Register training material
28 materials found

Keywords: R-programming  or Genome 


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: Pathway or network, Phylogenetics

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations

Resource type: Video

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

BiVi Genomes theme

Prof David Burt introduces the Genomes theme in bio-visualisation.
Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics

Resource type: Video

Visualization of Epigenetic Data

Esther Rheinbay (http://csb.mgh.harvard.edu/bradley_bernstein) talks about the current challenges of visualizing rapidly expanding epigenetic data and showcases some of the different tools which are available to researchers as part of the Integrative Genome Viewer...

Keywords: Genome, Molecular

Resource type: Video

Epigenome Browser

Ting Wang (http://wang.wustl.edu/) addresses many of the challenges of navigating the complexity of genomic data and showcases the WashU Epigenome Browser that he is developing. The browser aims to give investigators maximum flexibility to explore and navigate the available genomic data in...

Keywords: Genome, Molecular

Resource type: Slideshow, Video

Browsing 3D Genomes

Jim Zheng (http://www.uthouston.edu/sbmi/faculty-and-staff/jim-zheng.htm) talks about the importance of understanding the 3D structure of genome and gives an introduction into Genome3D framework (http://www.genome3d.org/) which allows integration of multi-scale structural and genomic data within...

Keywords: Genome, Molecular

Resource type: Video

Visualizing RNA Structures and Alignments

Paul Gardner (http://www.biol.canterbury.ac.nz/people/gardner.shtml) talks about the challenges of visualization of RNA Structures and Alignments in the context of Rfam database (http://rfam.sanger.ac.uk/), a collection of non-coding RNAs, structured cis-regulatory elements and self-splicing...

Keywords: Genome, Molecular

Resource type: Video

Non-coding RNA

Gisela Storz (http://irp.nih.gov/pi/gisela-storz) talks about the reliability and co-relation of anti-sense RNA sequence data. Comparison of RNA seq data across different experiments and from various sources reveals some discrepancies and lack of overlap. While the majority of RNA seq data is...

Keywords: Genome, Molecular

Resource type: Video

RNA-Seq

Cole Trapnell (http://www.broadinstitute.org/~cole/) focuses on isoform-resolution analysis of RNA -seq. RNA-seq is an assay used to determine the abundance of RNA transcripts in a transcriptome, the results of which can be used for gene discovery and expression analysis. In his talk Cole...

Keywords: Genome

Resource type: Video

Keynote on Visual Design Principles

Martin Krzywinski (http://mkweb.bcgsc.ca/) gives a great primer on the key principles of effective visual design in biological sciences. During the talk he highlights the principles with examples from various peer-reviewed publications and discusses the practical aspects of effective figure...

Keywords: Genome, HCI, Information visualisation, Communication

Resource type: Video

Metagenomics

Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community. She notes that there are some good analysis tools available for analysis at the 16S sequence and unassembled metagenome level, but more effort into...

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics, Populations

Resource type: Video

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: Pathway or network, Phylogenetics

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation

Resource type: Video

Graphical applica ons for visualiza on and analysis of genotype data sets

Poster presentation from 1st BiVi in 2014
Created at: 1st BiVi Annual Meeting.

Keywords: Genome

Resource type: Poster

Genomic Visualisations at TGAC

Anil S Thanki presents two visulaisation tools: TGAC Browser and Aequatus as 1st BiVi in 2014.
Created at: 1st BiVi Annual Meeting.

Keywords: Genome

Resource type: Video

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

Leeds Virtual Microscope and Orchestral

Dr Roy Ruddle discusses large displays for visualisation and the Leeds Virtual Microscope and Orchestral tools at 1st BiVi in 2014. Posters presented regarding the two tools discussed are also included.
Created at: 1st BiVi Annual Meeting.

Keywords: Genome

Resource type: Poster, Video

Evaluation of Helium: Visualisation of Large Scale Plant Pedigrees

Poster presentation at 1st BiVi in 2014 regarding the user evaluation of the Helium visualisaiton tool.
Created at: 1st BiVi Annual Meeting.

Keywords: Genome, Populations, HCI

Resource type: Poster

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

GeneProf Visualisations

Dr Simon Tomlinson discusses the GeneProf visualisation system at 1st BiVi in 2014.
Created at: 1st BiVi Annual Meeting.

Keywords: Genome, Molecular

Resource type: Video

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

BiVi theme: Genomes

Andy Yates introduces the Genomes session at 2nd BiVi in 2015.
Created at: 2nd BiVi Annual Meeting.

Keywords: Genome

Resource type: Slideshow

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

Aequatus-vis

Anil Thanki describes the Aequatus-vis JavaScript plugin to visualise homologous genes through alignment and phylogeny information at 2nd BiVi in 2015. aequatus-vis preserves teh interactive functionality of Aequatus, an open-source web based tool to visualise homologous genes with phylogenetic...

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics

Resource type: Slideshow

Joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles

Roland Schwarz's keynote about the joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles at 2nd BiVi in 2015.
Created at: 2nd BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Genome, Phylogenetics

Resource type: Slideshow

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: Pathway or network, Phylogenetics

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

Resource type: Video

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: Pathway or network, Phylogenetics

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Communication, Information visualisation

Resource type: Video

SeqMonk: Using visualisation to identify errors and biases in genome scale sequencing data

The increasing scale and complexity of genome scale studies has led to more widespread use of unsupervised analysis pipelines and reduced inspection and sanity checking of the underlying data.  Here we will illustrate how the use of interactive visualisation tools along with an explorative...

Keywords: Genome

Resource type: Video

Web-based Tools for Integrative Analysis of Pancreatic Cancer Data

Poster presentation at 3rd BiVi in April 2017.Presenitng a suite of web applications, developed for the PRECISION-Parc initiative, to provide integrative analyses of genomic and transcription data from patient primary samples, cell lines and xenografts, as well as clinical data on patient...

Scientific topics: Pathway or network

Keywords: Genome, Pathway

Resource type: Poster