Register event
8 events found

Sponsors: Oeiras Valley  or NanoSolveIT 

  • 3DAROC21 3C-based data analysis and 3D reconstruction of chromatin folding

    4 - 6 October 2021

    3DAROC21 3C-based data analysis and 3D reconstruction of chromatin folding https://tess.elixir-europe.org/events/3daroc21-3c-based-data-analysis-and-3d-reconstruction-of-chromatin-folding 3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are in close spatial proximity in the cell nucleus. Overall, those interaction matrices have been used to study how the genome folds within the nucleus, which is one of the most fascinating problems in modern biology. The rigorous analysis of those paired-reads using computational tools has been essential to fully exploit the experimental technique, and to study how the genome is folded in space. Currently, there is a clear expansion on the wealth of data on genome structure with the availability of many datasets of Hi-C experiments down to 1Kb resolution (see for example: http://hic.umassmed.edu/welcome/welcome.php or http://www.aidenlab.org/data.html). In this course, participants will learn to use TADbit, a software designed and developed to manage all dimensionalities of the Hi-C data: 1D - Map paired-end sequences to generate Hi-C interaction matrices 2D - Normalize matrices and identify constitutive domains (TADs, compartments) 3D - Generate populations of structures which satisfy the Hi-C interaction matrices 4D - Compare samples at different time points Participants can bring specific biological questions and/or their own 3C-based data to analyze during the course. At the end of the course, participants will be familiar with the TADbit software and will be able to fully analyze Hi-C data. Although the TADbit software is central in this course, alternative software will be discussed for each part of the analysis. 2021-10-04 09:00:00 UTC 2021-10-06 17:00:00 UTC Pedro Fernandes Instituto Gulbenkian de Ciência bicourses@igc.gulbenkian.pt Oeiras Valley experimental researchers and bioinformaticians at the graduate and post-graduate levels 20 workshops_and_courses registration_of_interest TADbit
  • 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
  • Assessing ethical impacts of nanomaterials in dentistry

    18 November 2021

    Assessing ethical impacts of nanomaterials in dentistry https://tess.elixir-europe.org/events/assessing-ethical-impacts-of-nanomaterials-in-dentistry On Thursday 18th November 2021, the NanoCommons, NanoSolveIT, and RiskGone teams, in a joint initiative with the NanoSafety Cluster, will offer an online workshop/hackathon on their Ethic Impacts Assessment Tool. Ethical Impacts Assessment (EIA) targets nanomaterials applied to improve properties of components of dental materials and dental hygiene products. The dental materials include composites, adhesive systems, impression materials and dental implants. The dental hygiene products include toothpaste, toothbrushes, and mouth rinse. In literature, innovative applications of nanotechnology in nanobiosensors for detecting oral cancer and nano-drug delivery are also mentioned. Identified ethical issues are health related, liberty and sustainable development (instead of environmental). A small-scale EIA was performed by Ineke Malsch. On this case study the freely available EIA tool (http://enaloscloud.novamechanics.com/riskgone/thresholdanalysis/) will be applied and its functionality presented. Attendees will be able to get hands-on experience during this 1.5 h workshop/hackathon. Expectation: Willing to learn new things and active participation in the interactive webinar. The webinar will take place on Thursday November 18th from 15:00 till 16:30 h CET. Feel free to join and please do not forget to register here: https://ukri.zoom.us/meeting/register/tJUvf-qqpzItHNQUvsU3L3FAd5rEyXk13Ul4 After registering, you will receive a confirmation email containing information about joining the workshop. Please, be aware that some personal information may be collected for statistical purposes, however, in a blinded and anonymous way. The workshop will be partially recorded for educational purposes. You will find updates with more information about NanoCommons and training materials here. Feel free to redistribute this information within your projects and networks. We are happy to have as many participants as possible and to help the community with the FAIRification of their data by offering insight into fully exploring and linking available data resources in a more straightforward way. The NanoCommons team will be happy to answer your questions and to guide you in your requests! 2021-11-18 15:00:00 UTC 2021-11-18 17:00:00 UTC Martin Himly, PLUS, Chair of EU NanoSafety Cluster WG-A PLUSUKCEHBNNUoBNovaMechanics NanoCommonsRiskGoneNanoSolveIT [] 80 workshops_and_courses [] concern assessment
  • IBIP21 Integrative Biological Interpretation using Proteomics

    22 - 26 November 2021

    Oeiras, Portugal

    IBIP21 Integrative Biological Interpretation using Proteomics https://tess.elixir-europe.org/events/ibip21-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. 2021-11-22 09:30:00 UTC 2021-11-26 18:30:00 UTC Pedro Fernandes R. Q.ta Grande 6, 6, Rua Quinta Grande, Oeiras, Portugal R. Q.ta Grande 6, 6, Rua Quinta Grande Oeiras Portugal 2780-156 Instituto Gulbenkian de Ciência The Gulbenkian Training Programme in Bioinformatics Pedro L. Fernandes, Organiser Instituto Gulbenkian de Ciência Rua da Quinta Grande, 6 2780-156 OEIRAS Portugal Oeiras Valley ResearchersBiologists, Genomicists, Computer Scientistsbioinformaticians 20 [] registration_of_interest ProteomicsIntegrativeGenomicsMass Spectroscopy
  • The NanoCommons Knowledge Base: how to find all data for one nanomaterial across multiple data sources

    2 December 2021

    The NanoCommons Knowledge Base: how to find all data for one nanomaterial across multiple data sources https://tess.elixir-europe.org/events/the-nanocommons-knowledge-base-how-to-find-all-data-for-one-nanomaterial-across-multiple-data-sources On Thursday 2nd December 2021, the NanoCommon team, in a joint initiative with the EU NanoSafety Cluster, will offer an online workshop/hackathon on their Knowledge Base (NC KB), termed “The NanoCommons Knowledge Base: how to find all data for one nanomaterial across multiple data sources”. Data retrievals & uploads will be showcased using the features of the NC KB (https://ssl.biomax.de/nanocommons/cgi/login_bioxm_portal.cgi) interlinking the results from several large projects’ real data sets and corresponding metadata sufficing the need for data FAIRness (Findability, Accessibility, Interoperability, Reusability) and its diverse functionalities will be presented in an interactive manner, thus, be tested for fitness-for-purpose by the attendees’ demands. Attendees will be able to get hands-on experience during this 2 h workshop/hackathon. Expectation: Willing to learn new things and active participation in the interactive webinar. The webinar will take place on Thursday December 2nd from 15:00 till 17:00 h CET. Feel free to join and please do not forget to register here: https://ukri.zoom.us/meeting/register/tJYtf-upqDMvGdRpjZos9mtYH0ZVG-1Ui7hq After registering, you will receive a confirmation email containing information about joining the workshop. Please, be aware that some personal information may be collected for statistical purposes, however, in a blinded and anonymous way. The workshop will be partially recorded for educational purposes. You will find updates with more information about NanoCommons and training materials here. Feel free to redistribute this information within your projects and networks. We are happy to have as many participants as possible and to help the community with the FAIRification of their data by offering insight into fully exploring and linking available data resources in a more straightforward way. The NanoCommons team will be happy to answer your questions and to guide you in your requests! 2021-12-02 15:00:00 UTC 2021-12-02 17:00:00 UTC Martin Himly, PLUS, Chair of EU NanoSafety Cluster WG-A BiomaxPLUSUKCEHBNNUoB7p9 NanoCommonsNanoSolveIT mixed audience workshops_and_courses [] data FAIRnessmetadata completenessnanosafety assessmentnanotoxicologyOntologies
  • Nanosafety and the semantic web: from natural language to computational processing

    8 - 9 December 2021

    Nanosafety and the semantic web: from natural language to computational processing https://tess.elixir-europe.org/events/nanosafety-and-the-semantic-web-from-natural-language-to-computational-processing On Wednesday 8th & Thursday 9th December 2021, the NanoCommon team, in a joint initiative with the EU NanoSafety Cluster, will offer an online workshop/hackathon on “Nanosafety and the semantic web: from natural language to computational processing”. The web is a large interlinked resource of information, which is largely represented in natural language. One of the main goals of the semantic web is to convert this data into formats suitable for computational processing. Within the nanosafety projects that the Department of Bioinformatics at Maastricht University (BiGCaT) is involved in, we talk a lot about Semantic Approaches and terms like the Web Ontology Language (OWL), Resource Description Framework (RDF), SPARQL queries and SPARQL endpoints are used regularly by members of our team. We have given workshops/tutorials/worksessions in the past, but always with a focus on the knowledge needed for a specific task we were working on. This means that many of our project partners understand part of the picture. We are therefore organizing a workshop covering the whole range of Semantic Approaches that we use within the nanosafety-projects. Starting with more general questions like “what is a triple and what is the link with ontologies and RDF?” all the way to writing SPARQL queries and exploring their capabilities, which by the end of the workshop everyone will be able to do and possibly implement in their own work. We will practice using and extending the eNanoMapper ontology and we will look at the SPARQL endpoints, semantic web applications and tools developed and used by BiGCaT within these nanosafety projects. The workshop will be spread out over two afternoons on the Thursday December 8th & 9th from 13:00 till 17:00 h CET. The afternoons will be filled with a mixture of lectures, tutorials, hands-on and Q&A sessions. Expectation: Willing to learn new things and active participation in the interactive webinar. Feel free to join and please do not forget to register here: https://ukri.zoom.us/meeting/register/tJMvcO2orzgrGdCjCCUSrDOkxGib4ZvgWOo5 After registering, you will receive a confirmation email containing information about joining the workshop. Please, be aware that some personal information may be collected for statistical purposes, however, in a blinded and anonymous way. The workshop will be partially recorded for educational purposes. You will find updates with more information about NanoCommons and training materials here. Feel free to redistribute this information within your projects and networks. We are happy to have as many participants as possible and to help the community with the FAIRification of their data by offering insight into fully exploring and linking available data resources in a more straightforward way. The NanoCommons team will be happy to answer your questions and to guide you in your requests! 2021-12-08 13:00:00 UTC 2021-12-09 17:00:00 UTC Martin Himly, PLUS, Chair of EU NanoSafety Cluster WG-A Maastricht University NanocommonsNanoSolveIT mixed audience 80 workshops_and_courses [] data FAIRnessmetadata completenessscientific quality assurancelinked datalife sciences
  • 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

Note, this map only displays events that have geolocation information in TeSS.
For the complete list of events in TeSS, click the grid tab.