Register training material
24 materials found

Keywords: Shell  or Cells and Organisms 


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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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 http://tess.elixir-uk.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...

Keywords: Cells and Organisms, Databases

Resource type: Video

Zegami: Digital Data Integration, Visualisation and Management http://tess.elixir-uk.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 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 http://tess.elixir-uk.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
Filename Expansion

Filename Expansion from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/05-expansion.md.

Keywords: Shell

Filename Expansion http://tess.elixir-uk.org/materials/filename-expansion Filename Expansion from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/05-expansion.md. Shell Intermediate
Job Control

Job Control from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/04-job.md.

Keywords: Shell

Job Control http://tess.elixir-uk.org/materials/job-control Job Control from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/04-job.md. Shell Intermediate
Instructor's Guide

Instructor's Guide from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/guide.md.

Keywords: Shell

Instructor's Guide http://tess.elixir-uk.org/materials/instructor-s-guide Instructor's Guide from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/guide.md. Shell Intermediate
Variables

Variables from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/03-var.md.

Keywords: Shell

Variables http://tess.elixir-uk.org/materials/variables Variables from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/03-var.md. Shell Intermediate
Loops

Loops from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/04-loop.md.

Keywords: Shell

Loops http://tess.elixir-uk.org/materials/loops Loops from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/04-loop.md. Shell Novice
Creating Things

Creating Things from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/02-create.md.

Keywords: Shell

Creating Things http://tess.elixir-uk.org/materials/creating-things Creating Things from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/02-create.md. Shell Novice
Shell Scripts

Shell Scripts from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/05-script.md.

Keywords: Shell

Shell Scripts http://tess.elixir-uk.org/materials/shell-scripts Shell Scripts from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/05-script.md. Shell Novice
Pipes and Filters

Pipes and Filters from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/03-pipefilter.md.

Keywords: Shell

Pipes and Filters http://tess.elixir-uk.org/materials/pipes-and-filters Pipes and Filters from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/03-pipefilter.md. Shell Novice
Introducing the Shell

Introducing the Shell from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/00-intro.md.

Keywords: Shell

Introducing the Shell http://tess.elixir-uk.org/materials/introducing-the-shell Introducing the Shell from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/00-intro.md. Shell Novice
Finding Things

Finding Things from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/06-find.md.

Keywords: Shell

Finding Things http://tess.elixir-uk.org/materials/finding-things Finding Things from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/06-find.md. Shell Novice
Files and Directories

Files and Directories from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/01-filedir.md.

Keywords: Shell

Files and Directories http://tess.elixir-uk.org/materials/files-and-directories Files and Directories from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/01-filedir.md. Shell Novice
Permissions

Permissions from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/01-perm.md.

Keywords: Shell

Permissions http://tess.elixir-uk.org/materials/permissions Permissions from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/01-perm.md. Shell Intermediate
Working Remotely

Working Remotely from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/02-ssh.md.

Keywords: Shell

Working Remotely http://tess.elixir-uk.org/materials/working-remotely Working Remotely from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/02-ssh.md. Shell Intermediate