Content Providers

  • DTLS - Dutch Techcentre For Life Sciences

    DTL focuses on the great potential of high-end technologies in pioneering life science research,...

    40 training materials
    4 upcoming events (196 past events)
    DTLS - Dutch Techcentre For Life Sciences https://tess.elixir-europe.org/content_providers/dtls-dutch-techcentre-for-life-sciences DTL focuses on the great potential of high-end technologies in pioneering life science research, and on the skills and solutions to professionally use computers to deal with the ever-growing data streams in research. /system/content_providers/images/000/000/003/original/logo.png?1469458221
  • Department of Bioinformatics - BiGCaT, Maastricht University

    The department of Bioinformatics-BiGCaT is part of NUTRIM the school of Nutrition and...

    8 training materials
    0 upcoming events (1 past event)
    Department of Bioinformatics - BiGCaT, Maastricht University https://tess.elixir-europe.org/content_providers/department-of-bioinformatics-bigcat-maastricht-university The department of Bioinformatics-BiGCaT is part of NUTRIM the school of Nutrition and Translational Research in Metabolism at Maastricht University, the Netherlands. It was founded in 2001 by Prof. dr. Chris Evelo aiming at employing bioinformatics approaches in systems biology to integrate experimental data and data with current knowledge. Integrative Systems Biology is being developed and applied in various research fields. The department has four core research areas; 1) Metabolic diseases, 2) Micronutrients, 3) Toxicity and risk Assessment and 4) Rare diseases. Within these areas different types of data, like transcriptomics, proteomics, metabolomics and (epi)genomics data, are collected , integrated and combined with existing knowledge /system/content_providers/images/000/000/093/original/logo_05_72dpi.gif?1528366508
  • WikiPathways

    WikiPathways is a database of biological pathways maintained by and for the scientific community.

    1 training material
    WikiPathways https://tess.elixir-europe.org/content_providers/wikipathways WikiPathways is a database of biological pathways maintained by and for the scientific community. /system/content_providers/images/000/000/660/original/wikipathways-logo-horizontal.svg?1668072305
  • Showing 30 materials out of 49. View all results.
    BridgeDbR Tutorial

    BridgeDb is a combination of an application programming interface (API), library, and set of data files for mapping identifiers for identical objects [1]. Identifier mapping databases are available for gene products and metabolites. This Bioconductor Vignette explains how to use BridgeDb in the R...

    Keywords: ELIXIR RIR, BridgeDb

    Resource type: Tutorial, Vignette

    #metawinterschool contribution by BiGCaT

    Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis.

    Scientific topics: Metabolomics

    Keywords: Metabolomics, Identifiers, ELIXIR RIR, BridgeDb

    Resource type: Tutorial

    How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene

    Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping. It explains how to download the IMS Docker and identifier mapping databases (link sets), load the link sets, and test the web interface.

    Scientific topics: Genetic variation, Genomics

    Keywords: ELIXIR RIR, BridgeDb

    Resource type: Tutorial

    Programming in the Life Sciences

    This is a OER around a six day course on using JavaScript to program the life sciences web, but with a focus on the Open PHACTS API.

    Scientific topics: Drug discovery, Pharmacology

    A network biology workflow to study transcriptomics data of the diabetic liver

    The described network biology workflow uses state-of-the-art pathway and network analysis methods to study the rewiring of the diabetic liver. The integration of experimental data and knowledge on disease-affected biological pathways, including regulatory elements like transcription factors or...

    Keywords: Biological networks, Network Visualization

    FAIR Data Stewardship - Data sharing, archiving and publishing

    In this workshop we focus on three aspects of FAIR data stewardship: Data sharing, publishing and archiving. Many scientists have an insufficient overview over data services, roles and their responsibilities towards safe data sharing, archiving and publishing. Shedding light on these roles helps...

    Keywords: Data Life Cycle, FAIR, data management, data stewardship, data repositories, data sharing, data publication

    Resource type: Slides, Training materials

    Essential Steps of the FAIRification Process

    Since 2014, a number of FAIR Stakeholders have developed tools and methods around the FAIRifcation of typical datasets. In the last 5 years, these efforts were field tested in a series of "Bring Your Own Data" Workshops" (https://www.dtls.nl/fair-data/byod/).

    This document records the...

    Keywords: FAIR, data stewardship, metadata, linked data

    Resource type: Training materials

    Helis Academy - Data Management Plans, why and how?

    Research Data Management
    The organisation of data throughout the research project
    everyday management of research data (storage, file naming, preservation)
    how will data be preserved and shared after the project is completed?

    Scientific topics: Data management

    Keywords: Data managment plan, Data Life Cycle

    Resource type: Slides, PDF

    Introduction to FAIR data stewardship

    FAIR data Stewardship: How to improve the reuse of nanosafety data

    Scientific topics: Data management

    Keywords: FAIR

    An introduction to the role of experimental data in Intellectual Property

    data ownership
    the role of experimental data in acquiring a patent
    the role of data in establishing a prior use right
    trade secrets

    Keywords: patents

    Resource type: PDF

    Helis Academy - Data Sharing, publishing and archiving

    Basic knowledge of:
    o Know what a repository is
    o Characteristics of Data Sharing, Archiving and Publishing
    o Knowledge of major platforms for Sharing, Archiving and Publishing

    Hands on experience:
    o Dataverse possibilities for sharing and publishing
    o Designing requirements digital...

    Keywords: data sharing, Data publishing, data archiving, data repositories, data management

    Resource type: Slides

    Helis Academy - Persistent identifiers and their use cases

    Managing increasing numbers of data objects
    Sharing data from different sourcesamongst researchers
    Data needs to be (globally) identifiable and addressable to ensure reuse of data
    Data citation
    Linking data from different source

    Keywords: Referencing data and code, Findability of data and code, Identifying data and code, data management

    Resource type: Slides

    FAIRification & Data modelling

    Wikidata
    fairification

    Keywords: FAIR, linked data, ontologies, metadata

    Resource type: Slides

    Introduction to Persistent Identifiers

    Module also available as self-study material in data carpentry style

    Scientific topics: Data management

    Keywords: system relevant metadata for data, PID metadata, Python API pyhandle, Persistent Identifiers

    Resource type: course materials

    Online course 'Learn to write your Data Management Plan'

    Writing a Data Management Plan can be new to you. ‘Learn to write your Data Management Plan’, an online self-study course, can help you decide how to take good care of your valuable research data.

    During the course you are writing your DMP step by step. As a result you have written a DMP for...

    Keywords: Data management plan, data management

    Resource type: e-learning

    Helis Academy - FAIRify your data

    FAIRify your data: FAIRification & Data modelling using linked data

    Keywords: linked data, Wikidata, data management

    Resource type: Slides

    Use Scholia and Wikidata to find scientific literature

    Scholia is a useful tool for finding scientific literature. Based on the main topic of a publication, you can find literature similar to a publication you are looking into or literature you didn’t know about or consider. Additionally, you can take advantage of all of the annotation work of others...

    Keywords: Literature

    Resource type: Tutorial

    SPARQLing Biology: a beginners course

    Course given at BioSB 2019 for biologists about SPARQL.

    Scientific topics: Biology

    Operations: Query and retrieval

    Keywords: Sparql queries, Sparql syntax

    Resource type: Tutorial

    BridgeDb-Matlab Usage Instructions

    Instructions on how to install and use the BridgeDb functionality in Matlab.

    Keywords: ELIXIR RIR, BridgeDb

    Workshop FAIR & Data stewardship for the 2020 ITN COSMIC

    This material is part of an introductory data stewardship workshop for the Marie Curie ITN COSMIC project (Combatting Disorders of Adaptive Immunity with Systems MedICine)

    FAIR and data stewardship - September 18th, 2020
    Organiser: PO5 (Dutch Techcentre For Life Sciences, DTL)
    Setup: Virtual...

    Scientific topics: FAIR data, Data management

    Operations: Analysis, Data handling

    Keywords: Data analysis, Data collection, Data management planning, Data preserving, Data processing, Data reuse, Data sharing

    Resource type: Slidedeck

    Workshop FAIR & Data stewardship for the 2020 ITN ProEVLifeCycle

    This material is part of an introductory FAIR data stewardship workshop for the Marie Curie ITN ProEVLifeCycle (The prostate cancer Extracellular Vesicle LifeCycle)

    FAIR and data stewardship - October 14th, 2020
    Organiser: Dutch Techcentre For Life Sciences, DTL
    Setup: Virtual meeting...

    Scientific topics: Data management, FAIR data

    Operations: Data handling, Analysis

    Keywords: Data analysis, Data management planning, Data processing, Data sharing, Data collection, Data preserving, Data reuse

    Resource type: Slidedeck

    Workshop FAIR & Data stewardship for the 2021 ITN ProEVLifeCycle

    This material is part of an follow up FAIR data stewardship workshop for the Marie Curie ITN ProEVLifeCycle (The prostate cancer Extracellular Vesicle LifeCycle)

    FAIR and data stewardship - November 3th, 2021
    Organiser: Dutch Techcentre For Life Sciences, DTL
    Setup: Virtual meeting...

    Scientific topics: Data management, FAIR data

    Operations: Data handling, Analysis

    Keywords: Data analysis, Data management planning, Data processing, Data sharing, Data collection, Data preserving, Data reuse

    Resource type: Slidedeck

    Helis Academy course FAIR data stewardship 2021, Day 1, Introduction Landscape Wrap up

    This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course
    Day 1, March 17, 2021

    https://www.aanmelder.nl/fair-data-stewardship-2021
    https://helisacademy.com/en/data-analysis-stewardship

    Topic: introduction, FAIR data stewardship...

    Scientific topics: Data management, FAIR data

    Operations: Analysis, Data handling

    Keywords: Data management planning, FAIR data

    Resource type: Slidedeck

    Helis Academy course FAIR data stewardship 2021, Day 2, Finding and capturing data part 1

    This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course
    Day 2, March 18, 2021

    https://www.aanmelder.nl/fair-data-stewardship-2021
    https://helisacademy.com/en/data-analysis-stewardship

    Topic: finding and capturing data

    Scientific topics: Data quality management, FAIR data

    Operations: Analysis

    Keywords: Data collection

    Resource type: Slidedeck

    Helis Academy course FAIR data stewardship 2021, Day 2, Finding and capturing data part 2

    This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course
    Day 2, March 18, 2021

    https://www.aanmelder.nl/fair-data-stewardship-2021
    https://helisacademy.com/en/data-analysis-stewardship

    Topic: finding and capturing data

    Scientific topics: Data management, FAIR data

    Operations: Data handling

    Keywords: Data collection

    Resource type: Slidedeck

    Helis Academy course FAIR data stewardship 2021, Day 1, Funder requirements

    This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course
    Day 1, March 17, 2021

    https://www.aanmelder.nl/fair-data-stewardship-2021
    https://helisacademy.com/en/data-analysis-stewardship

    Topic: funder requirements

    Scientific topics: FAIR data, Data management

    Operations: Data handling, Analysis

    Keywords: Data management planning, FAIR data

    Resource type: Slidedeck

    Helis Academy course FAIR data stewardship 2021, Day 1, Publisher requirements

    This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course
    Day 1, March 17, 2021

    https://www.aanmelder.nl/fair-data-stewardship-2021
    https://helisacademy.com/en/data-analysis-stewardship

    Topic: publisher requirements

    Scientific topics: FAIR data, Data management

    Operations: Data handling, Analysis

    Keywords: Data management planning, FAIR data, Data preserving, Data sharing

    Resource type: Slidedeck

    Helis Academy course FAIR data stewardship 2021, Day 1, Institute requirements

    This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course
    Day 1, March 17, 2021

    https://www.aanmelder.nl/fair-data-stewardship-2021
    https://helisacademy.com/en/data-analysis-stewardship

    Topic: institute requirements

    Scientific topics: FAIR data, Data management

    Operations: Data handling, Analysis

    Keywords: Data preserving, Data reuse, Data management planning, Data sharing, FAIR data

    Resource type: Slidedeck

    Helis Academy course FAIR data stewardship 2021, Day 2, Tools for processing and analysing data

    This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course
    Day 2, March 18, 2021

    https://www.aanmelder.nl/fair-data-stewardship-2021
    https://helisacademy.com/en/data-analysis-stewardship

    Topic: tools for processing and analysing data

    Scientific topics: FAIR data, Data management

    Operations: Data handling, Analysis

    Keywords: Data analysis, Data processing

    Resource type: Slidedeck

    Helis Academy course FAIR data stewardship 2021, Day 2, Infrastructure for storing and sharing data

    This presentation is part of the 3rd edition of the Helis Academy FAIR data stewardship (for life sciences) course
    Day 2, March 18, 2021

    https://www.aanmelder.nl/fair-data-stewardship-2021
    https://helisacademy.com/en/data-analysis-stewardship

    Topic: infrastructure for storing and sharing...

    Scientific topics: Data management, FAIR data

    Operations: Analysis, Data handling

    Keywords: Data analysis, Data processing, Data sharing

    Resource type: Slidedeck

    Showing 4 upcoming events. Found 197 past events. View all results.
    • Constraint-based modeling: Introduction and advanced topics

      13 - 17 February 2023

      Wageningen Campus, Netherlands

      ELIXIR node event
    • Integrated Modeling and Optimization (Fundamental)

      12 - 16 December 2022

      Wageningen Campus, Netherlands

      ELIXIR node event
    • Knowledge graphs in the life sciences

      13 - 17 March 2023

      Wageningen Campus, Netherlands

      ELIXIR node event
    • Algorithms for Biomolecular Networks (Advanced)

      26 - 30 June 2023

      Wageningen Campus, Netherlands

      ELIXIR node event