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86 events found

Content provider: VIB Bioinformatics Core  or ELIXIR Portugal 

  • 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
  • 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 [] [] [] [] [] []
  • 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 []
  • Electronic Lab Notebook Introduction - Ghent

    18 April 2017

    Ghent, Belgium

    Elixir node event
    Electronic Lab Notebook Introduction - Ghent https://tess.elixir-europe.org/events/electronic-lab-notebook-introduction-ghent-638a1f0b-2d27-4f09-b291-72bee6d64baa 2017-04-18 10:00:00 UTC 2017-04-18 12:00:00 UTC VIB Bioinformatics Core PC room V114 1st floor front building VIB-UGent Research Building, Ghent, Belgium PC room V114 1st floor front building VIB-UGent Research Building Ghent Belgium 9052 [] [] [] [] [] []
  • RNA-Seq prep course

    25 April 2017

    Leuven, Belgium

    Elixir node event
    RNA-Seq prep course https://tess.elixir-europe.org/events/rna-seq-prep-course 2017-04-25 09:30:00 UTC 2017-04-25 16:00:00 UTC VIB Bioinformatics Core Gasthuisberg O&N4 room 07.339, Leuven, Belgium Gasthuisberg O&N4 room 07.339 Leuven Belgium 3000 [] [] [] [] [] []
  • Initiation GIMP and Inkscape Ghent

    2 May 2017

    Ghent, Belgium

    Elixir node event
    Initiation GIMP and Inkscape Ghent https://tess.elixir-europe.org/events/initiation-gimp-and-inkscape-ghent 2017-05-02 09:00:00 UTC 2017-05-02 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Ghent, Belgium Bio-Accelerator Ghent Belgium 9052 [] [] [] [] [] []
  • Initiation GIMP and Inkscape Leuven

    4 May 2017

    Leuven, Belgium

    Elixir node event
    Initiation GIMP and Inkscape Leuven https://tess.elixir-europe.org/events/initiation-gimp-and-inkscape-leuven 2017-05-04 09:00:00 UTC 2017-05-04 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven, Leuven, Belgium Park Inn by Radisson Leuven Leuven Belgium 3010 [] [] [] [] [] []
  • Initiation GIMP and Inkscape - Ghent

    9 May 2017

    Ghent, Belgium

    Elixir node event
    Initiation GIMP and Inkscape - Ghent https://tess.elixir-europe.org/events/initiation-gimp-and-inkscape-ghent-bd18f6fb-c469-418d-8b9e-bd73e73ce890 2017-05-09 09:00:00 UTC 2017-05-09 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator Meeting Centre, Ghent, Belgium Bio-Accelerator Meeting Centre Ghent Belgium 9052 [] [] [] [] [] []
  • ELB17F Entry Level Bioinformatics

    11 May 2017

    Portugal

    Elixir node event
    ELB17F Entry Level Bioinformatics https://tess.elixir-europe.org/events/elb17f-entry-level-bioinformatics    IMPORTANT DATES for this Course   Deadline for applications: May 1st 2017   Course date: May 8th - May 12th 2017 Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants. Overview This is an entry level course aimed that those with a reasonable biological background butno significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved. Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products. This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools. Objectives The operation of the various programs used in the exercises will be explained, but only to the extent that allows a user to select parameters intelligently and to interpret results. The course will provide participants with an awareness of a wide range of bioinformatics tools and sufficient experience to use those tools in basic investigations with a relatively high degree of user independence. In the training course design, this is intentionally built-in, to allow us to show a wide range of analytical techniques while providing enough experience to break the ice in all of them. Target Audience This course is intended for those wishing to investigate how they might begin to exploit the ever expanding abundance of computing and data resources for researchers seeking help in using them. Course Pre-requisites Basic understanding of molecular biology. No particular computing expertise will be assumed. 2017-05-11 23:00:00 UTC 2017-05-11 23:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2781-901 [] [] [] [] [] []
  • Initiation to Cytoscape

    2 June 2017

    Leuven, Belgium

    Elixir node event
    Initiation to Cytoscape https://tess.elixir-europe.org/events/initiation-to-cytoscape In this course, you will be introduced to the basics of Cytoscape, and to more advanced functionalities such as data integration and data analysis using Cytoscape plugins. The list of topics covered in this hands-on training: Cytoscape is a free, Open Source bioinformatics environment for integration, visualisation, and query of biological networks.? Registration is open for VIB and non-VIB employees and is only available on this website. For any questions about this training, contact bits*Replace*With*At*Sign*vib.be 2017-06-02 09:30:00 UTC 2017-06-02 17:00:00 UTC VIB Bioinformatics Core Park Inn by Radisson Leuven Hotel, Leuven, Belgium Park Inn by Radisson Leuven Hotel Leuven Belgium 3010 [] [] [] [] [] []
  • In silico cloning with SnapGene, Leuven

    8 June 2017

    Leuven, Belgium

    Elixir node event
    In silico cloning with SnapGene, Leuven https://tess.elixir-europe.org/events/in-silico-cloning-with-snapgene-leuven 2017-06-08 13:30:00 UTC 2017-06-08 16:30:00 UTC VIB Bioinformatics Core O&N4 room 06.239 Gasthuisberg, Leuven, Belgium O&N4 room 06.239 Gasthuisberg Leuven Belgium 3000 [] [] [] [] [] []
  • In silico cloning with SnapGene, Ghent

    9 June 2017

    Ghent (Zwijnaarde), Belgium

    Elixir node event
    In silico cloning with SnapGene, Ghent https://tess.elixir-europe.org/events/in-silico-cloning-with-snapgene-ghent 2017-06-09 13:30:00 UTC 2017-06-09 16:30:00 UTC VIB Bioinformatics Core VIB Bioinformatics Core, Ghent (Zwijnaarde), Belgium VIB Bioinformatics Core Ghent (Zwijnaarde) Belgium 9052 [] [] [] [] [] []
  • Protein Structure Analysis

    15 June 2017

    Ghent, Belgium

    Elixir node event
    Protein Structure Analysis https://tess.elixir-europe.org/events/protein-structure-analysis-f095d4f5-e03b-4b1d-9f38-38dff017174a b'\r\n\r\n\n \r\n\r\n\n \r\n\r\n\n' 2017-06-15 09:30:00 UTC 2017-06-15 17:00:00 UTC ELIXIR Belgium VIB-UGent reseach Building FSVM PC room V114 (first floor), Ghent, Belgium VIB-UGent reseach Building FSVM PC room V114 (first floor) Ghent Belgium 9052 [] [] [] [] [] []
  • RODS17 Reproducible, Open Data Science

    20 June 2017

    Portugal

    Elixir node event
    RODS17 Reproducible, Open Data Science https://tess.elixir-europe.org/events/rods17-reproducible-open-data-science    IMPORTANT DATES for this Course    Deadline for applications: June 16th, 2017    Course date: June 21st - 23rd 2017 Course description In an age of increasingly complex and data-intensive, collaborative scientific practices, scandals of irreproducibility, and a growing societal ethos of transparency and accountability, a new paradigm has arisen: Open Science. In this three day course, we will introduce to you the three organizing principles and practices that undergird this paradigm: Open Access scholarly publishing Open Source software development Open Data integration and sharing For this, we will be introducing a set of technologies and ways of using them. The reasonable expectation is that the participants will feel empowered and start using them for the above purposes in a highly productive way. The use-cases that we will be working on are going to be based on bioinformatics, but the principles are very broadly applicable to other fields. You do not need to have any particular programming or otherwise computational experience beyond what is normally required from a scientist in graduate school and beyond, i.e., you should not be afraid of interacting with a computer and editing simple text files.   Target Audience Researchers and Students in all sectors of Biomedicine. Pre-course Reading W S Noble. 2009. A Quick Guide to Organizing Computational Biology Projects. PLoS Comput Biol 5(7): e1000424 https://doi.org/10.1371/journal.pcbi.1000424 E M Hart et al. 2016. Ten Simple Rules for Digital Data Storage. PLoS Comput Biol 12(10): e1005097 https://doi.org/10.1371/journal.pcbi.1005097 P E Bourne et al. 2017. Ten simple rules to consider regarding preprint submission 13(5): e1005473. https://doi.org/10.1371/journal.pcbi.1005473   2017-06-20 23:00:00 UTC 2017-06-20 23:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2780-156 [] [] [] [] [] []
  • IBSTATB17 - Introductory Biostatistics for Biologists

    10 September 2017

    Portugal

    Elixir node event
    IBSTATB17 - Introductory Biostatistics for Biologists https://tess.elixir-europe.org/events/ibstatb17-introductory-biostatistics-for-biologists This is one of our "Foundations" type courses, providing a systematic and detailed review of fundamental concepts and techniques in Biostatistics. Participants can expect to go through a set of exercises that are based on biomedical problems. These exercises are preceded by short lectures that are simple to follow. The lectures are designed to provide the conceptual framework that is needed to release the training power of the exercises, not to flood the participants with formality, which will be kept to a minimum. We will make use of a highly interactive methodology, taking advantage of our well equipped Bioinformatics training room. With this approach, we expect to bring the participants to a high degree of usage independence in using the methods that we cover. Main topics: Descriptive Statistics; Probability; Statistical Inference; Design of Experiments. Target Audience: Most participants must have had one or more semester courses in Statistics in their graduate education. For some, learning Statistics has happened a long time ago, and that makes it difficult to go back and manipulate the concepts with full confidence. For others, school days were just a while ago, but using that knowledge represents a serious effort. Opening a Statistics handbook, when you want to use Statistics righ away, is usually a painful experience, as concepts often show a less than obvious interdependence. Attending this course is a chance of revisiting those subjects in a systematic way, through a series of hands-on exercises, in a workflow that brings-in the skills in a seamless way. Course Pre-Requisites: Basic knowledge in Statistics is handy. Elementary skills in computer usage are needed. 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" Instructors:​             Ana Luísa Papoila holds a degree in Mathematics (Probability and Statistics) from the Faculdade de Ciências da Universidade de Lisboa (FCUL), a Master of Science in Statistics and Optimization, from the Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa (UNL) and a PhD in Statistics and Operational Research, in the field of Probability and Statistics, from the FCUL in 2006. Since then, she is an Assistant Professor in the NOVA Medical School / Faculdade de Ciências Médicas of UNL where she coordinates and teaches several undergraduate and postgraduate courses in Biostatistics. Her main areas of research interest are Applied Health Statistics and Epidemiology. She is an integrated member of the Centro de Estatística e Aplicações da Universidade de Lisboa (CEAUL) since 2007. She is also responsible for the area of statistics of the Division of Statistics and Epidemiology from the Research Center of Centro Hospitalar de Lisboa Central. In GTPB, she has been an instructor of the IBSTAT series, since 2014.            Affiliation: NOVA Medical School / Faculdade de Ciências Médicas of UNL, Lisboa, PT   Maria Fernanda Diamantino is an Assistant Professor at the Faculdade de Ciências da Universidade de Lisboa (FCUL) where she teaches since 1989. She obtained a Master of Science in Probability and Statistics (in the epidemiology area) and her PhD in Probability and Statistics in 2008, both at FCUL. Over the years, she has taught several undergraduate statistical courses in various areas, for example, biology, chemistry, geology, mathematics and informatics. She is a collaborator member of the Centro de Estatística e Aplicações da Universidade de Lisboa (CEAUL). She has been focusing her interests in biostatistics and applied health statistics and has taught postgraduate courses in those areas. In GTPB, she has been an instructor of the IBSTAT series, since 2014.             Affiliation: Faculdade de Ciências da Universidade de Lisboa, Lisboa, PT   Program: You can find here the detailed program.   Registration:  Register using here until August the 30th   Contact: For any questions about this course, please contact Pedro Fernandes (e-mail address below) 2017-09-10 23:00:00 UTC 2017-09-10 23:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2781-901 [] [] [] [] [] []
  • Biomolecular data mining: a hands-on training

    11 - 13 September 2017

    Antwerpen, Belgium

    Elixir node event
    Biomolecular data mining: a hands-on training https://tess.elixir-europe.org/events/biomolecular-data-mining-a-hands-on-training This course aims to introduce the core principles and biomedical applications of different data mining and machine learning techniques in a hands-on manner. It will tackle both unsupervised (clustering, frequent pattern mining, data projection) and supervised (classification) techniques. The methods that will be seen include hierarchical clustering, k- means clustering, item set mining, association rule mining, principle component analysis, support vector machines, random forests, bayesian networks and artificial neural networks. Attendees will be introduced to the basic operations of these data mining techniques, with a focus on the practical use and interpretation of these procedures rather than the mathematical formulas. In addition, attendants will be introduced to some important data processing and performance evaluation methods related to these data mining techniques. The software used in this course will be R. The course itself will consist of 50% theory lessons, 40% hands-on practicals and 10% application case studies. Organised by biomina: Dr. Pieter Meysman Prof. dr. Kris Laukens 2017-09-11 09:00:00 UTC 2017-09-13 17:00:00 UTC biomina Antwerpen Groenenborgerlaan, Antwerpen, Belgium Antwerpen Groenenborgerlaan Antwerpen Antwerpen Belgium 2020 Biomedical science Machine learning Data mining University of Antwerp Dr. Pieter Meysman Prof. dr. Kris Laukens ELIXIR Belgium and Flemish Region PhD studentsPostDocs 30 workshops_and_courses registration_of_interest []
  • Functional Plant Bioinformatics - PLAZA

    14 - 15 September 2017

    Ghent, Belgium

    Elixir node event
    Functional Plant Bioinformatics - PLAZA https://tess.elixir-europe.org/events/functional-plant-bioinformatics-plaza 2017-09-14 10:00:00 UTC 2017-09-15 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator Meeting Center, Ghent, Belgium Bio-Accelerator Meeting Center Ghent Belgium 9052 [] [] [] [] [] []
  • IO17 - Large-scale bioinformatics for Immuno-Oncology

    19 September 2017

    Portugal

    Elixir node event
    IO17 - Large-scale bioinformatics for Immuno-Oncology https://tess.elixir-europe.org/events/io17-large-scale-bioinformatics-for-immuno-oncology The immuno-oncology approach leverages on the unique capability of the immune system to recognize and kill tumour cells. This action is hampered by escape mechanisms put in place by tumour cells like, for instance, the engagement immune checkpoints, i.e. inhibitory molecules that modulate the amplitude and duration of immune responses. Immunotherapies that block checkpoint molecules are amongst the most promising approaches in immuno-oncology for the enhancement of antitumour immunity. Thanks to high-throughput technologies, such as next-generation sequencing (NGS) and proteomics, we have now access to large-scale tumour data that can be used to investigate the interplay between tumour and immune cells and the role of the immune system in tumour progression and response to therapy. In this course, you will learn to use bioinformatics tools and mathematical modelling techniques operating on high-throughput tumour data, in order to extract features that can be used to characterise this complex tumour-immune cell interface, such as: tumour antigens recognized by T cells tumour-infiltrating immune cells deregulated signalling pathways in cancer and immune cells A fully practical, hands-on approach will ensure that the newly acquire skills can be used with a great deal of autonomy. Target Audience: Motivated researchers, clinicians, and students who want to gain an understanding on how bioinformatics tools and simple (logic-based) modelling approaches can be used to investigate the tumour-immune cell interface and its underlying signalling pathways from high-throughput data. Course Pre-Requisites: Programming/scripting skills are helpful, but not mandatory. An understanding of elementary operations with R will be required. Elementary command line instructions in UNIX will be used, so minimal familiarity with navigation in directory trees, copying files and folders, etc. will be needed.  Instructors:​             Francesca Finotello received her PhD in Bioengineering in 2014 from the Department of Information Engineering, University of Padova (Italy). Her PhD thesis, entitled "Computational methods for the analysis of gene expression from RNA sequencing data", was awarded with the "Marco Ramoni" doctoral research award by the Italian National Bioengineering Group. She has an extensive experience on computational methods for the analysis of different types of next-generation sequencing (NGS) data, including RNA-seq and 16S ribosomal RNA gene sequencing of the human microbiota. Currently, she is a postdoctoral researcher in the Division of Bioinformatics of Medical University of Innsbruck (Austria). She is interested in bioinformatics and computational biology for cancer immunology and precision medicine, with a particular focus on in silico prediction of tumor neoantigens and deconvolution of tumour-infiltrating immune cells from NGS data. She is principal investigator of the research project "QuanTIseq: dissecting the immune contexture of human cancers" funded by the Österreichischen Krebshilfe Tirol (Austria) and aimed at developing a computational tool for the quantification of immune cell fractions from RNA-seq data of cell mixtures.            Affiliation: Division of Bioinformatics, Medical University of Innsbruck, AT   Federica Eduati received her PhD in Bioengineering in 2013 from the University of Padova, with a thesis (awarded the "Paolo Durst" best Italian PhD Thesis Award in Bioengineering) focusing on mechanistic modelling aspects of both large- and small-scale biological systems. In 2009 she participated to the DREAM4 "Predictive signaling network modeling" challenge classifying as best performing team. In 2011-2012 she was a visiting predoctoral fellow for 8 months in the Systems Biomedicine group at EBI. Since February 2013 she is a Postdoctoral EIPOD fellow - Marie Curie Fellow at EMBL (UK and Germany). Since May 2016 she is also a visiting scientist at JRC-COMBINE in RWTH Aachen (Germany). Currently, her main research interest is the investigation of why patients differentially respond to cancer therapy and how we can suggest personalized therapy. In particular, she is interested in approaching this problem by investigating signalling pathways, their deregulation in cancer and the specific effect of targeted therapy, using dynamic mathematical modelling approaches and machine learning techniques. She has also been working on the development of a microfluidics platform, which allows drug screening of live cells obtained from patient biopsies in a fast and cost-effective way. In 2013 she was also co-organizer of the NIEHS-NCATS-UNC DREAM Toxicogenetics Challenge, where 213 registered participants from more than 30 countries had to predict cell line-specific cytotoxicity to chemical compounds based on genomic data and chemical attributes.            Affiliation: European Molecular Biology Laboratory (EMBL), Heidelberg, DE; JRC-COMBINE (RWTH Aachen), Aachen, DE   Program: You can find here the detailed program.   Registration:  Register using here until August the 30th   Contact: For any questions about this course, please contact Pedro Fernandes (e-mail address below) 2017-09-19 23:00:00 UTC 2017-09-19 23:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2781-901 [] [] [] [] [] []
  • EMBL-EBI Bioinformatics Workshop

    1 October 2017

    Portugal

    Elixir node event
    EMBL-EBI Bioinformatics Workshop https://tess.elixir-europe.org/events/embl-ebi-bioinformatics-workshop In this course, participants will receive an introduction to EMBL-EBI and its public data resources, with a focus on functional genomics (e.g. microarray expression profiling, RNA-seq, ChIP-seq).  During the course,participants will acquire skills in the effective use of functional genomics databases: ArrayExpress (one of the ELIXIR core data resources) and Expression Atlas.  Such skills will include searching, retrieving and interpreting data relevant to their research areas of interests.  There will be interactive presentations, demonstrations and practical exercises to give trainees hands on experiences.To complement the sessions on functional genomics, there will be brief presentations on some related EMBL-EBI resources: EBI metagenomics and Reactome.  Since many EMBL-EBI resources are built to facilitate reproducible research, there will also be a session discussing the obstacles and barriers to data reproducibility in the research environment, illustrated by real-life examples.  Participants will learn about some handy data management techniques that help to alleviate reproducibility problems, many of which have already been implemented for over a decade at EMBL-EBI. Please note this course does not cover microarray, sequencing, metagenomic or network data analysis.   Course Organizers:​ Cymon Cox is a senior researcher at  CCMAR in Faro. He is the leader of  the Plant Systematics and Bioinformatics group.             Affiliation: Fundação para a Ciência (FCT) / CCMAR, Faro, PT   Amy Tang studied Human Genetics at the University of Nottingham for her bachelor degree.  She did her PhD at the Brockdorff's lab, then at MRC Clinical Sciences Centre / Imperial College London, working on the epigenetic control of X-chromosome inactivation in mouse early development. The project was split 50:50 into wet-lab and bioinformatics, this is when she first got interested in bioinformatics. After a short postdoc in the same lab, she returned to study at Imperial for a MSc in Bioinformatics and Systems Biology, which helped her move laterally from wet-lab to bioinformatics. Amy now leads the curation efforts for ArrayExpress and Expression Atlas databases in the Gene Expression Team, promoting reproducible research by maintaining curation quality, and also by driving the development of the user-friendly ArrayExpress data submission tool Annotare. To allow users make the most out of the databases and to educate researchers on best practices for reproducible research, she also manages all training activities for the Team, delivering most of the hands-on courses on functional genomics resources at EMBL-EBI and worldwide.  Through listening to Annotare submitters' needs and gathering feedback at training courses, she also acts as users' advocate and works with software developers to improve user experience of ArrayExpress and Expression Atlas websites. Before joining EMBL-EBI, Amy was a senior bioinformatician in the Ensembl GeneBuild team, curating gene models for key model organisms such as mouse and rat.           Affiliation: EMBL-EBI, UK   Adelino V. M. Canário is a full professor at University of Algarve (Portugal) is a specialist in fish physiology. He is the Director of the Centre of Marine Sciences (ccmar.ualg.pt) since 1994 and leads the Comparative and Molecular Endocrinology research group. He teaches Cell Biology to undergraduate students and Reproductive Biology to graduate students. He coordinates courses for graduate students on Molecular and Cellular Biology Techniques and marine Genomics. He is the promoter of 2 ongoing PhDs and has supervised to completion 12 PhDs (8 in the last 5 years). He is internationaly recognized expert in his field with over 140 published articles (H=26) in regulation of calcium homeostasis, fish reproductive physiology, hormone-behavour relationships, chemical communication and genomics. He has coordinated and participated in European Commission funded research including recently Marine Genomics Europe, Assemble and EMBRC (ESFRI infrastructure).           Affiliation: Fundação para a Ciência (FCT) / CCMAR, Faro, PT   Grace Mugumbate Scientific Training Officer - Training           Affiliation: EMBL-EBI, UK   Course Lecturers:​ Steven Jupe is a Knowledge Database Curator/Developer for the Hermjakob team at the EML-EBI.            Affiliation: EMBL-EBI, UK   Amy Tang (Bio above)           Affiliation: EMBL-EBI, UK   Audience: This course is aimed at wet-lab researchers who have minimum or no prior experience in bioinformatics, who want to explore, and use EMBL-EBI resources for their research. No knowledge of programming is required, but the trainer expects an undergraduate level knowledge of biology and/or biochemistry.   Modules and resources: During this course, you will learn about: EMBL-EBI data services: an overview of the free databases and data services covering a wide range of subject areas across biological sciences. ArrayExpress: a public archive of functional genomics data (e.g. expression microarrays, RNA-seq, ChIP-seq), often deposited as a pre-requisite of journal publication Expression Atlas: a public resource of systematically analysed gene and protein expression data from manually curated studies across many species (not limited to model organisms) Data management: the problems we face in poor reproducibility of published research results, and how to alleviate them with some simple data management techniques   Learning Outcomes: After this course, you should be able to: Define some of the public data services EMBL-EBI provides Explore functional genomics data in ArrayExpress effectively, and submit your own data with ease. Search for and interpret expression information using Expression Atlas Discuss the value of biocuration in safeguarding reproducibility of research data   Program: Time Topic Lecturer Day 1 - 2nd October 2017 09:00 - 09:30 Welcome and Introduction to EBI resources Amy Tang 09:30 - 10:30 ArrayExpress Amy Tang 10:30 - 11:00 Tea/coffee break   11:00 - 12:30 ArrayExpress Amy Tang 12:30 - 13:30 Lunch   13:30 - 14:30 ArrayExpress and data submission Amy Tang 14:30 - 15:00 Tea/coffee break   15:00 - 16:00 An introduction to EBI Metagenomics Amy Tang 16:00 - 17:00 Data management for reproducible research Amy Tang 17:00 End of Day 1   Day 2 - 3rd October 2017 09:00 - 10:30 Expression Atlas Amy Tang 10:30 - 11:00 Tea/coffee break   11:00 - 12:30 Expression Atlas Amy Tang 12:30 - 13:30 Lunch   13:30 - 15:00 Expression Atlas & RNAseq-er API Amy Tang 15:00 - 15:30 Tea/coffee break   15:30 - 16:30 Reactome (webinar) Steve Jupe (TBC) 16:30 - 17:00 Wrap up and feedback Amy Tang 17:00 End of course       Participation: Participation has a 50€ registration fee. Registration for this course is done at the Centre for Marine Sciences (CCMAR) , until September the 28th! A maximum of 20 participants will be accepted. If you require assistance in finding accommodation, please contact Cymon J. Cox (e-mail bellow). 2017-10-01 23:00:00 UTC 2017-10-01 23:00:00 UTC Centre for Marine Sciences (CCMAR), Portugal Centre for Marine Sciences (CCMAR) Portugal 8005-139 [] [] [] [] [] []
  • Python for Data Processing

    5 - 6 October 2017

    Heverlee, Belgium

    Elixir node event
    Python for Data Processing https://tess.elixir-europe.org/events/python-for-data-processing 2017-10-05 09:30:00 UTC 2017-10-06 17:00:00 UTC VIB Bioinformatics Core ICTS Education Center KUL Leslokaal A, Heverlee, Belgium ICTS Education Center KUL Leslokaal A Heverlee Belgium 3001 [] [] [] [] [] []
  • Introduction to gene regulation

    9 October 2017

    Gent, Belgium

    Elixir node event
    Introduction to gene regulation https://tess.elixir-europe.org/events/introduction-to-gene-regulation 2017-10-09 09:30:00 UTC 2017-10-09 17:00:00 UTC VIB Bioinformatics Core Bio-Accelerator, Gent, Belgium Bio-Accelerator Gent Belgium 9052 [] [] [] [] [] []
  • Genome assembly and annotation course 3

    23 - 27 October 2017

    Oeiras, Portugal

    Elixir node event
    Genome assembly and annotation course 3 https://tess.elixir-europe.org/events/genome-assembly-and-annotation-course-3 ELIXIR Genome assembly and annotation course 3, Oct 23-27 2017 at the Gulbenkian Institute of Science, Oeiras, Portugal 2017-10-23 09:00:00 UTC 2017-10-27 17:00:00 UTC ELIXIR PT, Instituto Gulbenkian Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande, Oeiras, Portugal Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande Oeiras Portugal Genomics Instituto Gulbenkian de Ciência [] life scientistsResearchersPhD students workshops_and_courses registration_of_interest genomics AssemblyTrainingeLearningEeLP
  • Electronic Lab Notebook Introduction Ghent

    25 October 2017

    Gent, Belgium

    Elixir node event
    Electronic Lab Notebook Introduction Ghent https://tess.elixir-europe.org/events/electronic-lab-notebook-introduction-ghent-fcc80d61-9755-4fe2-8067-00f12ea03c2f 2017-10-25 10:00:00 UTC 2017-10-25 12:00:00 UTC VIB Bioinformatics Core PC Room V114 First floor front building VIB Research Building, Gent, Belgium PC Room V114 First floor front building VIB Research Building Gent Belgium 9052 [] [] [] [] [] []
  • PM17 - Precision Medicine

    14 November 2017

    Portugal

    Elixir node event
    PM17 - Precision Medicine https://tess.elixir-europe.org/events/precision-medicine The implementation of cancer genomics into the clinic is becoming a reality. Personalized medicine or Precision medicine as other authors refers, uses molecular data of a specific patient to guide clinical decisions such as prevention, diagnosis and treatment. This will revolutionize healthcare and will play a dominant role in the future of cancer therapy. Bioinformatics analyses are essential to identify patients who will benefit from treatment based on their molecular profile, and to tailor chemotherapeutic regimens accordingly. The aim of the course is to present a complete computational pipeline for the analysis and interpretation of Next-Generation Sequencing (NGS) data such as exome sequencing or targeted panels that are commonly used in the clinic. We will address the implementation of large-scale genomic sequencing in clinical practice and the recently developed computational strategies for the analysis of NGS data with a particular emphasis on the interpretation of the results, selection of biomarkers of drug response and afford opportunities to match therapies with the characteristics of the individual patient's tumour.  Exercises and case studies focused on cancer will be used to illustrate the principles of how genetics influence led to refining diagnoses and personalized treatment of cancer disease. Target Audience: This course is intended for working healthcare professionals and Bioinformaticians working in the area. Course Pre-Requisites: The course assumes that attendees are not intimidated by the prospect of gaining experience working on UNIX-like operating systems (including the shell, and shell scripting). Attendees should understand some of the science behind high-throughput DNA sequencing and sequence analysis, as we will not go deeply into underlying theory (or the mechanics of given algorithms, for example) as such. What will be taught are technical solutions for automating and sharing such analyses in reusable compute environments, which will include (but is not limited to) beginner-level programming, and basic Linux provisioning. General computer literacy, (e.g. editing plain text data files, navigating using the command line) will be assumed. (*)  (*) Note: An optional free session will be arranged with the participants that may be interested, on the EVE of the first day (Monday, Nov 13th at 4PM), where we will ensure that every participant willing to attend can use the Linux operating system at the required level. Instructors:​             Fátima Al-Shahrour obtained her PhD from Universidad Autónoma de Madrid (UAM) in 2006. During her PhD she worked at the Bioinformatics Unit at Spanish National Cancer Research Center (CNIO, Madrid, Spain) and Centro de Investigaciones Príncipe Valencia (Valencia, Spain). During this period, her research work dealt with the development of new Bioinformatics tools for microarray gene expression analysis, with a particular focus on computational methods for the functional interpretation of high-throughput experiments. In 2007, she joined the Computational Biology and Bioinformatics group at Cancer Program at Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard (Cambridge, USA). In 2008, she got a staff position at Broad Institute of MIT and Harvard as a Computational Biologist. During this period, her research was focused on the study the biology and treatment of cancer under a genomic perspective using hematopoiesis as a model system. In 2012 she joined the Spanish National Cancer Research Centre (CNIO) to lead the Translational Bioinformatics Unit (TBU) in the Clinical Research Programme and since 2017 she is leading the Bioinformatics Unit (BU). -- The CNIO Bioinformatics Unit (BU) belongs to the Structural and Biocomputing Programme. This is a group with a large trajectory in bioinformatics for functional genomics, field in which the group has published numerous papers as well as developed distinct applications and programs widely used by the scientific community. BU's major research activity is focused on the development of new computational methodologies to perform genomic analysis of cancer patients' data, in order to identify new biomarkers and mechanisms of drug response. The main goal is to translate this knowledge into effective treatments for cancer patients. Since 2013, we extensively collaborate with hospitals to analyze next-generation sequencing data from patient's tumors. During this period, we have applied our analytical pipeline for the categorization and interpretation of patient's tumors and match them to effective drugs or treatments based on their genomic alterations.            Affiliation: Centro Nacional de Investigaciones Oncológicas, Madrid, ES Javier Perales is a PhD student working under the supervision of Fátima Al-Shahrour & Alfonso Valencia, at the Spanish National Cancer Research Centre. During his education, he has acquired knowledge in Molecular Biology, Genetics and Computational Biology. His research activity is focused on the genomic characterization of patient tumours by Next-Generation Sequencing technologies. He is interested on the development and integration of computational approaches for cancer genomics data in order to improve our understanding about the individual patient's disease.            Affiliation: Centro Nacional de Investigaciones Oncológicas, Madrid, ES Elena Piñeiro is a Bioinformatician working in the Bioinformatics Unit of the CNIO. Her work is mainly focused on the elaboration of pipelines for the analysis and prioritization of genomic variations obtained through NGS technologies and on the construction of a methodology for the personalized drug assignation according to the particular genomic profile of each patient.            Affiliation: Centro Nacional de Investigaciones Oncológicas, Madrid, ES   Program: You can find here the detailed program.   Registration:  Register using here until October the 18th   Contact: For any questions about this course, please contact Pedro Fernandes (e-mail address below) 2017-11-14 09:00:00 UTC 2017-11-14 00:00:00 UTC Instituto Gulbenkian de Ciência, Portugal Instituto Gulbenkian de Ciência Portugal 2781-901 [] [] [] [] [] []
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