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  • PostGIS paikkatietokannan käyttö

    11 - 12 April 2016

    Elixir node event
    PostGIS paikkatietokannan käyttö https://tess.elixir-europe.org/events/postgis-paikkatietokannan-kaytto PostGIS peruskurssi, missä opit asentamaan tietokannan, kyselemään ja analysoimaan sitä SQL-lausekkeilla ja konfiguroimaan muun muassa karttaprojektioihin liittyviä ongelmia. 2016-04-11 09:00:00 UTC 2016-04-12 16:15:00 UTC CSC 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. [] [] [] [] [] []
  • Webinar: Running array jobs in Taito

    12 April 2016

    Elixir node event
    Webinar: Running array jobs in Taito https://tess.elixir-europe.org/events/webinar-running-array-jobs-in-taito How to run array jobs in Taito. Join the webinar here: https://connect.funet.fi/webinar 2016-04-12 13:00:00 UTC 2016-04-12 13:30:00 UTC CSC Join the webinar here: https://connect.funet.fi/webinar Join the webinar here: https://connect.funet.fi/webinar [] [] [] [] [] []
  • Elmer FEM Course

    13 - 14 April 2016

    Elixir node event
    Elmer FEM Course https://tess.elixir-europe.org/events/elmer-fem-course Elmer FEM Course presents the basics of the open source finite element software for multi-physical problems. 2016-04-13 09:00:00 UTC 2016-04-14 16:30:00 UTC CSC 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. [] [] [] [] [] []
  • Advanced Threading and Optimization

    18 - 20 April 2016

    Elixir node event
    Advanced Threading and Optimization https://tess.elixir-europe.org/events/advanced-threading-and-optimization The course includes topics on code optimization for x86 platforms and efficient code parallelization using OpenMP threading. Advanced aspects of threading and optimization, such as new features of OpenMP 4.0, will be covered during the course. Some performance aspects of MPI will also be discussed. 2016-04-18 09:00:00 UTC 2016-04-20 16:00:00 UTC CSC 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. [] [] [] [] [] []
  • Webinar: Module system on Taito

    19 April 2016

    Elixir node event
    Webinar: Module system on Taito https://tess.elixir-europe.org/events/webinar-module-system-on-taito This webinar explains how to use the module system on Taito. 2016-04-19 13:00:00 UTC 2016-04-19 13:30:00 UTC CSC https://connect.funet.fi/webinar https://connect.funet.fi/webinar [] [] [] [] [] []
  • Webinar: Using FGCI grid

    26 April 2016

    Elixir node event
    Webinar: Using FGCI grid https://tess.elixir-europe.org/events/webinar-using-fgci-grid This webinar demonstrates, how camputing tasks can be submitted to the The Finnish Grid and Cloud Infrasructuire (FGCI). With the ARC middleware jobs can be submitted to FGCI as well from the servers of CSC and from the users local environment. 2016-04-26 13:30:00 UTC 2016-04-26 14:00:00 UTC CSC https://connect.funet.fi/webinar https://connect.funet.fi/webinar [] [] [] [] [] []
  • Vaadin meetup at CSC

    28 April 2016

    Elixir node event
    Vaadin meetup at CSC https://tess.elixir-europe.org/events/vaadin-meetup-at-csc This time our Vaadin meetup is hosted by CSC, the home of Finland's most powerful computers. We'll first hear how CSC is using Vaadin in their services, then we get a brief introduction to Spring Boot and Vaadin and the remaining time is reserved for informal Q&A and hacking. 2016-04-28 15:00:00 UTC 2016-04-28 18:00:00 UTC CSC 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. [] [] [] [] [] []
  • Protein Modeling with Discovery Studio

    10 May 2016

    Elixir node event
    Protein Modeling with Discovery Studio https://tess.elixir-europe.org/events/protein-modeling-with-discovery-studio This one day course provides introduction to Discovery Studio protein modeling enviroment. 2016-05-10 09:00:00 UTC 2016-05-10 17:00:00 UTC CSC 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. [] [] [] [] [] []
  • POSTPONED: cPouta Cloud Course

    11 May 2016

    Elixir node event
    POSTPONED: cPouta Cloud Course https://tess.elixir-europe.org/events/cpouta-cloud-course This course will give a practical introduction to using CSC's cPouta cloud service. 2016-05-11 09:00:00 UTC 2016-05-11 17:00:00 UTC CSC 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. [] [] [] [] [] []
  • Webinar: How to use Techila with R

    17 May 2016

    Elixir node event
    Webinar: How to use Techila with R https://tess.elixir-europe.org/events/webinar-how-to-use-techila-with-r In this webinar we learn how to run parallel R jobs using the Techila service. 2016-05-17 13:00:00 UTC 2016-05-17 13:30:00 UTC CSC https://connect.funet.fi/webinar https://connect.funet.fi/webinar [] [] [] [] [] []
  • FGCI ARC tutorial

    20 May 2016

    Elixir node event
    FGCI ARC tutorial https://tess.elixir-europe.org/events/fgci-arc-tutorial The tutorial is intended to help users of local clusters benefit from computing resources available at other FGCI (Finnish Grid and Cloud Infrastructure) sites via the NorduGrid ARC middleware. 2016-05-20 10:00:00 UTC 2016-05-20 15:00:00 UTC CSC 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. [] [] [] [] [] []
  • Introduction to the Techila HPC system - How to use Techila with R

    31 May 2016

    Elixir node event
    Introduction to the Techila HPC system - How to use Techila with R https://tess.elixir-europe.org/events/introduction-to-the-techila-hpc-system-how-to-use-techila-with-r This course will give a practical introduction on how to use the Techila HPC system with R. 2016-05-31 11:00:00 UTC 2016-05-31 15:00:00 UTC CSC 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. [] [] [] [] [] []
  • Funetin tekniset päivät ja vuosikokous 2016

    1 - 2 June 2016

    Elixir node event
    Funetin tekniset päivät ja vuosikokous 2016 https://tess.elixir-europe.org/events/funetin-tekniset-paivat-ja-vuosikokous-2016 Nämä Funet-jäsenorganisaatioiden edustajille tarkoitetut tapahtumat järjestetään Hankenilla, Helsingissä. Vuosikokouksen (1.6.. iltapäivä) mahdollisille osallistujille on lähetetty erillinen kutsu. 2016-06-01 09:30:00 UTC 2016-06-02 15:00:00 UTC CSC Hanken, Arkadiankatu 22, Helsinki. Katso Lisätiedot (vaatii sisäänkirjautumista) Hanken, Arkadiankatu 22, Helsinki. Katso Lisätiedot (vaatii sisäänkirjautumista) [] [] [] [] [] []
  • Obtaining a Converged Solution with Abaqus

    2 - 3 June 2016

    Elixir node event
    Obtaining a Converged Solution with Abaqus https://tess.elixir-europe.org/events/obtaining-a-converged-solution-with-abaqus Suomenkielinen kurssi Abaquksen käyttöön jo perehtyneille 2016-06-02 09:00:00 UTC 2016-06-03 17:00:00 UTC CSC Kurssi järjestetään CSC:n tiloissa, Keilaranta 14, Espoo. Kurssi järjestetään CSC:n tiloissa, Keilaranta 14, Espoo. [] [] [] [] [] []
  • OpenFOAM Introduction Course

    7 - 8 June 2016

    Elixir node event
    OpenFOAM Introduction Course https://tess.elixir-europe.org/events/openfoam-introduction-course OpenFOAM introduction course at University of Oulu 2016-06-07 09:00:00 UTC 2016-06-08 16:15:00 UTC CSC Mikroluokka YL124 Mikroluokka YL124 [] [] [] [] [] []
  • INTEGRATE Summer School 2016

    7 - 10 June 2016

    Elixir node event
    INTEGRATE Summer School 2016 https://tess.elixir-europe.org/events/integrate-summer-school-2016 HTS, Medicinal Chemistry, and Cell Biology in the Discovery of New Drugs Active Against Resistant G-negative Bacteria 2016-06-07 10:00:00 UTC 2016-06-10 14:00:00 UTC CSC 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. [] [] [] [] [] []
  • ELIXIR-EXCELERATE WP4 F2F Meeting

    8 - 10 June 2016

    Elixir node event
    ELIXIR-EXCELERATE WP4 F2F Meeting https://tess.elixir-europe.org/events/elixir-excelerate-wp4-workshop The ELIXIR-EXCELERATE WP4 F2F meeting in Helsinki will bring together WP4 participants to plan the work distribution and put together the upcoming deliverables. 2016-06-08 12:00:00 UTC 2016-06-10 17:00:00 UTC CSC The event is held mainly at the Hotel Katajanokka in Helsinki. The event is held mainly at the Hotel Katajanokka in Helsinki. [] [] [] [] [] []
  • Finnish OpenFOAM® User Day 2016

    9 June 2016

    Elixir node event
    Finnish OpenFOAM® User Day 2016 https://tess.elixir-europe.org/events/finnish-openfoam-user-day-2016 Annual OpenFOAM user meeting 2016-06-09 09:00:00 UTC 2016-06-09 17:00:00 UTC CSC Lecture room L4 Lecture room L4 [] [] [] [] [] []
  • ELIXIR Workshop Genomics

    7 - 8 November 2016

    Bruxelles, Belgium

    Elixir node event
    ELIXIR Workshop Genomics https://tess.elixir-europe.org/events/elixir-workshop-genomics Goal The fast generation of large amounts of data is fundamentally changing the way how research is done today. Many domains of research are challenged with managing, analyzing and sharing genomics data. This is not just a challenge, it is an oppurtunity to implement this workshop for researchers to learn basic handling of genomics concepts, skills and tools. This workshop is aimed at researchers in the life sciences at all career stage and is designed for learners with little to no prior knowledge of Linux and command line tools or biological networks in Cytoscape. A basic knowledge of programming in R is recommended. ​ Workshop Topics The main ambition or this workshop is that researchers get more familiar with genomics data and handle it in a more efficient way. The following topics will be covered during the workshop.   DAY 1 Introduction to Linux and the command line The first session will introduce you to the use of Linux and the command line for managing and analyzing genomics data.   DAY 2​ Data manipulation in R This session gives an introduction to the use of the R packages plyr and ggplot2 for data manipulation and subsequent graphing. Initiation Cytoscape In this tutorial, you will be introduced to the basics of Cytoscape (how to make a network, change the visualisation parameters such as the layout, ...), and to more advanced functionalities such as data integration and data analysis using Cytoscape plugins. 2016-11-07 09:00:00 UTC 2016-11-08 17:00:00 UTC ELIXIR Belgium Belgian Science Policy (BELSPO), 231, Avenue Louise, Bruxelles, Belgium Belgian Science Policy (BELSPO), 231, Avenue Louise Bruxelles Belgium Data visualisation Molecular interactions, pathways and networks Bioinformatics VIB christof.debo@vib.be ELIXIR-BE PhD studentsPost Docs [] [] Cytoscape R-programming Linux
  • CANCELED: Linux 1 - Introduction to Linux

    23 - 24 January 2017

    Elixir node event
    CANCELED: Linux 1 - Introduction to Linux https://tess.elixir-europe.org/events/linux-1-introduction-to-linux This two day course will cover the very basics of Unix/Linux. It serves as an introduction to those who are completely new to Linux. Both days have extended hands-on exercises. 2017-01-23 09:30:00 UTC 2017-01-24 16:30:00 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 [] []
  • CLC Bio Main Workbench, Leuven

    17 February 2017

    Leuven, Belgium

    Elixir node event
    CLC Bio Main Workbench, Leuven https://tess.elixir-europe.org/events/clc-bio-main-workbench-leuven You will learn to: work with the CLC Main Workbench user interface: create folders, import data, adjust settings... open sequences, view and manipulate annotations align sequences and perform BLAST searches virtually PCR-amplify a gene and insert it into a vector assemble sequences generated by Sanger sequencing into contigs and find conflicts between sequence reads​ 2017-02-17 13:00:00 UTC 2017-02-17 16:00:00 UTC VIB Bioinformatics Core O&N4 room 07.339 Gasthuisberg, Leuven, Belgium O&N4 room 07.339 Gasthuisberg Leuven Belgium 3000 [] [] [] [] [] []
  • GATK workshop

    20 - 22 February 2017

    Leuven, Belgium

    Elixir node event
    GATK workshop https://tess.elixir-europe.org/events/gatk-workshop This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn  why each step is essential to the variant discovery process what are the operations performed on the data at each step how to use the GATK tools to get the most accurate and reliable results out of your dataset. • samtools Familiarity with Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points​. The training will take 3 days, you can register for each day separately 2017-02-20 09:30:00 UTC 2017-02-22 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Vlaams-Brabant Belgium 3010 Sequence analysis [] [] [] [] [] GATKBroad's Genome Analysis Toolkit
  • Hands-on introduction to Perl programming

    6 - 13 March 2017

    Leuven, Belgium

    Elixir node event
    Hands-on introduction to Perl programming https://tess.elixir-europe.org/events/hands-on-introduction-to-perl-programming Learning the basics of Perl programming: different variables, reading files, writing files, regex. Being able to write small scripts to parse text files Using Perl in windows. Day 2 an example about parsing through a list of files introduction into Perl one-liners subroutines and libraries downloading and using libraries ​​​ 2017-03-06 09:30:00 UTC 2017-03-13 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • PDA17 Proteomics Data Analysis

    6 March 2017

    Oeiras, Portugal

    Elixir node event
    PDA17 Proteomics Data Analysis https://tess.elixir-europe.org/events/proteomics-data-analysis    IMPORTANT DATES for this Course   Deadline for applications: Feb 25th 2017 (New)   Course date: March 6th - March 10th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course description Mass spectrometry based proteomic experiments generate ever larger datasets and, as a consequence, complex data interpretation challenges. In this course, the concepts and methods required to tackle these challenges will be introduced, covering both protein identification and quantification. The core focus will be on shotgun proteomics data. Quantification through isobaric labels (iTRAQ, TMT) and label-free precursor peptide (MS1) ion intensities will also be introduced. The course will rely exclusively on free and user-friendly software, all of which can be directly applied in your lab upon your return from the course. An introduction to available online resources and repositories will also be given. Here you will see how to link the results from proteomic experiments with external data to conduct pathway, gene ontology and interaction analyses. In the course, you will also learn how to submit data to the ProteomeXchange online repositories, and how to browse and reprocess publicly available data from these repositories. The course will provide a solid basis for beginners, but also new perspectives to those already familiar with standard data interpretation procedures in proteomics. Note: this is a highly interactive course. It requires that the participants interact with each other and with the course instructors, in order to reach the learning outcomes in full. Course Pre-requisites The participants should have a basic knowledge about mass spectrometry based proteomics. Experience in analyzing proteomics data is an advantage, but not mandatory. The course does not require advanced computer skills. 2017-03-06 09:30:00 UTC 2017-03-06 09:30:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto Gulbenkian de Ciência Oeiras Portugal 2781-901 Mass spectrometry Proteomics Instituto Gulbenkian de Ciência bicourses@igc.gulbenkian.pt [] [] 20 workshops_and_courses registration_of_interest []
  • PGDH17 Population Genetics and Demographic History: model-based approaches

    13 March 2017

    Oeiras, Portugal

    Elixir node event
    PGDH17 Population Genetics and Demographic History: model-based approaches https://tess.elixir-europe.org/events/pgdh17-population-genetics-and-demographic-history    IMPORTANT DATES for this Course    Deadline for applications: Mar 6th 2017 (New)    Course date: March 13th - March 17th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Course description Genetic and genomic data are increasingly used by ecologists and evolutionary biologists in general. It has thus become important for many biologists with different levels of experience to produce and analyse genetic (and genomic) data. In this course we will take a practical approach to the analysis of genetic and genomic data, but we will also provide some of the theoretical background required to understand the outputs of the software used. This course will be organised so as to mix lectures where important notions are introduced with practicals where freely available software will be used. While this will not be the focus of the course, we will also introduce and discuss genealogical (coalescent-based) simulation methods and those based on forward-in-time simulations. Altogether this will allow to discuss the potentialities and limitations of the tools available to the community. In this five-day course we will introduce the main concepts that underlie many of the models that are frequently used in population genetics. We will focus on the importance of demographic history (e.g. effective sizes and migration patterns) in shaping genetic data. We will go through the basic notions that are central to population genetics, insisting particularly on the statistics used to measure genetic diversity and population differentiation. The course will also cover a short introduction to coalescent theory, Bayesian inference in population genetics and data simulation. We will also introduce two methods that have been recently developed to analyse genomic data. The PSMC of Li and Durbin reconstructs the demographic history of a species or population with the genome of a single individual. The Rehh package is an R implementation of the Extended Haplotype Homozygosity (EHH) test for selective sweeps and looks for signals of selection based on the analysis of genomic regions. Most theory will be put into practice in practical sessions, analyzing real and/or simulated datasets. In these sessions, we will look at measures of genetic diversity and differentiation and use methods to infer demographic history. We will learn how to perform coalescent simulations of genetic/genomic data (using SPAms and ms). We will also show how to simulated data for PSMC analyses. This will allow users to compare the PSMC obtained with real data to those obtained for the models they used. We will also look at how habitat fragmentation can be simulated using an in-house program. Some exercises will make use of R scripts (R being a freely available statistical program). Basic R knowledge is a pre-requisite but we will provide a short introduction to R. The R statistical package is a very powerful tool to analyse data outputs from many population genetics software, and can also be used to simulate genetic data under simple demographic scenarios. Course Pre-requisites Basic molecular population genetics and molecular ecology. Basic R knowldedge. Basic knowledge of genomic data. 2017-03-13 09:30:00 UTC 2017-03-13 09:30:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto Gulbenkian de Ciência Oeiras Portugal 2781-901 Genomics Population genetics [] bicourses@igc.gulbenkian.pt [] [] 20 workshops_and_courses registration_of_interest []
  • Prep course for Biopython

    31 March 2017

    Leuven, Belgium

    Elixir node event
    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 [] [] [] [] [] []
  • Metagenomics Data Analysis Workshop @ CSC

    3 - 6 April 2017

    Espoo, Finland

    Elixir node event
    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 CSC [] Anyone workshops_and_courses registration_of_interest EXCELERATEMarine Metagenomics
  • Metagenomics data analysis

    3 - 6 April 2017

    Elixir node event
    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 (computer classroom Dogmi and auditorium). 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 (computer classroom Dogmi and auditorium). The address is Keilaranta 14, Espoo, Finland. You can reach us by public transportation, read more. [] [] [] workshops_and_courses [] []
  • ABSTAT17 - Advanced Biostatistics for Bioinformatics Tool Users using R

    9 April 2017

    Portugal

    Elixir node event
    ABSTAT17 - Advanced Biostatistics for Bioinformatics Tool Users using R https://tess.elixir-europe.org/events/abstat17-advanced-biostatistics-for-bioinformatics-tool-users-using-r    IMPORTANT DATES for this Course    Deadline for applications: April 3rd 2017    Course date: April 10th - 13th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. Course description This course is targeted for Biostatistical techniques often employed in analytical tools for high throughput data and multivariate data. Participants can expect to attend a thorough set of lectures that will reveal the conceptual frameworks that are needed to understand the methods. Extensive hands-on practice will be the main vehicle for providing the skills and user independence. To keep things in context, the course is exclusively based on biological examples. We will be using custom-built R scripts and packages that are available from the CRAN and/or Bioconductor repositories. Care has been taken not to use any proprietary data or software, so that the hands-on experience can carry on after the course, providing maximum user independence. We will be using custom-built R scripts and packages that are available from the CRAN and Bioconductor repositories. Methodology This intensive course will introduce a relatively high number of concepts and methods. To keep it highly practical, we will spend most of the time in hands-on sessions. - We will focus on each method using examples taken from biological data. - We will then dissect the method, identifying the concepts and exploring their interrelationships. - The applicability and limitations of each method will be emphasized. - The use of the method will be illustrated using appropriate Bioinformatics tools and biological data resources. Target Audience Everybody using Bioinformatics methods is implicitly using statistical methods. Moreover, proper judgement of the results often calls for a deeper level of understanding than what is required to solve scholarly exercises. We will look into particular areas such Simulation, Bayesian Inference, Hidden Markov Chains and Multivariate Data Analysis methods with the attitude, eyes and brains of an experienced statistician that wants to understand how the methods work and systematic way. Course Pre-requisites Intermediate level knowledge in Statistics is necessary. There is no time to provide basic knowledge, so we will need to assume that accepted candidates have self-assessed for it in the following areas: - probability - conditional probability - distributions - statistical tests - hypothesis testing - inference A suitable candidate will need to be able to answer 8 out of the 10 questions readily, without help. --> This level can also be obtained by attending another course in GTPB: The IBSTAT course. Basic Familiarity with the R environment will be necessary. Please follow the exercise that we provide. Install R from http://cran.r-project.org/ following the instructions. Download and unzip the Tutorial folder that is made available here. Then: - Visualize the slides in "Tutorial R.pdf" - Follow the exercise in "Basic_Exercise.pdf" - For reference, we also provide a script with a correct set of R statements in sequence "Tutorial_script.R" Additionally, we suggest that candidates acquire familiarity with RStudio by visiting the following resources: - Introduction to RStudio (basics) - Tutorial R and R Studio (complete) R Studio will be used in the course to ease-up interaction and increase productivity, but people that prefer the original R environment on the command line will be able to follow that preference. 2017-04-09 23:00:00 UTC 2017-04-09 23:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2781-901 [] [] [] [] [] []
  • ADER17 - Analysis of Differential Expression with RNAseq

    17 April 2017

    Oeiras, Portugal

    Elixir node event
    ADER17 - Analysis of Differential Expression with RNAseq https://tess.elixir-europe.org/events/ader17-analysis-of-differential-expression-with-rnaseq    IMPORTANT DATES for this Course   Deadline for applications: April 10th 2017   Course dates: April 17th - April 20th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application, until we reach 20 participants. Course description Overview High-throughput technologies allow us to detect transcripts present in a cell or tissue. This course covers practical aspects of the analysis of differential gene expression by RNAseq. Participants will be presented with real world examples and work with them in the training room, covering all the steps of RNAseq analysis, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. We we will also cover some of the initial steps of secondary analysis, such as functional enrichment of the obtained gene lists. Target Audiences Life Scientists who want to be able to use NGS data to evaluate gene expression (RNAseq). Computational researchers that wish to get acquainted with the concepts and methodologies used in RNAseq are also welcome. Participants are encouraged to bring their own data and will have the opportunity to apply the concepts learned in the course. Pre-requisites Familiarity with elementary statistics and a few basics of scripting in R. Please have a look at the following resources and gauge your ability to use R in statitics at the basic level: Introduction to Data Science with R Videos from Coursera's four week course in R Statistics at Square One - BMJ Basic Unix command line skills, such as being able to navigate in a directory tree and copy files. See, for example, "Session 1" of the Software Carpentry training for a Unix introduction (Shell-novice material from the Software Carpentry Foundation). 2017-04-17 07:30:00 UTC 2017-04-17 07:30:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto Gulbenkian de Ciência Oeiras Portugal 1000-029 Transcriptomics RNA-Seq [] bicourses@igc.gulbenkian.pt [] [] 20 workshops_and_courses registration_of_interest []
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