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Keywords: Exploratory-analysis  or metagenomics  or Populations  or Galaxy 


Galaxy Proteomics workshop Prague 2018

Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic

Scientific topics: Proteomics

Keywords: Galaxy, training, proteomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

Galaxy Proteomics workshop Prague 2018 https://tess.elixir-europe.org/materials/galaxy-proteomics-workshop-prague-2018 Materials from the ELIXIR workshop “Galaxy Proteomics workshop Prague 2018”, Oct 4-5 2018 at the IOCB, Prague, Czech Republic Andrea Argentini Frederik Coppens Pavel Dvorak Matthias Fahrner Melanie Foell Björn Grüning Martin Hubalek Hana Pergl Sustkova Marek Vrbacky Proteomics Galaxy, training, proteomics, eLearning, EeLP life scientists Researchers PhD Students
ELIXIR TtR course: Basic genomics using advanced analysis tools

Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia

Scientific topics: Genomics

Keywords: Galaxy, training, Genomics, eLearning, EeLP

Resource type: course materials, Training materials, Slides

ELIXIR TtR course: Basic genomics using advanced analysis tools https://tess.elixir-europe.org/materials/elixir-ttr-course-basic-genomics-using-advanced-analysis-tools Materials from the ELIXIR workshop “ELIXIR TtR course: Basic genomics using advanced analysis tools”, Nov 5-6 2018 at the University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia Christophe Antoniewski Olivier Inizan Genomics Galaxy, training, Genomics, eLearning, EeLP life scientists beginner bioinformaticians Postgraduate students
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

Introducing Bivi.co https://tess.elixir-europe.org/materials/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. Prof. Jessie Kennedy Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations 2016-12-08
Infectious Disease Host/Pathogen Relationships

Bruno Sobral demonstrates how collaboration with the bench scientists to learn about their needs, uses and challenges can lead to design of more effective resources for data exploration and analysis. He emphasises the importance of designing in a user-centric manner and highlights the importance...

Keywords: Populations, HCI

Resource type: Video

Infectious Disease Host/Pathogen Relationships https://tess.elixir-europe.org/materials/infectious-disease-host-pathogen-relationships Bruno Sobral demonstrates how collaboration with the bench scientists to learn about their needs, uses and challenges can lead to design of more effective resources for data exploration and analysis. He emphasises the importance of designing in a user-centric manner and highlights the importance of human-computer interface professionals in the design process.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Populations, HCI 2017-01-31
Metagenomics

Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community. She notes that there are some good analysis tools available for analysis at the 16S sequence and unassembled metagenome level, but more effort into...

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics, Populations

Resource type: Video

Metagenomics https://tess.elixir-europe.org/materials/metagenomics-6625dde2-a7da-4cc2-a51d-14c1c31b51b2 Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community. She notes that there are some good analysis tools available for analysis at the 16S sequence and unassembled metagenome level, but more effort into analysis and visualisation solutions are required at the microbial community and ecosystem level.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Phylogenetics Genome, Phylogenetics, Populations 2017-01-31
Geographic & Evolutionary Visualization

Daniel Janies showcases SupraMap, a web-based app that integrates genetic sequences of pathogens with geographic data points to map the spread of diseases and track mutations.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013.

Scientific topics: Phylogenetics

Keywords: Phylogenetics, Populations

Resource type: Video

Geographic & Evolutionary Visualization https://tess.elixir-europe.org/materials/geographic-amp-evolutionary-visualization Daniel Janies showcases SupraMap, a web-based app that integrates genetic sequences of pathogens with geographic data points to map the spread of diseases and track mutations.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Phylogenetics Phylogenetics, Populations 2017-01-31
BBSRC: Data and Data Visualisation

Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014. 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, Information visualisation

Resource type: Video

BBSRC: Data and Data Visualisation https://tess.elixir-europe.org/materials/bbsrc-data-and-data-visualisation Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting. Michael Ball Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation 2017-02-01
Evaluation of Helium: Visualisation of Large Scale Plant Pedigrees

Poster presentation at 1st BiVi in 2014 regarding the user evaluation of the Helium visualisaiton tool. Created at: 1st BiVi Annual Meeting.

Keywords: Genome, Populations, HCI

Resource type: Poster

Evaluation of Helium: Visualisation of Large Scale Plant Pedigrees https://tess.elixir-europe.org/materials/evaluation-of-helium-visualisation-of-large-scale-plant-pedigrees Poster presentation at 1st BiVi in 2014 regarding the user evaluation of the Helium visualisaiton tool. Created at: 1st BiVi Annual Meeting. Dr. Paul Shaw Genome, Populations, HCI 2017-02-02
Art and Science: A partnership catalyzing discovery in biomedicine

A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our...

Scientific topics: Phylogenetics, Pathway or network

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

Resource type: Video

Art and Science: A partnership catalyzing discovery in biomedicine https://tess.elixir-europe.org/materials/art-and-science-a-partnership-catalyzing-discovery-in-biomedicine A 3rd BiVi 2017 Keynote Presentation by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of MedicineChaired by: Geoff BartonThe data generated by the biomedical research community hold tremendous potential to inform our understanding and treatment of disease. The challenge is to ensure that technical and non-technical researchers can access, use and learn from this wealth of data and analytical resources. Bang will present examples of solutions developed at the Broad Institute that draw on art and design to enable scientific discovery.Bang Wong is the creative director of the Broad Institute of MIT & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at the Johns Hopkins University School of Medicine. His work focuses on the design and development of computation-visualization tools to meet the analytical challenges of research data. He leads the data visualization initiative at the Broad and is the founding author of Points of View published by Nature Methods, a series of articles that focus on the fundamental aspects of data presentation in science. Created at: 3rd BiVi Annual Meeting (2017). Bang Wong Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation 2017-05-12
Visualising dynamic genetics in human populations

Genetic and environmental variation affect all complex human traits and disorders. Recent large-scale genome-wide association studies have identified some of the specific genetic variants, and we often assume these associations will hold true irrespective of context. However, our research shows...

Keywords: Populations

Resource type: Video

Visualising dynamic genetics in human populations https://tess.elixir-europe.org/materials/visualising-dynamic-genetics-in-human-populations Genetic and environmental variation affect all complex human traits and disorders. Recent large-scale genome-wide association studies have identified some of the specific genetic variants, and we often assume these associations will hold true irrespective of context. However, our research shows that the relationship between genotype and phenotype can change across a lifetime or in different environments. For example, some genetic variants may have larger effects in adulthood or in the centre of cities. Data visualisation plays a vital role in bringing researchers together across disciplines to understand these dynamic patterns of gene-environment interaction. Created at: 3rd BiVi Annual Meeting (2017). Oliver Davis Populations 2017-05-15
PhenoMeNal: accessing metabolomics workflows in Galaxy

A description of PhenoMeNal and when to use it, the creation of a cloud research environment and how to access Galaxy workflows via PhenoMeNal.

Scientific topics: Chemical biology, Metabolomics

Keywords: Galaxy

PhenoMeNal: accessing metabolomics workflows in Galaxy https://tess.elixir-europe.org/materials/phenomenal-accessing-metabolomics-workflows-in-galaxy A description of PhenoMeNal and when to use it, the creation of a cloud research environment and how to access Galaxy workflows via PhenoMeNal. Chemical biology Metabolomics Galaxy Beginners
Exercices on Galaxy: metagenomics

Find Rapidly OTU with Galaxy Solution

Keywords: Galaxy, Metagenomics

Exercices on Galaxy: metagenomics https://tess.elixir-europe.org/materials/exercices-on-galaxy-metagenomics Find Rapidly OTU with Galaxy Solution Galaxy, Metagenomics
ToolShed upload and tool-iuc PR

Questions What is a Tool Shed? How to install tools and workflows from a Tool Shed into a Galaxy instance? What are the Tool Shed repository types? How to publish with Planemo? Objectives Discover what is a Tool Shed Be able to install tools and workflows from a Tool Shed into a...

Keywords: Galaxy

ToolShed upload and tool-iuc PR https://tess.elixir-europe.org/materials/toolshed-upload-and-tool-iuc-pr Questions What is a Tool Shed? How to install tools and workflows from a Tool Shed into a Galaxy instance? What are the Tool Shed repository types? How to publish with Planemo? Objectives Discover what is a Tool Shed Be able to install tools and workflows from a Tool Shed into a Galaxy instance Be able to publish tools with Planemo Galaxy
BioBlend API

BioBlend module, a python library to use Galaxy API

Keywords: API, Galaxy, Python

BioBlend API https://tess.elixir-europe.org/materials/bioblend-api BioBlend module, a python library to use Galaxy API API, Galaxy, Python
Galaxy Configuration Hierarchy

How to configure your local instance of Galaxy

Keywords: Galaxy

Galaxy Configuration Hierarchy https://tess.elixir-europe.org/materials/galaxy-configuration-hierarchy How to configure your local instance of Galaxy Galaxy
Galaxy Visualisation - Slides

Questions How can visualization plugins benefit science? Objectives Implement a first Galaxy visualization Understand the client side vs. server side principle

Keywords: Galaxy

Galaxy Visualisation - Slides https://tess.elixir-europe.org/materials/galaxy-visualisation-slides Questions How can visualization plugins benefit science? Objectives Implement a first Galaxy visualization Understand the client side vs. server side principle Galaxy
Galaxy Interactive Tour

Questions What is a Galaxy Interactive Tour? How to create a Galaxy Interactive Tour? Objectives Discover what is a Galaxy Interactive Tour Be able to create a Galaxy Interactive Tour Be able to add a Galaxy Interactive Tour in a Galaxy instance

Keywords: Galaxy

Galaxy Interactive Tour https://tess.elixir-europe.org/materials/galaxy-interactive-tour Questions What is a Galaxy Interactive Tour? How to create a Galaxy Interactive Tour? Objectives Discover what is a Galaxy Interactive Tour Be able to create a Galaxy Interactive Tour Be able to add a Galaxy Interactive Tour in a Galaxy instance Galaxy
Tool development and integration into Galaxy

Questions: What is a tool for Galaxy? How to build a tool/wrapper with the good practices? How to deal with the tool environment? Objectives: Discover what is a wrapper and its structure Use the Planemo utilities to develop a good wrapper Deal with the dependencies Write functional...

Keywords: Galaxy

Tool development and integration into Galaxy https://tess.elixir-europe.org/materials/tool-development-and-integration-into-galaxy Questions: What is a tool for Galaxy? How to build a tool/wrapper with the good practices? How to deal with the tool environment? Objectives: Discover what is a wrapper and its structure Use the Planemo utilities to develop a good wrapper Deal with the dependencies Write functional tests Make a tool ready for publishing in a ToolShed Galaxy
Galaxy Installation

How to install a local instance of Galaxy

Keywords: Galaxy

Galaxy Installation https://tess.elixir-europe.org/materials/galaxy-installation How to install a local instance of Galaxy Galaxy
Galaxy Handlers

Galaxy is a web application that uses handlers to perform actions. There are two main types of actions that are carried out by handlers: Respond to user requests; These actions are carried out by web handlers Manage the execution of tools; These actions are performed by job handlers. By...

Keywords: Galaxy

Galaxy Handlers https://tess.elixir-europe.org/materials/galaxy-handlers Galaxy is a web application that uses handlers to perform actions. There are two main types of actions that are carried out by handlers: Respond to user requests; These actions are carried out by web handlers Manage the execution of tools; These actions are performed by job handlers. By default, Galaxy is configured to run a single handler that handles both user queries and jobs. Depending on the number of users accessing your Galaxy instance or the number of jobs you need to manage you may need to start web handlers or additional job handlers. Galaxy
Development in Galaxy

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Here, you will find some materials to learn how to contribute to Galaxy project.

Keywords: Galaxy

Development in Galaxy https://tess.elixir-europe.org/materials/development-in-galaxy Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ... Here, you will find some materials to learn how to contribute to Galaxy project. Galaxy
Training on Galaxy : Metagenomics

Find Rapidly OTU with Galaxy Solution

Keywords: Galaxy, Metagenomics

Training on Galaxy : Metagenomics https://tess.elixir-europe.org/materials/training-on-galaxy-metagenomics Find Rapidly OTU with Galaxy Solution Galaxy, Metagenomics
Initiation to Galaxy

DNA-sequence analysis: from raw reads to variants calling within the galaxy environement.

Keywords: DNA Analysis, Galaxy, Variant calling

Initiation to Galaxy https://tess.elixir-europe.org/materials/initiation-to-galaxy DNA-sequence analysis: from raw reads to variants calling within the galaxy environement. DNA Analysis, Galaxy, Variant calling
Docker and Galaxy

Questions Why Docker? What is it? How to use Docker? How to integrate Galaxy in Docker to facilitate its deployment? Objectives Docker basics Galaxy Docker image (usage) Galaxy Docker (internals) Galaxy flavours

Keywords: Docker, Galaxy

Docker and Galaxy https://tess.elixir-europe.org/materials/docker-and-galaxy Questions Why Docker? What is it? How to use Docker? How to integrate Galaxy in Docker to facilitate its deployment? Objectives Docker basics Galaxy Docker image (usage) Galaxy Docker (internals) Galaxy flavours Docker, Galaxy
Galactic Database

How to choose a database for Galaxy and configure it

Keywords: Galaxy

Galactic Database https://tess.elixir-europe.org/materials/galactic-database How to choose a database for Galaxy and configure it Galaxy
Connecting Galaxy to a compute cluster

Problems Running jobs on the Galaxy server negatively impacts Galaxy UI performance Even adding one other host helps Can restart Galaxy without interrupting jobs Solution: Connecter Galaxy to a computing cluster

Keywords: Cluster, Galaxy

Connecting Galaxy to a compute cluster https://tess.elixir-europe.org/materials/connecting-galaxy-to-a-compute-cluster Problems Running jobs on the Galaxy server negatively impacts Galaxy UI performance Even adding one other host helps Can restart Galaxy without interrupting jobs Solution: Connecter Galaxy to a computing cluster Cluster, Galaxy
Users, Groups, and Quotas in Galaxy

How to handle Users, Groups, and Quotas in Galaxy

Keywords: Galaxy

Users, Groups, and Quotas in Galaxy https://tess.elixir-europe.org/materials/users-groups-and-quotas-in-galaxy How to handle Users, Groups, and Quotas in Galaxy Galaxy
Defining and importing genomes, Data Managers into Galaxy

Intro to built in datasets Built in data hierarchy Some problems Data Managers

Keywords: Galaxy

Defining and importing genomes, Data Managers into Galaxy https://tess.elixir-europe.org/materials/defining-and-importing-genomes-data-managers-into-galaxy Intro to built in datasets Built in data hierarchy Some problems Data Managers Galaxy
Galaxy Docker Training Tutorial

Galaxy docker integration Enable Galaxy to use BioContainers (Docker) Galaxy with Docker swarm

Keywords: Docker, Galaxy

Galaxy Docker Training Tutorial https://tess.elixir-europe.org/materials/galaxy-docker-training-tutorial Galaxy docker integration Enable Galaxy to use BioContainers (Docker) Galaxy with Docker swarm Docker, Galaxy
(Proxy) Web Server Choices and Configuration

Installation and configuration of NGiNX for Galaxy

Keywords: Galaxy, NGiNX

(Proxy) Web Server Choices and Configuration https://tess.elixir-europe.org/materials/proxy-web-server-choices-and-configuration Installation and configuration of NGiNX for Galaxy Galaxy, NGiNX