One Health

Recently added tutorials, slides, FAQs, and events in the one-health topic

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🎥 Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

By: Wolfgang Maier

A 55M long recording is now available.

Published: 2024-09-27T00:00:00+00:00
Tags: variant-analysis, covid19, virology, one-health

🎥 Recording of Identification of AMR genes in an assembled bacterial genome

By: Saim Momin

A 26M long recording is now available.

Published: 2024-09-24T00:00:00+00:00
Tags: genome-annotation, gmod, illumina, amr, one-health, jbrowse1, microgalaxy

📰 4th Mycobacterium tuberculosis complex NGS made easy

Tuberculosis (TB) is a big killer in many countries of the world, particularly in those with low and middle income. Next-generation sequencing has been key in improving our understanding of drug resistance acquisition and of transmission of Mycobacterium tuberculosis. Yet, the need for expertise guiding NGS implementation in laboratories and the lack of bioinformatic expertise, are main obstacles hindering the implementation of NGS into TB programs.

Published: 2024-07-08T00:00:00+00:00
Tags: news, NGS, Tuberculosis, Drug-resistance, transmission, evolution, one-health, microbiome

📅 Galaxy Training Academy 2024

The Galaxy Academy is a self-paced online training event for beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we will have a different topic and focus every day.

Published: 2024-06-11T15:07:31+00:00
Tags: event, microbiome, single-cell, proteomics, introduction, galaxy-interface, ecology, assembly, one-health, statistics

🎥 Recording of M. tuberculosis Variant Analysis

By: Peter van Heusden

A 1H17M long recording is now available.

Published: 2024-06-11T00:00:00+00:00
Tags: variant-analysis, prokaryote, one-health, microgalaxy, tuberculosis

📅 Mycobacterium tuberculosis complex NGS made easy

These series of webinars and tutorials aim at improving basic and applied knowledge associated with next-generation sequencing (NGS) technologies and their applications in the field of Tuberculosis (TB).

Published: 2024-06-03T09:32:41+00:00
Tags: event, one-health, tuberculosis, NGS, Galaxy, training, microbiome

📰 Learn to use MINERVA Platform's COVID-19 Disease Map with Galaxy

By: Helena Rasche, Marek Ostaszewski

As part of the work of BeYond COVID, we have developed a new integration between the MINERVA Platform’s COVID-19 Disease Map and Galaxy! Datasets created within Galaxy can now be seamlessly visualized in the MINERVA Platform, allowing you to explore your data in the context of the COVID-19 Disease Map.

Published: 2024-03-28T00:00:00+00:00
Tags: news, by-covid, pathways, minerva, gtn infrastructure, new feature, one-health, transcriptomics

🛤️ Detection of AMR genes in bacterial genomes

This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy.

Published: 2024-01-23T16:20:06+00:00
Tags: learning-pathway, amr, bacteria, microgalaxy, one-health, microbiome

📚 Identification of AMR genes in an assembled bacterial genome

By: Bazante Sanders, Bérénice Batut

Antimicrobial resistance (AMR) is a global phenomenon with no geographical or species boundaries, which poses an important threat to human, animal and environmental health. It is a complex and growing problem that compromises our ability to treat bacterial infections.

Published: 2024-01-23T16:20:06+00:00
Tags: genome-annotation, gmod, illumina, amr, one-health, jbrowse1, microgalaxy

📚 Pox virus genome analysis from tiled-amplicon sequencing data

By: Wolfgang Maier, Tomas Klingström

Pox viruses (Poxviridae) are a large family of viruses, and members of it have various vertebrate and arthropod species as their natural hosts. The most widely known species in the family are the now extinct variola virus from the genus orthopoxvirus as the cause of smallpox, and vaccinia virus, a related, likely horsepox virus, which served as the source for the smallpox vaccine that allowed eradication of that disease.

Published: 2023-05-15T10:22:16+00:00
Tags: variant-analysis, virology, one-health

🎥 Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

By: Wolfgang Maier

A 55M long recording is now available.

Published: 2023-05-10T00:00:00+00:00
Tags: variant-analysis, covid19, virology, one-health

📰 New GTN Feature Tag-based Topics enables new SARS-CoV-2 topic

By: Helena Rasche, Wolfgang Maier

The GTN has long struggled with the rigid hierarchy of a single level of classification: topics. All materials had to be organised into a single topic, even when their contents sometimes spanned multiple topics! We added subtopics a while back to help further organise these tutorials, but that still did not solve the issue of needing to collect multiple learn materials in a single location for people to access.

Published: 2023-01-23T00:00:00+00:00
Tags: news, new topic, new feature, one-health

📚 Avian influenza viral strain analysis from gene segment sequencing data

By: Wolfgang Maier

Of the four species of influenza viruses (Influenza A-D), Influenza A is the most virulent in human hosts and subtypes of it have been responsible for all historic flu pandemics.

Published: 2022-11-21T16:45:21+00:00
Tags: variant-analysis, virology, one-health

📚 Tree thinking for tuberculosis evolution and epidemiology

By: Christoph Stritt, Daniela Brites, Galo A. Goig

Published: 2022-03-16T10:37:17+00:00
Tags: evolution, prokaryote, one-health, phylogenetics, microgalaxy

📚 Identifying tuberculosis transmission links: from SNPs to transmission clusters

By: Galo A. Goig, Daniela Brites, Christoph Stritt

In a disease outbreak situation, to understand the dynamics and the size of the outbreak, it is essential to detect transmission clusters to distinguish likely outbreak cases from unrelated background cases. Such detection is nowadays often based on actual sequencing data that enables quantitative conclusions about differences between pathogen isolates.

Published: 2022-03-16T08:35:43+00:00
Tags: evolution, prokaryote, one-health, microgalaxy

🎥 Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

By: Wolfgang Maier

A 1H30M long recording is now available.

Published: 2021-08-09T00:00:00+00:00
Tags: variant-analysis, covid19, virology, one-health

📚 Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

By: Wolfgang Maier, Bérénice Batut

Sequence-based monitoring of global infectious disease crises, such as the COVID-19 pandemic, requires capacity to generate and analyze large volumes of sequencing data in near real time. These data have proven essential for surveilling the emergence and spread of new viral variants, and for understanding the evolutionary dynamics of the virus.

Published: 2021-06-30T06:20:05+00:00
Tags: variant-analysis, covid19, virology, one-health

📰 New Tutorial: Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

By: Bérénice Batut, Wolfgang Maier

Effectively monitoring global infectious disease crises, such as the COVID-19 pandemic, requires capacity to generate and analyze large volumes of sequencing data in near real time. These data have proven essential for monitoring the emergence and spread of new variants, and for understanding the evolutionary dynamics of the virus.

Published: 2021-06-30T00:00:00+00:00
Tags: news, new tutorial, variant-analysis, covid-19, one-health

🎥 Recording of M. tuberculosis Variant Analysis

By: Peter van Heusden

A 40M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: variant-analysis, prokaryote, one-health, microgalaxy, tuberculosis

🎥 Recording of From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis

By: Anton Nekrutenko

A 15M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: variant-analysis, covid19, virology, one-health

📚 M. tuberculosis Variant Analysis

By: Peter van Heusden, Simon Gladman, Thoba Lose

Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, in 2018 there were 10.0 million new cases of TB worldwide and 1.4 million deaths due to the disease, making TB the world’s most deadly infectious disease. The publication of the genome of M. tuberculosis H37Rv in 1998 gave researchers a powerful new tool for understanding this pathogen. This genome has been revised since then, with the latest version being available

Published: 2020-07-25T20:58:54+00:00
Tags: variant-analysis, prokaryote, one-health, microgalaxy, tuberculosis

📚 From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis

The aim of this tutorial is twofold:

Published: 2020-06-24T15:38:29+00:00
Tags: variant-analysis, covid19, virology, one-health

📚 Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring

By: Simon Bray

This tutorial provides a companion to the work performed in March 2020 by InformaticsMatters, the Diamond Light Source, and the European Galaxy Team to perform virtual screening on candidate ligands for the SARS-CoV-2 main protease (MPro). This work is described in our dedicated site.

Published: 2020-03-27T13:26:13+00:00
Tags: computational-chemistry, covid19, one-health