Register training material
86 materials found

Content provider: CINECA PROJECT  or Bioinformatics Visualization 


GA4GH Passports and ELIXIR AAI

The training (delivered 23 June 2021) consisted of one hour of presentations (recorded stream), followed by a hands-on exercise with a Virtual Machine. In the hands-on part the trainees integrate their VM to ELIXIR AAI as an OpenID Connect client to...

Keywords: AAI , GA4GH, Passports, Auhtorisation

Resource type: Training materials, Video

CINECA discovery service catalog

This series of three videos describes and demonstrates the CINECA service catalog:

The first video introduces the Service Catalog, a searchable listing of query services available atop CINECA cohort data, and explains where it fits into CINECA’s set of interactive queries and data...

Keywords: Cohort data, Standards, federated data analysis, Beacon queries

Resource type: Series of videos

A common framework for designing portable federated pipelines

This video describes a common framework for designing portable federated pipelines. The joint cohort genotyping pipeline is provided as a specific implementation example. The ability of the pipeline to run in different environments, accessing the data via different protocols, and applying the...

Scientific topics: Data architecture, analysis and design

Keywords: data access, federated data analysis

Resource type: Video

FAIR software tools

In this talk, I will discuss the importance of the FAIR principles for the software tools we use to process data. Ranging from small analysis scripts to full fledged data processing pipelines, software needs to be FAIR to enable other researchers to reproduce our own experiments and reuse our...

Scientific topics: Software engineering

Keywords: FAIR, software tools, Software

Resource type: Video

Making cohort data FAIR

Cohort studies, which recruit groups of individuals who share common characteristics and follow them over a period of time, are a robust and essential method in biomedical research for understanding the links between risk factors and diseases. Through questionnaires, medical assessments, and...

Scientific topics: Data management, Data integration and warehousing

Keywords: FAIR data, Cohort data, Ontologies, Standards

Resource type: Video

Introduction to FAIR principles - Open science through FAIR health data networks: dream or reality?

Since the FAIR data principles were published in 2016, many organizations including science funders and governments have adopted these principles to promote and foster true open science collaborations. However, to define a vision and create a video of a Personal Health Train that leverages...

Scientific topics: Data management

Keywords: FAIR data, Health data, Open science

Resource type: Video

Data Gravity in the Life Sciences: Lessons learned from the HCA and other federated data projects

We live in an era of cloud computing. Many of the services in the life sciences are keenly planning cloud transformations, seeking to create globally distributed ecosystems of harmonised data based on standards from organisations like GA4GH. CINECA faces similar challenges, gathering cohort...

Scientific topics: Data architecture, analysis and design

Keywords: Cloud computing, Data analysis, Standards, Translational research

Resource type: Video

Annotating data using next generation biobanking ontology (NGBO)

This video explains why we need data standardization and how to annotate data using next generation biobanking ontology (NGBO).

This video is part of the CINECA online training series, where you can learn about concepts and tools relevant to federated analysis of cohort data.

Scientific topics: Ontology and terminology, Data integration and warehousing

Keywords: Standards, Ontologies, Data Integration, data harmonization, Standardised vocabulary

Resource type: Video

Applying data standards to the harmonization of COVID-19 datasets from different sources

This video describes how public health genomics has played a key role in international responses to the COVID-19 pandemic, and how data standards are being used to harmonize data across jurisdictions for Canadian COVID-19 surveillance and outbreak investigations.

The video is aimed at anyone...

Scientific topics: Data integration and warehousing

Keywords: Data integration, Standards, Standardised vocabulary, data harmonization, Ontologies

Resource type: Video

Useful ontologies for harmonizing cohort data

This video describes a community of practice for interoperable ontology building called the OBO Foundry, and highlights a number of well curated and maintained ontologies that are useful for annotating cohort data.

The video is aimed at anyone interested in data standardization and/or the...

Scientific topics: Ontology and terminology, Data management, Data integration and warehousing

Keywords: Ontologies, Cohort data, data annotation

Resource type: Video

Status Update Code of Conduct: Teaming up & Talking about it

Committed to the drafting of a Code of Conduct for the sector of health research according to Art. 40 GDPR, our initiative is advancing slowly but steadily. Throughout Europe, national jurisdictions differ to a great deal in their interpretations of the GDPR, especially in regard to its...

Keywords: GDPR, Healthcare research, data harmonization

Resource type: Video

Annotating data using ontologies

This video highlights examples of tools and ontologies which can be used for annotating health data, and how ontologies help to support data ecosystems.

Scientific topics: Ontology and terminology, Data integration and warehousing, Data management

Keywords: Ontologies, Annotation, Data integration

Resource type: Video

Solutions for overcoming cohort data integration challenges using ontology: an introduction

Ontologies are collections of well-defined, hierarchical, controlled vocabulary, linked by logical relationships. This video introduces the concept and benefits of implementing ontologies for solving data integration issues when data is generated by different research groups.

Scientific topics: Data management, Data integration and warehousing, Ontology and terminology

Keywords: Ontologies, Data integration, Annotation

Resource type: Video

Data harmonization and enrichment using EMBL-EBI ontology tools

This video explains how the Zooma annotation tool, the OxO mapping service and the Ontology Lookup Service (OLS) can be used to harmonise and enrich biological and biomedical data.
The EMBL-EBI Ontology Tools can be used by both biological curators and software developers. Biological curators...

Scientific topics: Ontology and terminology, Data submission, annotation, and curation, Data management

Keywords: CINECA, data harmonization, Annotation, Ontologies

Resource type: Video

Introducing Bivi.co

Introduction to the Bivi community presented as the introductory talk at the 1st Bivi Annual Meeting.
Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations

Resource type: Video

Jalview

Dr James Proctor of the University of Dundee discusses the Jalview tool in the Vis Tools & Bio Challenges session of the 1st BiVi Annual Meeting
Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Genome, Molecular, Phylogenetics

Resource type: Poster, Video

Validation and Visualisation of Electron Microscopy Density Fits

Poster presentation by Dr Maya Topf at 1st BiVi Annual Meeting in 2014
Created at: 1st BiVi Annual Meeting.

Resource type: Poster

BiVi Genomes theme

Prof David Burt introduces the Genomes theme in bio-visualisation.
Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics

Resource type: Video

Visualization of Epigenetic Data

Esther Rheinbay (http://csb.mgh.harvard.edu/bradley_bernstein) talks about the current challenges of visualizing rapidly expanding epigenetic data and showcases some of the different tools which are available to researchers as part of the Integrative Genome Viewer...

Keywords: Genome, Molecular

Resource type: Video

Keynote on Visual Analytics & Human/Computer Interfaces

Sara Irina Fabrikant discusses how analysis of scientific data can be enhanced using information visualization, visual analytics, cognition principles, and graphical user interface design. She focuses on the use of evaluation to valid visualization approaches. This talk was presented at VIZBI...

Keywords: Information visualisation

Resource type: Video

Epigenome Browser

Ting Wang (http://wang.wustl.edu/) addresses many of the challenges of navigating the complexity of genomic data and showcases the WashU Epigenome Browser that he is developing. The browser aims to give investigators maximum flexibility to explore and navigate the available genomic data in...

Keywords: Genome, Molecular

Resource type: Slideshow, Video

Browsing 3D Genomes

Jim Zheng (http://www.uthouston.edu/sbmi/faculty-and-staff/jim-zheng.htm) talks about the importance of understanding the 3D structure of genome and gives an introduction into Genome3D framework (http://www.genome3d.org/) which allows integration of multi-scale structural and genomic data within...

Keywords: Genome, Molecular

Resource type: Video

enRoute: BioVis Best Paper

Alexander Lex (http://alexander-lex.com/) talks about enRoute, a tool for dynamic path extraction from biological pathway maps for in-depth experimental data analysis. He highlights the inherent problem with correlating real-life heterogeneous data to pathways, namely that they rarely follow the...

Scientific topics: Pathway or network

Keywords: Pathway

Resource type: Video

Visualizing RNA Structures and Alignments

Paul Gardner (http://www.biol.canterbury.ac.nz/people/gardner.shtml) talks about the challenges of visualization of RNA Structures and Alignments in the context of Rfam database (http://rfam.sanger.ac.uk/), a collection of non-coding RNAs, structured cis-regulatory elements and self-splicing...

Keywords: Genome, Molecular

Resource type: Video

Non-coding RNA

Gisela Storz (http://irp.nih.gov/pi/gisela-storz) talks about the reliability and co-relation of anti-sense RNA sequence data. Comparison of RNA seq data across different experiments and from various sources reveals some discrepancies and lack of overlap. While the majority of RNA seq data is...

Keywords: Genome, Molecular

Resource type: Video

Visualizing Protein Structures and Features

Sean O'Donoghue (http://odonoghuelab.org) talks about molecular spatial data and the emerging issue of sequence-structure gap mainly due to experimental difficulties in obtaining reliable (or any) structure information for a given protein. In his talk, he also gives a brief demonstration of...

Keywords: Molecular

Resource type: Video

RNA-Seq

Cole Trapnell (http://www.broadinstitute.org/~cole/) focuses on isoform-resolution analysis of RNA -seq. RNA-seq is an assay used to determine the abundance of RNA transcripts in a transcriptome, the results of which can be used for gene discovery and expression analysis. In his talk Cole...

Keywords: Genome

Resource type: Video

Comparison and assemblies

Thomas Ferrin (http://www.cgl.ucsf.edu/home/tef/) talks about visualization tools for interactive modeling of biological structures with an emphasis on Chimera (http://www.cgl.ucsf.edu/chimera/), an extensible molecular modeling software.This talk was presented at VIZBI 2013, an international...

Keywords: Molecular

Resource type: Video

Evolution of Protein Structure and Function

Ian Sillitoe (http://orengogroup.info/) talks about the protein structure classification with particular emphasis on superfamily-centric taxonomy which is used in the CATH (http://www.cathdb.info/) database.This video was filmed and distributed with permission under a Creative Commons...

Keywords: Molecular

Resource type: Video

Visualizing odors with insect brains

Martin Strauch presents a brief overview of his BioVis 2012 Honorable Mention paper on visualising odors with insect brains.This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.

Keywords: Anatomy Physiology and Atlases

Resource type: Video