) 10:45-11:15 The metagenomics data life-cycle: standards and best practice (TBD) 11:15-12:00 HANDS-ON EXERCISES: Using the META-pipe platform (Nils Willassen, Espen Robertsen, Erik Hjerde) Introduction, taxonomic classification 12:00-13:00 Lunch 13:00-16:30 HANDS-ON EXERCISES: Using the META-pipe platform continued (Nils Willassen, Espen Robertsen, Erik Hjerde) / / coffee break included Taxonomic classification continued Functional assignment Day 4, Thursday 6.4.2017: Comparative metagenomics and other analysis 9:00-12:00 HANDS-ON EXERCISES: Using the META-pipe platform continued (Nils Willassen, Espen Robertsen, Erik Hjerde) / / coffee break included Visualization of data Comparative metagenomics 12:00-13:00 Lunch 13:00-14:30 LECTURES AND WRAP-UP 13:00-13:35 Arctic metagenomes as a scaffold for understanding metatranscriptomic data (Jenni Hultman) 13:35-14:00 Genome assembly from metagenomic reads (Jenni Hultman) 14:00-14:30 Feedback and wrap up   Language:  EnglishPrice:          Free of charge https://events.prace-ri.eu/event/602/ 2017-04-03 06:00:00 UTC 2017-04-06 14:00:00 UTC ELIXIR EXCELERATE project and PRACE CSC Finland Oy, Espoo, Finland CSC Finland Oy Espoo Finland
  • Metagenomics Data Analysis Workshop @ CSC

    3 - 6 Apr 2017

    Metagenomics Data Analysis Workshop @ CSC https://tess.elixir-europe.org/events/metagenomics-data-analysis-workshop-csc-80a1d085-6d5e-4f3d-867d-85fd61847e8e Description Metagenomics investigates the composition and function of microbial communities in different environments based on direct isolation of genetic material. It has been accelerated by the advances in high-throughput sequencing technologies, and the increasing data sizes require efficient analysis methods and advanced computing approaches. This international workshop covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the workshop has also an optional day on community analysis of amplicon sequencing data. Finally, international databases and standards for storing the data are introduced. The workshop consists of lectures and hands-on exercises. User-friendly analysis platforms META-pipe and Chipster are used in the exercises, so no programming skills are required, and the workshop is thus suitable for everybody. META-pipe has been developed by ELIXIR-Norway, and it offers tools for pre-processing (Prinseq, FastQC), assembly (MetaRay/Ray, Mira), taxonomic classification (LC-classifier), gene prediction (Glimmer/MGA), functional analysis (Blast, Priam, InterProScan) and visualization (Metarep). META-pipe analysis jobs use a Spark cluster in the cloud for computation. Chipster offers over 360 analysis tools for different kinds of high-thoughput data. For community analysis of amplicon sequencing data it has tools for pre-processing (Prinseq, Trimmomatic, FastQC, Mothur), taxonomic classification (Mothur), and statistical analysis for marker gene studies (R packages vegan, rich, biodiversityR, pegas and labdsv).  The workshop is organized in collaboration with the ELIXIR EXCELERATE project. Lecturers Nils Willassen (ELIXIR-Norway) Espen Robertsen (ELIXIR-Norway) Erik Hjerde (ELIXIR-Norway) Inge Alexander Raknes (ELIXIR-Norway) Rob Finn (EBI) Anu Mikkonen (University of Jyväskylä) Jenni Hultman (University of Helsinki) Petri Auvinen (University of Helsinki) Jarno Tuimala (RS training) Maria Lehtivaara (CSC) Kimmo Mattila (CSC) Eija Korpelainen (CSC) Program Please note that there might be still small changes to the schedule. Day 1, Monday 3.4.2017: OPTIONAL MODULE - Community analysis of amplicon sequencing data 9:00-10:45 LECTURES Who's there? Community analysis by amplicon sequencing (Anu Mikkonen) Short demo: Using QIIME in parallel fashion in HPC environments (Kimmo Mattila) 10:45-11:00 Coffee break 11:00-12:30 HANDS-ON SESSION: Using the Chipster software to analyze 16S rRNA data (Eija Korpelainen, Maria Lehtivaara, Anu Mikkonen) Introduction to Chipster Data preprocessing with Mothur-based tools and FastQC 12:30-13:30 Lunch 13:30-16:30 HANDS-ON SESSION: Using Chipster continues (Eija Korpelainen, Maria Lehtivaara, Anu Mikkonen and Jarno Tuimala) // coffee break included Data preprocessing with Mothur-based tools Taxonomic classification with Mothur-based tools Statistical analysis of marker gene data: Comparing diversity and abundance between groups Visualization Day 2, Tuesday 4.4.2017: Sample preparation, sequencing, quality control, filtering and assembly 9:00-12:30 LECTURES 9:00-10:15 Selecting and preparing samples for metaomics (Anu Mikkonen) Your samples are only as good as your sample preparation routines are, and your results are only as valid as your experimental design is. This talk will discuss, showing plenty of real-life examples, all the things that can go wrong before you even send your DNA samples out for the sequencing. The talk includes lots of practical recommendations on what to do before, or sometimes instead of, metagenomics analysis. 10:15-10:45 Sequencing technologies for metagenomics (Petri Auvinen) 10:45-11:00 Coffee break 11:00-11:30 Metagenomics analysis – an overview (Nils Willassen) 11:30-12:00 META-pipe analysis platform overview (Espen Robertsen, Erik Hjerde) 12:00-12:30 Metagenomics in the cloud (TBD) 12:30-13:15 Lunch 13:15-16:30 HANDS-ON EXERCISES: Using the META-pipe platform (Nils Willassen, Espen Robertsen, Erik Hjerde) / / coffee break included Quality control and filtering Assembly Validation Day 3, Wednesday 5.4.2017: Taxonomic and functional analysis 9:00-11:30 LECTURES 9:00-9:30 Providing the generalist EBI metagenomics platform: challenges and issues (Rob Finn) 9:30-9:50 The metagenomics data life-cycle: standards and best practice (Rob Finn) 9:50-10:20 New data resources for marine metagenomics (Nils Willassen) 10:20-10:35 Coffee break 10:35-11:15 Taxonomic classification and functional assignment (Espen Robertsen, Erik Hjerde) 11:15-12:00 HANDS-ON EXERCISES: Using the META-pipe platform (Nils Willassen, Espen Robertsen, Erik Hjerde) Introduction, taxonomic classification 12:00-13:00 Lunch 13:00-16:30 HANDS-ON EXERCISES: Using the META-pipe platform continued (Nils Willassen, Espen Robertsen, Erik Hjerde) / / coffee break included Taxonomic classification continued Functional assignment Day 4, Thursday 6.4.2017: Comparative metagenomics and other analysis 9:00-12:00 HANDS-ON EXERCISES: Using the META-pipe platform continued (Nils Willassen, Espen Robertsen, Erik Hjerde) / / coffee break included Visualization of data Comparative metagenomics 12:00-13:00 Lunch 13:00-14:30 LECTURES AND WRAP-UP 13:00-13:35 Arctic metagenomes as a scaffold for understanding metatranscriptomic data (Jenni Hultman) 13:35-14:00 Genome assembly from metagenomic reads (Jenni Hultman) 14:00-14:30 Feedback and wrap up   Language:  EnglishPrice:          Free of charge https://events.prace-ri.eu/event/602/ 2017-04-03 06:00:00 UTC 2017-04-06 14:00:00 UTC
  • Advanced Topics in High Performance Computing @ LRZ

    3 - 6 Apr 2017

    Advanced Topics in High Performance Computing @ LRZ https://tess.elixir-europe.org/events/advanced-topics-in-high-performance-computing-lrz-cfd3d16c-037e-411b-b54d-fadf598664fa In this add-on course to the parallel programming course special topics are treated in more depth, in particular node-level optimisation, I/O, Intel Xeon Phi and PGAS concepts. It is provided in collaboration of Erlangen Regional Computing Centre (RRZE) and LRZ within KONWIHR. The course is a PRACE Advanced Training Center 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/Hager) Day 2 (09:00-17:00) 09:00-12:30 Parallel I/O with MPI IO (Wittmann) 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 Introduction into Intel Xeon Phi Programming (Weinberg) Day 4 (09:00-17:00) PGAS programming with coarray Fortran and Unified Parallel C (Bader) https://events.prace-ri.eu/event/535/ 2017-04-03 07:00:00 UTC 2017-04-06 15:00:00 UTC
  • Programming the Manycore Knights Landing Processor @ EPCC at Leeds

    3 - 4 Apr 2017

    Programming the Manycore Knights Landing Processor @ EPCC at Leeds https://tess.elixir-europe.org/events/programming-the-manycore-knights-landing-processor-epcc-at-leeds ARCHER has recently added a small Cray XC40 cluster containing Intel's Knights Landing (KNL) processors. This system is intended to allow the UK computational simulation community to test their codes on the KNL processors, optimise codes for this new hardware, and evaluate the suitability of KNL for their applications. In this course we will introduce the KNL system associated with ARCHER, descibe how it can be used, and present the technical details of the KNL processor. Details Knights Landing is Intel's latest Xeon Phi many-core processor. It offers large amounts of floating point performance (the theoretical peak is 3TFlop/s using double precision data) in a single processor for applications that can use it efficiently. The KNL hardware is significantly different to the previous generation of Xeon Phi, and contains specialised hardware that may beneficial for scientific applications. In this course we will describe the KNL hardware, explain how to use the various new features it presents, and explain how to access and use KNL processors through the ARCHER service. There will be a number of hands-on practical sessions, and all attendees will be given KNL access for the duration of the course. This course is free to all academics. Intended learning outcomes On completion of this course students should be able to: Understand the Knights Landing (KNL) processor. Understand how to access and run jobs on the ARCHER KNL cluster. Understand the impact of vectorisation on performance on KNL. Understand how to check if an application is vectorising and modify applications to improve vectorisation Use the different memory available in the nodes. Pre-requisites Some understanding of at least one of the following programming Languages: Fortran, C or C++. Timetable to follow Course Materials to follow https://events.prace-ri.eu/event/608/ 2017-04-03 08:00:00 UTC 2017-04-04 16:30:00 UTC
  • Basic statistics and data handling

    3 - 5 Apr 2017

    Cambridge, United Kingdom

    Basic statistics and data handling https://tess.elixir-europe.org/events/basic-statistics-and-data-handling-eefdec71-300e-43f3-ae60-9d17eab0f745 This three day course is intended to open doors to applying statistics - whether directly increasing skills and personally undertaking analyses, or by expanding knowledge towards identifying collaborators. The end goal is to drive confident engagement with data analysis and further training - increasing the quality and reliability of interpretation, and putting that interpretation and subsequent presentation into the hands of the researcher. Each day of the course will deliver a mixture of lectures, workshops and hands-on practicals – and will focus on the following specific elements. Day 1 focuses on basic approaches and the computer skills required to do downstream analysis. Covering: Basic skills for data manipulation in R. How to prepare your data effectively. Principles of experimental design and how this influences analysis. On day 2, participants will explore the core concepts of statistics – so that they can begin to see how they can be applied to their own work, and to also help with better critical evaluation of the work of others. Covering: Basic statistics concepts and practice: power, variability, false discovery, t-test, effect size, simulations to understand what a p-value means. On day 3 we will continue to explore core concepts of statistic, focusing on linear regression and multiple testing correction. This event is supported by a BBSRC Strategic Training Awards for Research Skills (STARS) grant. 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=2034285&course-title=Basic%20statistics%20and%20data%20handling).'' 2017-04-03 08:30:00 UTC 2017-04-05 16:30:00 UTC University of Cambridge Craik-Marshall Building, Cambridge, United Kingdom Craik-Marshall Building Cambridge United Kingdom CB2 3AR
  • Metagenomics data analysis

    3 - 6 Apr 2017

    Metagenomics data analysis https://tess.elixir-europe.org/events/metagenomics-data-analysis This international workshop covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. It has also an optional module on community analysis of amplicon sequencing data. 2017-04-03 09:00:00 UTC 2017-04-06 17:00:00 UTC The course takes place at the training facilities of CSC. The address is Keilaranta 14, Espoo, Finland. You can reach us by public transportation, read more. The course takes place at the training facilities of CSC. The address is Keilaranta 14, Espoo, Finland. You can reach us by public transportation, read more.
  • Advanced R Programming

    3 - 4 Apr 2017

    Advanced R Programming https://tess.elixir-europe.org/events/advanced-r-programming 2017-04-03 09:00:00 UTC 2017-04-04 00:00:00 UTC
  • Special Aspects of Bioinformatics for Proteomics - Proteomic Forum 2017

    03 Apr 2017

    Special Aspects of Bioinformatics for Proteomics - Proteomic Forum 2017 https://tess.elixir-europe.org/events/special-aspects-of-bioinformatics-for-proteomics-proteomic-forum-2017 2017-04-03 09:00:00 UTC 2017-04-03 00:00:00 UTC
  • Making Babies in the 21st Century

    03 Apr - 15 May 2017

    Making Babies in the 21st Century https://tess.elixir-europe.org/events/making-babies-in-the-21st-century-e67b5e17-71f1-4351-b7b0-52af5b9902c1 Explores the new reproductive technologies, the opportunities they provide, and the profound social challenges they pose. 2017-04-03 09:00:00 UTC 2017-05-15 00:00:00 UTC UCL (University College London)
  • Introduction to Next Generation Sequencing (April) 2017

    3 - 6 Apr 2017

    Cambridge, GB

    Introduction to Next Generation Sequencing (April) 2017 https://tess.elixir-europe.org/events/introduction-to-next-generation-sequencing-april-2017 This course will provide an introduction to the technology, data analysis, tools and resources for next generation sequencing (NGS) data. 2017-04-03 12:00:00 UTC 2017-04-06 16:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 1, Cambridge, GB European Bioinformatics Institute (EMBL-EBI) - Training Room 1 Cambridge GB CB10 1SD
  • Introduction to Next Generation Sequencing (April)

    3 - 6 Apr 2017

    Cambridge, GB

    Introduction to Next Generation Sequencing (April) https://tess.elixir-europe.org/events/introduction-to-next-generation-sequencing-april-5f4bf11b-0957-4a11-b217-777b7eca707e This course will provide an introduction to the technology, data analysis, tools and resources for next generation sequencing (NGS) data. 2017-04-03 12:00:00 UTC 2017-04-06 16:00:00 UTC European Bioinformatics Institute (EMBL-EBI) - Training Room 1, Cambridge, GB European Bioinformatics Institute (EMBL-EBI) - Training Room 1 Cambridge GB CB10 1SD

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