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Keywords: Exploratory-analysis  or metagenomics  or Anatomy Physiology and Atlases  or Genomics 


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
Visualizing odors with insect brains

Martin Strauch presents a brief overview of his BioVis 2012 Honorable Mention paper on visualising odors with insect brains.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013.

Keywords: Anatomy Physiology and Atlases

Resource type: Video

Visualizing odors with insect brains https://tess.elixir-europe.org/materials/visualizing-odors-with-insect-brains Martin Strauch presents a brief overview of his BioVis 2012 Honorable Mention paper on visualising odors with insect brains.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Martin Strauch Anatomy Physiology and Atlases 2017-01-31
Developmental Anatomy

Sean Megason (http://megason.med.harvard.edu/) talks about the challenges and caveats of multiscale imaging, visualisation and analysis and highlights some of the tools that are used for processing and analysis of in toto imaging such as GoFigure2 (http://www.gofigure2.org/) and ACME...

Keywords: Anatomy Physiology and Atlases

Resource type: Video

Developmental Anatomy https://tess.elixir-europe.org/materials/developmental-anatomy Sean Megason (http://megason.med.harvard.edu/) talks about the challenges and caveats of multiscale imaging, visualisation and analysis and highlights some of the tools that are used for processing and analysis of in toto imaging such as GoFigure2 (http://www.gofigure2.org/) and ACME (https://wiki.med.harvard.edu/SysBio/Megason/ACME).  This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Anatomy Physiology and Atlases 2017-01-31
Physiology & Function

Daniel Haehn talks about visualising medical and scientific data (such as MRI and CT scans, microscopy scan stacks etc.) in 3D and introduces some of the open-source tools available.This video was filmed and distributed with permission under a Creative Common license. Created at: VIZBI 2013.

Keywords: Anatomy Physiology and Atlases

Resource type: Video

Physiology & Function https://tess.elixir-europe.org/materials/physiology-amp-function Daniel Haehn talks about visualising medical and scientific data (such as MRI and CT scans, microscopy scan stacks etc.) in 3D and introduces some of the open-source tools available.This video was filmed and distributed with permission under a Creative Common license. Created at: VIZBI 2013. Anatomy Physiology and Atlases 2017-01-31
Genes into Geometry

Mark Henkelman gives an introduction on the use of 3D imaging in neuroanatomy to explore consequences of genetic alterations on anatomical structures and infer function.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013.

Keywords: Anatomy Physiology and Atlases

Resource type: Video

Genes into Geometry https://tess.elixir-europe.org/materials/genes-into-geometry Mark Henkelman gives an introduction on the use of 3D imaging in neuroanatomy to explore consequences of genetic alterations on anatomical structures and infer function.This video was filmed and distributed with permission under a Creative Commons license. Created at: VIZBI 2013. Anatomy Physiology and Atlases 2017-01-31
BiVi theme: Anatomy, Physiology and Atlases

Prof Richard Baldock discusses bio-visualisation within the Anatomy, Physiology and Atlases theme Created at: 1st BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases

Resource type: Video

BiVi theme: Anatomy, Physiology and Atlases https://tess.elixir-europe.org/materials/bivi-theme-anatomy-physiology-and-atlases Prof Richard Baldock discusses bio-visualisation within the Anatomy, Physiology and Atlases theme Created at: 1st BiVi Annual Meeting. Prof. Richard Baldock Anatomy Physiology and Atlases 2017-02-01
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
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
BiVi theme: Anatomy, Physiology and Atlases 2015

Richard Baldock and Bernard de Bono introduce session on bio-visualisation in Anatomy, Physiology and Atlases at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases

Resource type: Slideshow

BiVi theme: Anatomy, Physiology and Atlases 2015 https://tess.elixir-europe.org/materials/bivi-theme-anatomy-physiology-and-atlases-2015 Richard Baldock and Bernard de Bono introduce session on bio-visualisation in Anatomy, Physiology and Atlases at 2nd BiVi in 2015. Created at: 2nd BiVi Annual Meeting. Prof. Richard Baldock Anatomy Physiology and Atlases 2017-02-03
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
MARender: A Simple JavaScript Library for Biomedical Visualisation

Bill Hill and Richard Baldock describe MARender, a simple JavaScipt library for biomedical visualisation at 2nd BiVi in 2015.  Created at: 2nd BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases, Information visualisation

Resource type: Slideshow

MARender: A Simple JavaScript Library for Biomedical Visualisation https://tess.elixir-europe.org/materials/marender-a-simple-javascript-library-for-biomedical-visualisation Bill Hill and Richard Baldock describe MARender, a simple JavaScipt library for biomedical visualisation at 2nd BiVi in 2015.  Created at: 2nd BiVi Annual Meeting. Mr. William Edward Hill Anatomy Physiology and Atlases, Information visualisation 2017-02-03
BioJS

Dr Manuel Corpas discusses the BioJS Javascript component library at the 1st BiVi Annual Meeting in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Genome, Molecular, Pathway, Phylogenetics

Resource type: Video

BioJS https://tess.elixir-europe.org/materials/biojs-6f4125d4-aca1-407d-b0c7-02345f3b3900 Dr Manuel Corpas discusses the BioJS Javascript component library at the 1st BiVi Annual Meeting in 2014. Created at: 1st BiVi Annual Meeting. Dr. Manuel Corpas Phylogenetics Pathway or network Anatomy Physiology and Atlases, Genome, Molecular, Pathway, Phylogenetics 2016-12-08
ApiNATOMY visualisation of multiscale physiology circuitboards

Bernard de Bono presents a talk on using ApiNATOMY for the visualisation of multiscale physiology circuitboards at 3rd BiVi Annual Meeting in April 2017. Created at: 3rd BiVi Annual Meeting (2017).

Keywords: Anatomy Physiology and Atlases

Resource type: Video

ApiNATOMY visualisation of multiscale physiology circuitboards https://tess.elixir-europe.org/materials/apinatomy-visualisation-of-multiscale-physiology-circuitboards Bernard de Bono presents a talk on using ApiNATOMY for the visualisation of multiscale physiology circuitboards at 3rd BiVi Annual Meeting in April 2017. Created at: 3rd BiVi Annual Meeting (2017). Dr. Bernard de Bono Anatomy Physiology and Atlases 2017-05-12
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
Galaxy: Initiation II

Galaxy II: common tools, quality control; alignment; data managment

Keywords: Genomics

Galaxy: Initiation II https://tess.elixir-europe.org/materials/galaxy-initiation-ii Galaxy II: common tools, quality control; alignment; data managment Genomics
Differential analysis of RNA-Seq data

Design, describe, explore and model

Keywords: Genomics, RNA-seq

Differential analysis of RNA-Seq data https://tess.elixir-europe.org/materials/differential-analysis-of-rna-seq-data Design, describe, explore and model Genomics, RNA-seq
DNA-seq analysis: From raw reads to processed alignments

Objectives: Mapping the DNA-seq data to the reference genome Process the alignments for the variant calling

Keywords: Alignment, DNA-seq, Genomics, Variant calling

DNA-seq analysis: From raw reads to processed alignments https://tess.elixir-europe.org/materials/dna-seq-analysis-from-raw-reads-to-processed-alignments Objectives: Mapping the DNA-seq data to the reference genome Process the alignments for the variant calling Alignment, DNA-seq, Genomics, Variant calling
Variants: alignment and pre-treatment; GATK

Variant calling practical session

Keywords: Genomics

Variants: alignment and pre-treatment; GATK https://tess.elixir-europe.org/materials/variants-alignment-and-pre-treatment-gatk-d2d0443e-60d2-48f0-bbec-53b94eb5b003 Variant calling practical session Genomics
Third generation sequencing : the revolution of long reads

Introduction on sequencing: available technologies, library types, applications ...

Keywords: Genomics

Third generation sequencing : the revolution of long reads https://tess.elixir-europe.org/materials/third-generation-sequencing-the-revolution-of-long-reads Introduction on sequencing: available technologies, library types, applications ... Genomics
Exploring Microscope Platform

How to use the Microscope Platform to annotate and analyze microbial genomes.

Keywords: Annotation, Genomics, Metabolomics, Microbial evolution, Sequence analysis, Transcriptomics

Exploring Microscope Platform https://tess.elixir-europe.org/materials/exploring-microscope-platform How to use the Microscope Platform to annotate and analyze microbial genomes. Annotation, Genomics, Metabolomics, Microbial evolution, Sequence analysis, Transcriptomics
Variant Filtering

Some use cases : - Extract a subset of variants (localization, type) - Combine variants from several analyses - Compare obtained variants from several data types (RNA ...

Keywords: Genomics

Variant Filtering https://tess.elixir-europe.org/materials/variant-filtering Some use cases : - Extract a subset of variants (localization, type) - Combine variants from several analyses - Compare obtained variants from several data types (RNA ... Genomics
REPET: TEdenovo tutorial

The TEdenovo pipeline follows a philosophy in three first steps: Detection of repeated sequences (potential TE) Clustering of these sequences Generation of consensus sequences for each cluster, representing the ancestral TE

Keywords: Annotation, Genomics

REPET: TEdenovo tutorial https://tess.elixir-europe.org/materials/repet-tedenovo-tutorial The TEdenovo pipeline follows a philosophy in three first steps: Detection of repeated sequences (potential TE) Clustering of these sequences Generation of consensus sequences for each cluster, representing the ancestral TE Annotation, Genomics
NGS data exploration with the MicroScope Platform

Exploring data annotation on the genomics and transcriptomics levels with the MicroScope Platform and its tools

Keywords: Genomics, NGS, RNA-seq, SNP, Transcriptomics

NGS data exploration with the MicroScope Platform https://tess.elixir-europe.org/materials/ngs-data-exploration-with-the-microscope-platform Exploring data annotation on the genomics and transcriptomics levels with the MicroScope Platform and its tools Genomics, NGS, RNA-seq, SNP, Transcriptomics
Variants: alignment and pre-treatment; GATK

Variant calling practical session

Keywords: Genomics

Variants: alignment and pre-treatment; GATK https://tess.elixir-europe.org/materials/variants-alignment-and-pre-treatment-gatk Variant calling practical session Genomics
RGP finder: prediction of Genomic Islands

Prediction of Region of Genomic Plasticity (RGPs) and CoDing Sequences (CDSs) and visualization

Keywords: CDS, Data visualization, Genomics, RGP

RGP finder: prediction of Genomic Islands https://tess.elixir-europe.org/materials/rgp-finder-prediction-of-genomic-islands Prediction of Region of Genomic Plasticity (RGPs) and CoDing Sequences (CDSs) and visualization CDS, Data visualization, Genomics, RGP
PASTEClassifier Tutorial

The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features and similarity to classify TEs ( Hoede C. et al. 2014 )

Keywords: Genomics, Transposons

PASTEClassifier Tutorial https://tess.elixir-europe.org/materials/pasteclassifier-tutorial The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features and similarity to classify TEs ( Hoede C. et al. 2014 ) Genomics, Transposons
Chip-seq Analysis

Quality, normalisation and peak calling

Keywords: Chip-seq, Genomics

Chip-seq Analysis https://tess.elixir-europe.org/materials/chip-seq-analysis Quality, normalisation and peak calling Chip-seq, Genomics
Exploring microbiomes with the MicroScope Platform

This module is separated in different courses: MicroScope: General overview, Keyword search and gene cart functionalities Functional annotation of microbial genomes Functional annotation of microbial genomes: Prediction of enzymatic functions Relational...

Keywords: Annotation, Genomics, Metabolomics, Microbial evolution, Transcriptomics

Exploring microbiomes with the MicroScope Platform https://tess.elixir-europe.org/materials/exploring-microbiomes-with-the-microscope-platform This module is separated in different courses: MicroScope: General overview, Keyword search and gene cart functionalities Functional annotation of microbial genomes Functional annotation of microbial genomes: Prediction of enzymatic functions Relational annotation of bacterial genomes: synteny Automatic functional assignation and expert annotation of genes Relational annotation of bacterial genomes: phylogenetic profiles Relational annotation of bacterial genomes: pan-genome analysis Relational annotation of bacterial genomes: metabolic pathways Syntactic re-annotation of public microbial genomes Syntactic annotation of microbial genomes Annotation, Genomics, Metabolomics, Microbial evolution, Transcriptomics
REPET: TEdannot Tutorial

TEannot is able to annote a genome using DNA sequences library. This library can be a predicted TE library built by TEdenovo

Keywords: Annotation, Genomics

REPET: TEdannot Tutorial https://tess.elixir-europe.org/materials/repet-tedannot-tutorial TEannot is able to annote a genome using DNA sequences library. This library can be a predicted TE library built by TEdenovo Annotation, Genomics