Register training material
32 materials found

Content provider: Coursera  or CINECA PROJECT 


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

Access Bioinformatics Databases with Biopython

In this 1-hour long project-based course, you will learn how to access, parse, and visualize data from various bioinformatics sequence and structural online databases such as ENTREZ, PDB, KEGG and NCBI using Biopython.
You will also interact with various bioinformatics file formats such as FASTA,...

Keywords: data-science, life-sciences, data-analysis, health-informatics

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

Bacterial Bioinformatics

This course provides demonstrations and exercises for performing common genomics-based analysis tasks of bacterial sequence data. It uses PATRIC, the PathoSystems Resource Integration Center, as the platform for analysis. PATRIC is the NIH/NIAID-funded bacterial Bioinformatics Resource Center,...

Keywords: life-sciences, health-informatics, research

Plant Bioinformatics Capstone

The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply...

Keywords: physical-science-and-engineering, life-sciences, research-methods, basic-science

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

Research Data Management and Sharing

This course will provide learners with an introduction to research data management and sharing. After completing this course, learners will understand the diversity of data and their management needs across the research data lifecycle, be able to identify the components of good data management...

Scientific topics: Data management

Resource type: e-learning

Plant Bioinformatics

The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply...

Keywords: life-sciences, physical-science-and-engineering, health-informatics, research-methods

Big Data, Genes, and Medicine

This course distills for you expert knowledge and skills mastered by professionals in Health Big Data Science and Bioinformatics. You will learn exciting facts about the human body biology and chemistry, genetics, and medicine that will be intertwined with the science of Big Data and skills to...

Keywords: life-sciences, computer-science, bioinformatics, algorithms

Bioinformatics: Life Sciences on Your Computer

What makes bioinformatics education exciting is that people of a variety of education levels can get started quickly, with just a computer and internet access.

Keywords: life-sciences, bioinformatics

Bioinformatic Methods II

Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful...

Keywords: life-sciences, bioinformatics

Bioinformatics Capstone: Big Data in Biology

In this course, you will learn how to use the BaseSpace cloud platform developed by Illumina (our industry partner) to apply several standard bioinformatics software approaches to real biological data.

In particular, in a series of Application Challenges will see how genome assembly can be used...

Keywords: life-sciences, computer-science, health-informatics, algorithms

Bioinformatics: Introduction and Methods 生物信息学: 导论与方法

A big welcome to “Bioinformatics: Introduction and Methods” from Peking University! In this MOOC you will become familiar with the concepts and computational methods in the exciting interdisciplinary field of bioinformatics and their applications in biology, the knowledge and skills in...

Keywords: life-sciences, health-informatics

Finding Hidden Messages in DNA (Bioinformatics I)

Named a top 50 MOOC of all time by Class Central!

This course begins a series of classes illustrating the power of computing in modern biology. Please join us on the frontier of bioinformatics to look for hidden messages in DNA without ever needing to put on a lab coat.

In the first half of the...

Keywords: life-sciences, computer-science, health-informatics, algorithms

Finding Mutations in DNA and Proteins (Bioinformatics VI)

In previous courses in the Specialization, we have discussed how to sequence and compare genomes. This course will cover advanced topics in finding mutations lurking within DNA and proteins.

In the first half of the course, we would like to ask how an individual's genome differs from the...

Keywords: life-sciences, computer-science, health-informatics, algorithms

Genome Sequencing (Bioinformatics II)

You may have heard a lot about genome sequencing and its potential to usher in an era of personalized medicine, but what does it mean to sequence a genome?

Biologists still cannot read the nucleotides of an entire genome as you would read a book from beginning to end. However, they can read...

Keywords: life-sciences, computer-science, health-informatics, algorithms

Bioinformatic Methods I

Large-scale biology projects such as the sequencing of the human genome and gene expression surveys using RNA-seq, microarrays and other technologies have created a wealth of data for biologists. However, the challenge facing scientists is analyzing and even accessing these data to extract useful...

Keywords: life-sciences, bioinformatics

Biology Meets Programming: Bioinformatics for Beginners

Are you interested in learning how to program (in Python) within a scientific setting?

This course will cover algorithms for solving various biological problems along with a handful of programming challenges helping you implement these algorithms in Python. It offers a gently-paced introduction...

Keywords: life-sciences, computer-science, health-informatics, software-development

Genomic Data Science and Clustering (Bioinformatics V)

How do we infer which genes orchestrate various processes in the cell? How did humans migrate out of Africa and spread around the world? In this class, we will see that these two seemingly different questions can be addressed using similar algorithmic and machine learning techniques arising from...

Keywords: life-sciences, computer-science, health-informatics, algorithms