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...

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,...

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...

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...

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...

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...

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...

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...

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.

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...

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...

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...

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,...

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...

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

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.

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...

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...

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...

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...

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.

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...

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...

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...

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...

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...

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...

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...

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...

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...