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Keywords: Exploratory-analysis  or metagenomics  or Cells and Organisms  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
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
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
Visualization of NGS data with IGV

Visualisation of next-gen sequencing data with Integrative Genomics Viewer

Keywords: Data visualization, Genomics, NGS

Visualization of NGS data with IGV https://tess.elixir-europe.org/materials/visualization-of-ngs-data-with-igv Visualisation of next-gen sequencing data with Integrative Genomics Viewer Data visualization, Genomics, NGS
Differential gene expression analysis : Practical part

RNA-seq: Differential gene expression analysis practical session

Keywords: Genomics, RNA-seq

Differential gene expression analysis : Practical part https://tess.elixir-europe.org/materials/differential-gene-expression-analysis-practical-part RNA-seq: Differential gene expression analysis practical session Genomics, RNA-seq
RNA-seq: Differential gene expression analysis

Transcriptome analysis provides information about the identity and quantity of all RNA molecules

Keywords: Genomics, RNA-seq

RNA-seq: Differential gene expression analysis https://tess.elixir-europe.org/materials/rna-seq-differential-gene-expression-analysis Transcriptome analysis provides information about the identity and quantity of all RNA molecules Genomics, RNA-seq