Register training material
9 materials found

Contributors: Prof. Tom Freeman  or Michael Krone  or Jalview Coordinator  or Dr. Nils Gehlenborg  or Vicky Schneider 


Jalview

Dr James Proctor of the University of Dundee discusses the Jalview tool in the Vis Tools & Bio Challenges session of the 1st BiVi Annual Meeting Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Genome, Molecular, Phylogenetics

Resource type: Poster, Video

Jalview https://tess.elixir-europe.org/materials/jalview Dr James Proctor of the University of Dundee discusses the Jalview tool in the Vis Tools & Bio Challenges session of the 1st BiVi Annual Meeting Created at: 1st BiVi Annual Meeting. Dr. Jim Procter Jalview Coordinator Phylogenetics Genome, Molecular, Phylogenetics 2016-12-08
Visualization Approaches for Biomedical Omics Data: Putting It All Together

Dr Nils Gehlenborg gives his keynote at 1st BiVi in 2014. The rapid proliferation of high quality, low cost genome-wide measurement technologies such as whole-genome and transcriptome sequencing, as well as advances in epigenomics and proteomics, are enabling researchers to perform studies that...

Keywords: Genome, Molecular

Resource type: Video

Visualization Approaches for Biomedical Omics Data: Putting It All Together https://tess.elixir-europe.org/materials/visualization-approaches-for-biomedical-omics-data-putting-it-all-together Dr Nils Gehlenborg gives his keynote at 1st BiVi in 2014. The rapid proliferation of high quality, low cost genome-wide measurement technologies such as whole-genome and transcriptome sequencing, as well as advances in epigenomics and proteomics, are enabling researchers to perform studies that generate heterogeneous datasets for cohorts of thousands of individuals. A common feature of these studies is that a collection of genome-wide, molecular data types and phenotypic or clinical characterizations are available for each individual. These data can be used to identify the molecular basis of diseases and to characterize and describe the variations that are relevant for improved diagnosis, prognosis and targeted treatment of patients. An example for a study in which this approach has been successfully applied is The Cancer Genome Atlas project (http://cancergenome.nih.gov).In this talk Dr Gehlenborg discusses how visualization approaches can be applied to enable exploration and support analysis of data generated by such studies. Specifically, he reviews techniques and tools for visual exploration of individual omics data types, their ability to scale to large numbers of individuals or samples, and emerging techniques that integrate multiple omics data types for interactive visual analysis. He also examines technical and legal challenges that developers of such visualization tools are facing. To conclude the talk, he outlines research opportunities for the biological data visualization community that address major challenges in this domain. Created at: 1st BiVi Annual Meeting. Dr. Nils Gehlenborg Genome, Molecular 2017-02-02
BiVi theme: Pathways

Prof Tom Freeman discusses bio-visualisation within the Pathway theme at 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Pathway or network

Keywords: Pathway

Resource type: Video

BiVi theme: Pathways https://tess.elixir-europe.org/materials/bivi-theme-pathways Prof Tom Freeman discusses bio-visualisation within the Pathway theme at 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting. Prof. Tom Freeman Pathway or network Pathway 2017-02-02
Visualization of Biomolecular Structures: State of the Art

Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on...

Keywords: Molecular, Information visualisation

Resource type: Slideshow

Visualization of Biomolecular Structures: State of the Art https://tess.elixir-europe.org/materials/visualization-of-biomolecular-structures-state-of-the-art Structural properties of molecules are of primary concern in many fields. This report provides a comprehensive overview on techniques that have been developed in the fields of molecular graphics and visualization with a focus on applications in structural biology. The field heavily relies on computerized geometric and visual representations of three-dimensional, complex, large, and time-varying molecular structures. The report presents a taxonomy that demonstrates which areas of molecular visualization have already been extensively investigated and where the field is currently heading. It discusses visualizations for molecular structures, strategies for efficient display regarding image quality and frame rate, covers different aspects of level of detail, and reviews visualizations illustrating the dynamic aspects of molecular simulation data. The report concludes with an outlook on promising and important research topics to enable further success in advancing the knowledge about interaction of molecular structures.Categories and Subject Descriptors (according to ACM CCS): I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling-Curve, surface, solid, and object representations Created at: EuroVis 2015. Barbara Kozlikova Michael Krone Molecular, Information visualisation 2017-02-28
NGS overview

This course covers: Sequencing technologies Applications Categories of analysis Sample preparation Potential services in NGS Appendix

Scientific topics: Sequencing, High-throughput sequencing

Keywords: bioinformatics, Australia

NGS overview https://tess.elixir-europe.org/materials/ngs-overview This course covers: Sequencing technologies Applications Categories of analysis Sample preparation Potential services in NGS Appendix Vicky Schneider Sequencing High-throughput sequencing bioinformatics, Australia Biologists
Python Overview

Introduction to Python

Keywords: bioinformatics, Australia

Python Overview https://tess.elixir-europe.org/materials/python-overview Introduction to Python Vicky Schneider bioinformatics, Australia Biologists
Galaxy workflows

This workshop/tutorial will familiarise you with the Galaxy workflow engine. It will cover the following topics: Logging in to the server How to construct and use a workflow by various methods How to share a workflow

Scientific topics: Workflows

Keywords: bioinformatics

Galaxy workflows https://tess.elixir-europe.org/materials/galaxy-workflows This workshop/tutorial will familiarise you with the Galaxy workflow engine. It will cover the following topics: Logging in to the server How to construct and use a workflow by various methods How to share a workflow Vicky Schneider Workflows bioinformatics Biologists
What is GenomeSpace?

GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses...

Keywords: bioinformatics, GVL

What is GenomeSpace? https://tess.elixir-europe.org/materials/what-is-genomespace GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses and visualizations in each of them. The tools retain their native look and feel, with GenomeSpace providing frictionless conduits between them through a lightweight interoperability layer. Vicky Schneider bioinformatics, GVL Biologists
Introduction to Galaxy

Basic Introduction to Galaxy

Keywords: bioinformatics

Introduction to Galaxy https://tess.elixir-europe.org/materials/introduction-to-galaxy Basic Introduction to Galaxy Vicky Schneider bioinformatics Biologists