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68 materials found

Keywords: Exploratory-analysis  or metagenomics  or Cells and Organisms  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
Biological Networks

Scooter Morris (http://www.cgl.ucsf.edu/home/scooter/) talks about the opportunities and challenges in mapping biological networks and gives an brief overview of Cytoscape (http://www.cytoscape.org/), an open source bioinformatics software platform for visualizing molecular interaction...

Scientific topics: Pathway or network

Keywords: Cells and Organisms, Pathway

Resource type: Video

Biological Networks https://tess.elixir-europe.org/materials/biological-networks Scooter Morris (http://www.cgl.ucsf.edu/home/scooter/) talks about the opportunities and challenges in mapping biological networks and gives an brief overview of Cytoscape (http://www.cytoscape.org/), an open source bioinformatics software platform for visualizing molecular interaction networks.(PLEASE NOTE: There is a small formatting problem with the presentation slides for the first 2 min of the talk only). This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Dr. Scooter Morris Pathway or network Cells and Organisms, Pathway 2017-01-31
Cellular Image Data

Peter Sorger (http://sorger.med.harvard.edu/) and Bang Wong (http://bang.clearscience.info/) talk about the challenges of visualising large sets of multidimensional data (e.g. single cell imaging, dose-response assays, multiplex biochemistry etc.).This video was filmed and distributed with...

Keywords: Cells and Organisms

Resource type: Video

Cellular Image Data https://tess.elixir-europe.org/materials/cellular-image-data Peter Sorger (http://sorger.med.harvard.edu/) and Bang Wong (http://bang.clearscience.info/) talk about the challenges of visualising large sets of multidimensional data (e.g. single cell imaging, dose-response assays, multiplex biochemistry etc.).This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Bang Wong Cells and Organisms 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
Cell lineage visualisation

Dr A J Pretorius discusses Cell-o-pane, a cell lineage visulaisation tool at 1st BiVi in 2014. As assoicated poster also presented a the meeting is included. Created at: 1st BiVi Annual Meeting.

Keywords: Cells and Organisms, Molecular

Resource type: Video

Cell lineage visualisation https://tess.elixir-europe.org/materials/cell-lineage-visualisation Dr A J Pretorius discusses Cell-o-pane, a cell lineage visulaisation tool at 1st BiVi in 2014. As assoicated poster also presented a the meeting is included. Created at: 1st BiVi Annual Meeting. Dr. A.J. Pretorius Cells and Organisms, Molecular 2017-02-01
BioLayout Express 3D

Derek Wright discusses the BioLayout Express visualisation tool at 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Pathway or network

Keywords: Cells and Organisms, Genome, Pathway

Resource type: Video

BioLayout Express 3D https://tess.elixir-europe.org/materials/biolayout-express-3d Derek Wright discusses the BioLayout Express visualisation tool at 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting. Derek Wright Pathway or network Cells and Organisms, Genome, Pathway 2017-02-02
Zegami: A tool for image data exploration

Stephen Taylor discusses the Zegami visualisation tool at 1st BiVi in 2014. An associated poster is also available. Created at: 1st BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome

Resource type: Poster, Video

Zegami: A tool for image data exploration https://tess.elixir-europe.org/materials/zegami-a-tool-for-image-data-exploration Stephen Taylor discusses the Zegami visualisation tool at 1st BiVi in 2014. An associated poster is also available. Created at: 1st BiVi Annual Meeting. Stephen Taylor Anatomy Physiology and Atlases, Cells and Organisms, Genome 2017-02-02
Zegami: Image visualisation, annotation and searching

Stephen Taylor describes and demonstrates Zegami at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome

Resource type: Slideshow

Zegami: Image visualisation, annotation and searching https://tess.elixir-europe.org/materials/zegami-image-visualisation-annotation-and-searching Stephen Taylor describes and demonstrates Zegami at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Stephen Taylor Anatomy Physiology and Atlases, Cells and Organisms, Genome 2017-02-03
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
Zegami: Digital Data Integration, Visualisation and Management

Stephen Taylor discusses Zegami with examples and latest developments at 3rd BiVi in April 2017.Zegami has the potential to do for images what the spreadsheet did for number calculations. It provides a way of manipulating images and derived values (from the images themselves or annotated...

Scientific topics: Database management

Keywords: Cells and Organisms, Databases

Resource type: Video

Zegami: Digital Data Integration, Visualisation and Management https://tess.elixir-europe.org/materials/zegami-digital-data-integration-visualisation-and-management Stephen Taylor discusses Zegami with examples and latest developments at 3rd BiVi in April 2017.Zegami has the potential to do for images what the spreadsheet did for number calculations. It provides a way of manipulating images and derived values (from the images themselves or annotated metadata) on a massive scale allowing querying and organisation of large image based collections. The talk will show various examples of its usage in biology and beyond, and will look at new features such as annotation to build training sets for machine learning. Created at: 3rd BiVi Annual Meeting (2017). Stephen Taylor Database management Cells and Organisms, Databases 2017-05-12
Model organism analysis using Intermine

Poster presented at 3rd BiVi in April 2017.InterMine is an open source data warehouse based in the University of Cambridge. We integrate data from disparate sources and provide a single unified interface, allowing you to access your data via an easy-to-use webapp or API. InterMine has over 30...

Keywords: Cells and Organisms

Resource type: Poster

Model organism analysis using Intermine https://tess.elixir-europe.org/materials/model-organism-analysis-using-intermine Poster presented at 3rd BiVi in April 2017.InterMine is an open source data warehouse based in the University of Cambridge. We integrate data from disparate sources and provide a single unified interface, allowing you to access your data via an easy-to-use webapp or API. InterMine has over 30 different instances worldwide, covering model organisms, plants, mitochondrial DNA, drug targeting, and more.  Created at: 3rd BiVi Annual Meeting (2017). Ms. Yo Yehudi Cells and Organisms 2017-05-30
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 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 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 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
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
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
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