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9 materials found

Contributors: Michael Ball  or Vicky Schneider  or Manimozhiyan Arumugam  or Prof. Marc Streit  or Anatole Chessel 


Introductory image processing on biological images using python.

A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples.

Resource type: Jupyter notebook, PDF

Introductory image processing on biological images using python. https://tess.elixir-europe.org/materials/introductory-image-processing-on-biological-images-using-python A jupyter notebook python practical designed to give students a introduction to opening and processing image files derived from biological samples. Anatole Chessel Volker Baecker Bioimage Analysts Image Analysts Computer Vision scientists bioinformaticians computational scientists Biophysicists Biologists Microscopists Python for Biologists PhD students
Text-mining exercises

Hands-on exercises using a variety of text-mining tools and databases based on text mining, to interpret the results from microbiome studies.

Scientific topics: Data mining, Natural language processing, Metagenomics, Microbial ecology

Text-mining exercises https://tess.elixir-europe.org/materials/text-mining-exercises Hands-on exercises using a variety of text-mining tools and databases based on text mining, to interpret the results from microbiome studies. Manimozhiyan Arumugam Data mining Natural language processing Metagenomics Microbial ecology Bioinformaticians Biologists
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
From Visual Exploration of Biomedical Data to Storytelling and Back Again

A 3rd BiVi 2017 Keynote Presentation by Marc Streit who discusses visual exploration and sharing discoveries with examples from the Caleydo project.Chaired by Tom FreemanThe primary goal of visual data exploration tools is to enable the discovery of new insights. To justify and reproduce...

Keywords: Communication, Information visualisation

Resource type: Video

From Visual Exploration of Biomedical Data to Storytelling and Back Again https://tess.elixir-europe.org/materials/from-visual-exploration-of-biomedical-data-to-storytelling-and-back-again A 3rd BiVi 2017 Keynote Presentation by Marc Streit who discusses visual exploration and sharing discoveries with examples from the Caleydo project.Chaired by Tom FreemanThe primary goal of visual data exploration tools is to enable the discovery of new insights. To justify and reproduce insights, the discovery process needs to be documented and communicated. A common approach to documenting and presenting findings is to capture visualizations as images or videos. Images, however, are insufficient for telling the story of a visual discovery, as they lack full provenance information and context. Videos are difficult to produce and edit, particularly due to the nonlinear nature of the exploration process. Most importantly, however, neither approach provides the opportunity to return to any point in the exploration in order to review the state of the visualization in detail or to conduct additional analyses.In this talk, Marc introduces their efforts to more tightly integrate biomedical data exploration with the presentation of discoveries. Based on provenance data captured during the exploration process, users can extract key steps, add annotations, and author 'Vistories', visual stories based on the history of the exploration. These Vistories can be shared for others to view, but also to retrace and extend the original analysis. Marc demonstrates how such methods can increase the reproducibility of cancer research and drug discovery.The presented work is part of the Caleydo project, which is a long-running collaboration between JKU Linz, Harvard University and the University of Utah.Marc Streit is a tenured Associate Professor at the Institute of Computer Graphics at Johannes Kepler University Linz where he leads the Visual Data Science group. He finished his PhD at the Institute for Computer Graphics and Vision at Graz University of Technology in early 2011 and moved to Linz later that year. In 2012 he was a visiting researcher at the Center for Biomedical Informatics (CBMI) at Harvard Medical School. As part of a Fulbright scholarship for research and lecturing he was a visiting professor at the Visual Computing Group at Harvard Paulson School in 2014. Marc also teaches courses at the Imperial College Business School and Salzburg University of Applied Sciences.His scientific areas of interest include visualization, visual analytics, and biological data visualization, where he is particularly interested in the integrated analysis of large heterogeneous data. Together with his team he develops novel visual analysis tools for cancer research, drug discovery, and other biomedical applications. Most of his research is embedded in the open-source project Caleydo, where he is one of the project leaders and founding-members. Since 2016 he is a CEO of the JKU spin-off company datavisyn.Marc won Best Paper Awards at InfoVis'13, BioVis’12, InfoVis’11, GI’10 and Honorable Mention Awards at EuroVis'16, CHI'14, InfoVis'14 and EuroVis’12. He is a co-author of the Nature Methods Points of View column. In 2013 he co-edited the Special Issue on Visual Analytics in the IEEE Computer journal. Additionally, he actively contributes to the scientific community by serving on the organizing and program committee of several scientific events as well as by acting as a reviewer for high-quality journals and conferences. He was program chair of the IEEE Visualization in Data Science Symposium and papers and now general chair of BioVis, the Symposium on Biological Data Visualization. Created at: 3rd BiVi Annual Meeting (2017). Prof. Marc Streit Communication, Information visualisation 2017-05-15
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