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15 events found

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  • 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
  • BioData.pt Business Forum: Advanced data management for added value

    6 May 2019

    Oeiras, Portugal

    Elixir node event
    BioData.pt Business Forum: Advanced data management for added value https://tess.elixir-europe.org/events/biodata-pt-business-forum Research and development institutions annually produce zetabytes of biological information, of which only terabytes are used by the bio-industry. There is a large biological information, the big biodata, still to be explored by the bio-industry, which can add value into new products and services. The BioData.pt Business Forum: advanced data management for added value, organized by BioData.pt and PBio, will bring together four national companies related to the health sector, the sea, agriculture and bioindustry, and tell their stories to inspire new ideas and new businesses. There will also be an opportunity to discuss best practices in curation, management and use of biodata, as well as the use of bioinformatics tools essential to its success. 2019-05-06 14:30:00 UTC 2019-05-06 18:00:00 UTC Biodata.pt Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande, Oeiras, Portugal Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande Oeiras Portugal 2780-156 Instituto Gulbenkian de CiênciaBiodata.pt - Elixir's portuguese node of the european projec info@biodata.pt [] Clinical ScientistsbioinformaticiansBiologists, Genomicists, Computer Scientistssoftware developers, bioinformaticiansbiology and bioinformatics sophomore undergraduatesbiocurators Institutions and other external Institutions or individualsIndustry health professionalsplant researchersBiomedical researchers studies human diseases or developmental biology 120 meetings_and_conferences [] Biodata, Bioinformatics, Biodata
  • Computational PANGenomics

    9 - 13 September 2019

    Oeiras, Portugal

    Elixir node event
    Computational PANGenomics https://tess.elixir-europe.org/events/computational-pangenomics Reference genomes have become central to bioinformatics approaches, and form the core of standard analyses using contemporary sequencing data. However, the use of linear reference genomes, which provide the sequence of one representative genome for a species, is increasingly becoming a limitation as the number of sequenced genomes grows. In particular, they tend to bias us away from the observation of variation in the genomes we study. A general solution to this problem is to use a pangenome that incorporates both sequence and variation from many individuals as our reference system. This pangenome is naturally modelled as a graph with annotations and can provide all the functionality traditionally provided by linear reference genomes. Unlike linear reference genomes, a pangenome readily incorporates both small and large variation, allowing bias-free genotyping at known alleles. In this course, we will explore the use of modern bioinformatic tools that allow researchers to use pangenomes as their reference system when engaging in studies of organisms of all types. Such techniques will aid any researcher working on organisms of high genetic diversity or on organisms lacking a high-quality reference genome. This course targets all researchers interested in learning about an exciting paradigm shift in computational genomics. 2019-09-09 09:30:00 UTC 2019-09-13 17:00:00 UTC The Gulbenkian Training Programme in Bioinformatics Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande, Oeiras, Portugal Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande Oeiras Portugal 2781-901 Instituto Gulbenkian de Ciência, Biodata.pt - Elixir's portuguese node of the european project bicourses@igc.gulbenkian.pt [] This course is oriented towards biologists and bioinformaticians. The course will be of particular interest to researchers investigating organisms without a reference genome or populations featuring high levels of genetic diversity. 20 workshops_and_courses registration_of_interest BioinformaticsGenomics
  • Integrative Biological Interpretation using Proteomics

    4 - 7 November 2019

    Oeiras, Portugal

    Elixir node event
    Integrative Biological Interpretation using Proteomics https://tess.elixir-europe.org/events/integrative-biological-interpretation-using-proteomics Quantitative proteomics by mass spectrometry has become an essential tool for multi-omics studies aiming at answering important biological questions in a system-wide perspective. Proteomics data contain rich and deep information that can become challenging to extract, interpret, and interface with other experimental outcomes. This training course is aimed at researchers who are not expert in proteomics and want to integrate quantitative proteomics results into wider biomedical experiments. We will focus on quality control from an end-user perspective, link to the underlying genomic context, multivariate analysis, protein complexes investigation, and compare different platforms for biological interpretation. After the training, participants will be able to critically interpret results, troubleshoot analyses, and will be ready to successfully attend more specialized training e.g. in proteogenomics or biological network analysis. 2019-11-04 09:30:00 UTC 2019-11-07 18:00:00 UTC The Gulbenkian Training Programme in Bioinformatics, Biodata.pt - Elixir's portuguese node of the european project R. Q.ta Grande 6, 6, Rua Quinta Grande, Oeiras, Portugal R. Q.ta Grande 6, 6, Rua Quinta Grande Oeiras Portugal 2781-901 Instituto Gulbenkian de Ciência bicourses@igc.gulbenkian.pt [] This training course is aimed at researchers who are not expert in proteomics and want to integrate quantitative proteomics results into wider biomedical experiments. 20 workshops_and_courses registration_of_interest BioinformaticsProteomics
  • Ready for BioData Management? - Introduction to Data Management Plans

    10 January 2020

    Oeiras, Portugal

    Elixir node event
    Ready for BioData Management? - Introduction to Data Management Plans https://tess.elixir-europe.org/events/ready-for-biodata-management-introduction-to-data-management-plans Ready For BioData Management? – Introduction to Data Management Plans is an introductory one-day workshop aiming at disseminating Data Management best practices and teaching the basics of making and using Data Management Plans (DMPs) in the context of research activities. The workshop features two introductory lectures on Data Management and DMPs, followed by a hands-on DMP exercise where participants will form groups to fill in a DMP for a mock research project on our custom canvas. The produced DMPs will then be presented, discussed and evaluated. The event is free to attend, but registration is required. 2020-01-10 09:30:00 UTC 2020-01-10 17:00:00 UTC BioData.pt ITQB NOVA, Avenida da República, Oeiras, Portugal ITQB NOVA, Avenida da República Oeiras Oeiras Portugal 2780-157 Data management INESC-ID - Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento info@biodata.pt [] Life Science ResearchersPhD studentsMaster studentsTechnicians 30 workshops_and_courses registration_of_interest Data managment plan
  • Practical Statistics for the Life Sciences

    20 - 24 January 2020

    Oeiras, Portugal

    Elixir node event
    Practical Statistics for the Life Sciences https://tess.elixir-europe.org/events/practical-statistics-for-the-life-sciences This intermediate level course is one of our Foundations courses. It covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. The course positions applied statistics, starting from important aspects of experimental design and data exploration. We then move into statistical modeling and data analysis. We will focus on the link between linear regression and analysis of variance. Together, these methods contribute to the study of General Linear Models. The course also introduces the basics of non-parametric testing, and addresses categorical data analysis and logistic regression. The concepts and methods are exclusively introduced via case-studies in the life sciences. For every study we elaborate on a concrete research question and then provide a study design, which is followed by data exploration. Next, we will focus on how to model the data and elaborate on the link between model parameters and the subject matter research question. 2020-01-20 09:30:00 UTC 2020-01-24 18:00:00 UTC The Gulbenkian Training Programme in Bioinformatics, Biodata.pt - Elixir's portuguese node of the european project Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande, Oeiras, Portugal Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande Oeiras Portugal 2780-156 Instituto Gulbenkian de Ciência bicourses@igc.gulbenkian.pt [] Life Science Researchers 20 workshops_and_courses registration_of_interest Statistics
  • PO21 Precision Oncology

    25 - 29 October 2021

    Oeiras, Portugal

    Elixir node event
    PO21 Precision Oncology https://tess.elixir-europe.org/events/po21-precision-oncology Precision Oncology (PO) is already revolutionizing healthcare and will play a dominant role in the future of cancer therapy. PO integrates tumor multi-omic profiles and data that reflect the course of the disease, lifestyle and environment to guide clinical decisions during cancer patient journey such as prevention, diagnosis and treatment. 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 tumor. 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. Although focused on cancer, some of the principles and steps could be extrapolated to other complex diseases. 2021-10-25 09:30:00 UTC 2021-10-29 18:30:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto Gulbenkian de Ciência Oeiras Oeiras Portugal 2780-156 Oncology IGC - Instituto Gulbenkian de Ciência Pedro L Fernandes, Training Coordinator, pfern@igc.gubenkian.pt Oeiras Valley healthcare professionals Bioinformaticians 14 workshops_and_courses [] Clinical oncologyVariant callingDrug Targetting
  • AM21 Applied Metagenomics

    2 - 5 November 2021

    Oeiras, Portugal

    Elixir node event
    AM21 Applied Metagenomics https://tess.elixir-europe.org/events/am21-applied-metagenomics This course will give a comprehensive introduction to the research field of metagenomics. It will cover the basic concepts of microbiome analysis of shotgun metagenomic data using state of the art bioinformatics (amplicon sequencing will not be covered). The analysis methods that are being introduced are generic for all types of microbiomes, but we will be using data from the human microbiome as showcases. The course will start with the main preprocessing steps of raw sequence data, before various downstream analysis will be covered separately. These include taxonomic analysis, assembly, binning, and finally functional analysis with focus on antibiotic resistance genes. The theoretical part for each topic will be introduced via lectures, followed by practical hands-on exercises. 2021-11-02 09:30:00 UTC 2021-11-05 18:00:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto Gulbenkian de Ciência Oeiras Oeiras Portugal 2780-156 Metagenomic sequencing Metagenomics IGC - Instituto Gulbenkian de Ciência Pedro L. Fernandes, Training Coordinator, pfern@igc.gulbenkian.pt Oeiras Valley bioinformaticiansMicrobiologistsDrug resistance 10 [] [] Metagenomics
  • PSLS21 - Practical Statistics for the Life Sciences 2021

    8 - 12 November 2021

    Oeiras, Portugal

    Elixir node event
    PSLS21 - Practical Statistics for the Life Sciences 2021 https://tess.elixir-europe.org/events/psls21 This intermediate level course is one of our Foundations courses. It covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. The course positions applied statistics, starting from important aspects of experimental design and data exploration. We then move into statistical modeling and data analysis. We will focus on the link between linear regression and analysis of variance. Together, these methods contribute to the study of General Linear Models. The course also introduces the basics of non-parametric testing, and addresses categorical data analysis and logistic regression. The concepts and methods are exclusively introduced via case-studies in the life sciences. For every study we elaborate on a concrete research question and then provide a study design, which is followed by data exploration. Next, we will focus on how to model the data and elaborate on the link between model parameters and the subject matter research question. 2021-11-08 09:30:00 UTC 2021-11-12 18:30:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto Gulbenkian de Ciência Oeiras Portugal Portugal 2780-156 Statistics and probability IGC - Instituto Gulbenkian de Ciência pfern@igc.gulbenkian.pt [] [] 17 workshops_and_courses registration_of_interest []
  • Machine Learning

    15 - 17 November 2021

    Oeiras, Portugal

    Elixir node event
    Machine Learning https://tess.elixir-europe.org/events/machine-learning With the rise in high-throughput sequencing technologies, the volume of omics data has grown exponentially in recent times and a major issue is to mine useful knowledge from these data which are also heterogeneous in nature. Machine learning (ML) is a discipline in which computers perform automated learning without being programmed explicitly and assist humans to make sense of large and complex data sets. The analysis of complex high-volume data is not trivial and classical tools cannot be used to explore their full potential. Machine learning can thus be very useful in mining large omics datasets to uncover new insights that can advance the field of bioinformatics. This 3 day course will introduce participants to the machine learning taxonomy and the applications of common machine learning algorithms to omics data. The course will cover the common methods being used to analyse different omics data sets by providing a practical context through the use of basic but widely used R libraries. The course will comprise a number of hands-on exercises and challenges where the participants will acquire a first understanding of the standard ML processes, as well as the practical skills in applying them on familiar problems and publicly available real-world data sets. Instructors: Vandrille Duchemin, University of Basel, CH Crhistian Cardona, University of Tuebingen, DE 2021-11-15 09:30:00 UTC 2021-11-17 18:00:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto Gulbenkian de Ciência Oeiras Portugal 2780-156 Machine learning Instituto Gulbenkian de Ciência pfern@igc-gulbenkian.pt To register your interest, please send an e-mail to bicourses@igc.gulbenkian.pt with "Machine Learning" in the subject line UNTIL November 11th 2021, stating the reason why you would be interested in attending this course in a single paragraph. ELIXIR PhD Studentspost-docsScientistsstudents 17 workshops_and_courses registration_of_interest Machine Learning, Introductory, Novice / Entry-level, Supervised learning, Unsupervised learning, Principal Component Analysis, K-means, Hierarchical Clustering, Decision Trees, Random Forest, Regression
  • PSLS22 - Practical Statistics for the Life Sciences

    28 March - 1 April 2022

    Oeiras, Portugal

    Elixir node event
    PSLS22 - Practical Statistics for the Life Sciences https://tess.elixir-europe.org/events/psls22 This intermediate level course is one of our Foundations courses. It covers essential statistical concepts and methods for extracting insights from empirical data in the life sciences. The course positions applied statistics, starting from important aspects of experimental design and data exploration. We then move into statistical modeling and data analysis. We will focus on the link between linear regression and analysis of variance. Together, these methods contribute to the study of General Linear Models. The course also introduces the basics of non-parametric testing, and addresses categorical data analysis and logistic regression. The concepts and methods are exclusively introduced via case-studies in the life sciences. For every study we elaborate on a concrete research question and then provide a study design, which is followed by data exploration. Next, we will focus on how to model the data and elaborate on the link between model parameters and the subject matter research question. 2022-03-28 09:30:00 UTC 2022-04-01 18:30:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande, Oeiras, Portugal Instituto Gulbenkian de Ciência (IGC), 6, Rua Quinta Grande Oeiras Portugal Portugal 2780-156 Statistics and probability Instituto Gulbenkian de Ciência bicourses@igc.gulbenkian.pt [] PhD studentspost-docsLife Science Researchers 20 workshops_and_courses [] data visualizationData analysisGeneral Linear Models
  • PO22 Precision Oncology

    9 - 13 May 2022

    Oeiras, Portugal

    Elixir node event
    PO22 Precision Oncology https://tess.elixir-europe.org/events/po22-precision-oncology Precision Oncology (PO) is already revolutionizing healthcare and will play a dominant role in the future of cancer therapy. PO integrates tumor multi-omic profiles and data that reflect the course of the disease, lifestyle and environment to guide clinical decisions during cancer patient journey such as prevention, diagnosis and treatment. 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 tumor. 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. Although focused on cancer, some of the principles and steps could be extrapolated to other complex diseases. 2022-05-09 09:30:00 UTC 2022-05-13 18:00:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto Gulbenkian de Ciência Oeiras Portugal 2780-156 Biotherapeutics Bioinformatics Biomarkers Oncology Instituto Gulbenkian de Ciência bicourses@igc.gulbenkian.pt Pedro L Fernandes, Training Coordinator [] oncologistsBiologists and bioinformaticians who are dealing with high-throughput gene expression data or other high-throughput data and would like to learn state-of-the-art methods for mining and analysing such data. 20 workshops_and_courses [] cancergene panelschemotherapydrug prioritization
  • CPANG22 - Computational Pangenomics

    23 - 27 May 2022

    Oeiras, Portugal

    Elixir node event
    CPANG22 - Computational Pangenomics https://tess.elixir-europe.org/events/cpang22-computational-pangenomics 2022-05-23 09:30:00 UTC 2022-05-27 18:00:00 UTC Pedro Fernandes Oeiras, Portugal Oeiras Portugal 2780-156 Genomics Instituto Gulbenkian de Ciência bicourses@igc.gulbenkian.pt Oeiras Valley Bioinformaticians and wet-lab biologists who can program in Perl. 20 workshops_and_courses registration_of_interest Computational Pangenomics
  • IBIP22 - Integrative Biological Interpretation using Proteomics

    20 - 24 June 2022

    Oeiras, Portugal

    Elixir node event
    IBIP22 - Integrative Biological Interpretation using Proteomics https://tess.elixir-europe.org/events/ibip22-integrative-biological-interpretation-using-proteomics Quantitative proteomics by mass spectrometry has become an essential tool for multi-omics studies aiming at answering important biological questions in a system-wide perspective. Proteomics data contain rich and deep information that can become challenging to extract, interpret, and interface with other experimental outcomes. This training course is aimed at researchers who are not expert in proteomics and want to integrate quantitative proteomics results into wider biomedical experiments. We will focus on quality control from an end-user perspective, link to the underlying genomic context, multivariate analysis, protein complexes investigation, and compare different platforms for biological interpretation. 2022-06-20 09:30:00 UTC 2022-06-24 18:30:00 UTC Pedro Fernandes Rua da Quinta Grande, 6, Oeiras, Portugal Rua da Quinta Grande, 6 Oeiras Portugal 2780-156 Proteogenomics Instituto Gulbenkian de Ciência bicourses@igc.gulbenkian.pt Oeiras Valley [] 20 [] registration_of_interest []
  • PDA22 Proteomics Data Analysis

    12 - 16 September 2022

    Oeiras, Portugal

    Elixir node event
    PDA22 Proteomics Data Analysis https://tess.elixir-europe.org/events/pda22-proteomics-data-analysis 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 peptide and protein identification, quantification, and differential analysis. Moreover, more advanced experimental designs and blocking will also be introduced. The core focus will be on shotgun proteomics data, and quantification using label-free precursor peptide (MS1) ion intensities. The course will rely exclusively on free and user-friendly software, all of which can be directly applied in your lab upon returning from the course. You will also learn how to submit data to PRIDE/ProteomeXchange, which is a common requirement for publication in the field, and how to browse and reprocess publicly available data from online repositories. The course will thus provide a solid basis for beginners, but will also bring new perspectives to those already familiar with standard d ata 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. 2022-09-12 09:30:00 UTC 2022-09-16 18:30:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência, Oeiras, Portugal Instituto Gulbenkian de Ciência Oeiras Portugal 2780-156 Instituto Gulbenkian de Ciência bicourses@igc.gulbenkian.pt Oeiras Valley PhD StudentsBiologists and bioinformaticians who are dealing with high-throughput gene expression data or other high-throughput data and would like to learn state-of-the-art methods for mining and analysing such data.post-doctoral researchers and principle investigators working in wet-lab biology. Participants who are looking for a basic introduction to the bioinformatics resources offered by the EMBL-EBI and want to know more about accessing biological data and tools.computational and statistical techniques are used to identify and validate the causal links between targets 20 workshops_and_courses registration_of_interest Proteomics

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