Bioinformatics Visualization

The Biological Visualisation Network (BiVi) provides a forum for dissemination, training and discussion for life-scientists to discover and promote complex data visualisation ideas and solutions. BiVi, funded by the BBSRC, is a central resource for information on bio-visualisation and is supplemented with annual meetings for networking and educational purposes, focussed around emerging trends in visualisation and challenges facing biology.

Bioinformatics Visualization http://tess.elixir-uk.org/content_providers/bioinformatics-visualization The Biological Visualisation Network (BiVi) provides a forum for dissemination, training and discussion for life-scientists to discover and promote complex data visualisation ideas and solutions. BiVi, funded by the BBSRC, is a central resource for information on bio-visualisation and is supplemented with annual meetings for networking and educational purposes, focussed around emerging trends in visualisation and challenges facing biology. /system/content_providers/images/000/000/077/original/logo.png?1498706596
Showing 72 materials out of 72. View all results.
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

BiVi theme: Anatomy, Physiology and Atlases

Prof Richard Baldock discusses bio-visualisation within the Anatomy, Physiology and Atlases theme
Created at: 1st BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases

Resource type: 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

Comparison and assemblies

Thomas Ferrin (http://www.cgl.ucsf.edu/home/tef/) talks about visualization tools for interactive modeling of biological structures with an emphasis on Chimera (http://www.cgl.ucsf.edu/chimera/), an extensible molecular modeling software.This talk was presented at VIZBI 2013, an international...

Keywords: 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

BiVi theme: Anatomy, Physiology and Atlases 2015

Richard Baldock and Bernard de Bono introduce session on bio-visualisation in Anatomy, Physiology and Atlases at 2nd BiVi in 2015.
Created at: 2nd BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases

Resource type: Slideshow

Validation and Visualisation of Electron Microscopy Density Fits

Poster presentation by Dr Maya Topf at 1st BiVi Annual Meeting in 2014
Created at: 1st BiVi Annual Meeting.

Resource type: Poster

XiNET: A molecular interaction viewer

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

Keywords: Molecular

Resource type: Poster

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

Visualisation of cross-linking/mass spectrometry data

Colin Combe discusses the visualisation of cross-linking/mass spectrometry data at 1st BiVi in 2014.
Created at: 1st BiVi Annual Meeting.

Keywords: Molecular

Resource type: Poster, Video

Genes into Geometry

Mark Henkelman gives an introduction on the use of 3D imaging in neuroanatomy to explore consequences of genetic alterations on anatomical structures and infer function.This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.

Keywords: Anatomy Physiology and Atlases

Resource type: Video

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

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

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

Foldsynth

Prof. Frederic Fol Leymarie discusses the Foldsynth project at 1st BiVi in 2014. A poster presented at the meeting is also included.
Created at: 1st BiVi Annual Meeting.

Keywords: Molecular

Resource type: Poster, Video

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

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

Visualizing odors with insect brains

Martin Strauch presents a brief overview of his BioVis 2012 Honorable Mention paper on visualising odors with insect brains.This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.

Keywords: Anatomy Physiology and Atlases

Resource type: Video

BiVi theme: Molecular

Prof Michael Sternberg introduces bio-visualisation in the Molecular theme from a user perspective at 1st BiVi in 2014.
Created at: 1st BiVi Annual Meeting.

Keywords: Molecular

Resource type: Video

Evolution of Protein Structure and Function

Ian Sillitoe (http://orengogroup.info/) talks about the protein structure classification with particular emphasis on superfamily-centric taxonomy which is used in the CATH (http://www.cathdb.info/) database.This video was filmed and distributed with permission under a Creative Commons...

Keywords: Molecular

Resource type: Video

Physiology & Function

Daniel Haehn talks about visualising medical and scientific data (such as MRI and CT scans, microscopy scan stacks etc.) in 3D and introduces some of the open-source tools available.This video was filmed and distributed with permission under a Creative Common license.
Created at: VIZBI 2013.

Keywords: Anatomy Physiology and Atlases

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

Geographic & Evolutionary Visualization

Daniel Janies showcases SupraMap, a web-based app that integrates genetic sequences of pathogens with geographic data points to map the spread of diseases and track mutations.This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.

Scientific topics: Phylogenetics

Keywords: Phylogenetics, Populations

Resource type: Video

Pathway visualization in the Reactome pathway database

Reactome provides curated human biological pathways representing the consensus view of the molecular events involved. Pathway Diagrams show mechanistic details, using a style based on SBGN. A unique Overview represents all pathways in a single view. Analysis results and expression data are...

Scientific topics: Pathway or network

Keywords: Pathway

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

ViCTree-Virus Taxonomy Classification Framework

Poster presentation at 3rd BiVi in April 2017.
Created at: 3rd BiVi Annual Meeting (2017).

Scientific topics: Phylogenetics

Keywords: Phylogenetics

Resource type: Poster

XiGUI- Visual Interface to Cross-Linking Mass Spectrometry Data

Poster presentation at 3rd BiVi in April 2017.
Created at: 3rd BiVi Annual Meeting (2017).

Keywords: Molecular

Resource type: Poster

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

Visualising dynamic genetics in human populations

Genetic and environmental variation affect all complex human traits and disorders. Recent large-scale genome-wide association studies have identified some of the specific genetic variants, and we often assume these associations will hold true irrespective of context. However, our research shows...

Keywords: Populations

Resource type: Video

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

ApiNATOMY visualisation of multiscale physiology circuitboards

Bernard de Bono presents a talk on using ApiNATOMY for the visualisation of multiscale physiology circuitboards at 3rd BiVi Annual Meeting in April 2017.
Created at: 3rd BiVi Annual Meeting (2017).

Keywords: Anatomy Physiology and Atlases

Resource type: 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

BiVi theme: Phylogenetics

Prof Rod Page discusses bio-visualisation and the Phylogenetics theme at 1st BiVi in 2014.
Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics

Keywords: Phylogenetics

Resource type: Video

Foldsynth: From proteins to DNA

Prof Frederic Fol Leymarie demonstrates Foldsynth 2.0 visualisation tool at 2nd BiVi in 2015.
Created at: 2nd BiVi Annual Meeting.

Keywords: Molecular

Resource type: Video

Reactome

Kostas Sidiropoulos disceusses the visualsation of biomolecular pathways and Reactome, a free, open-source, curated and peer-reviewed knowledge-base of biomolecular pathways at 2nd BiVi in 2015.
Created at: 2nd BiVi Annual Meeting.

Scientific topics: Pathway or network

Keywords: Pathway, Databases

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

Interacting with large biomolecules using haptic feedback

Dr Stephen Laycock describes using InteractinHaptiMOL to interact with large biomolecules using haptic feedback at 2nd BiVi in 2015.
Created at: 2nd BiVi Annual Meeting.

Keywords: Molecular

Resource type: Slideshow

MARender: A Simple JavaScript Library for Biomedical Visualisation

Bill Hill and Richard Baldock describe MARender, a simple JavaScipt library for biomedical visualisation at 2nd BiVi in 2015. 
Created at: 2nd BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases, Information visualisation

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

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

Intermine 2.0

Yo Yehudi describes Intermine, an open source data warehouse and analysis system at 2nd BiVi in 2015
Created at: 2nd BiVi Annual Meeting.

Keywords: Databases

Resource type: Slideshow

BiVi theme: Molecular - Structural molecular graphics

Prof Michael Sternberg introduces the Molecular bio-visualsation session at 2nd BiVi in 2015.
Created at: 2nd BiVi Annual Meeting.

Keywords: Molecular

Resource type: Slideshow

Revise and Redraw—Visual Design Principles for Scientific Data

Martin Krzywinski's keynote from 1st BiVi in 2014. He discusses visual design principles and communicating effectively in pictures.This talk distills core concepts of information design into practical guidelines for creating scientific figures. We will explain how to generate visual vocabularies...

Keywords: HCI, Communication

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

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

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

OME Bio-Formats and OMERO

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

Resource type: Poster

Making Science Beautiful

In this presentation David Goodsell reveals the beauty of science through his scientific and artistic endeavors. He explores the visual techniques which have been used to communicate the detail of the molecular biology world to different audiences.David Goodsell (http://bit.ly/DGoodsell) is an...

Keywords: Molecular, 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

Infectious Disease Host/Pathogen Relationships

Bruno Sobral demonstrates how collaboration with the bench scientists to learn about their needs, uses and challenges can lead to design of more effective resources for data exploration and analysis. He emphasises the importance of designing in a user-centric manner and highlights the importance...

Keywords: Populations, HCI

Resource type: Video

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

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

Data visualization in proteomics

Martin Miller talks about visualization of proteome data with particular emphasis on modeling phosphorylation sites. He gives a brief introduction into different methods for the analysis of the single cell proteome from antibody-based methods to mass spectrometry and fluorescence tagging. With...

Keywords: 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

enRoute: BioVis Best Paper

Alexander Lex (http://alexander-lex.com/) talks about enRoute, a tool for dynamic path extraction from biological pathway maps for in-depth experimental data analysis. He highlights the inherent problem with correlating real-life heterogeneous data to pathways, namely that they rarely follow the...

Scientific topics: Pathway or network

Keywords: Pathway

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

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

Developmental Anatomy

Sean Megason (http://megason.med.harvard.edu/) talks about the challenges and caveats of multiscale imaging, visualisation and analysis and highlights some of the tools that are used for processing and analysis of in toto imaging such as GoFigure2 (http://www.gofigure2.org/) and ACME...

Keywords: Anatomy Physiology and Atlases

Resource type: Video

Keynote on Communicating Science Visually

Felice Frankel delivers her keynote address in which she talks about how to effectively use visual tools to communicate science.This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.

Keywords: Communication

Resource type: Video

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

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: Phylogenetics, Pathway or network

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

Resource type: Video

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

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

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

Visualizing Protein Structures and Features

Sean O'Donoghue (http://odonoghuelab.org) talks about molecular spatial data and the emerging issue of sequence-structure gap mainly due to experimental difficulties in obtaining reliable (or any) structure information for a given protein. In his talk, he also gives a brief demonstration of...

Keywords: Molecular

Resource type: Video

Keynote on Visual Analytics & Human/Computer Interfaces

Sara Irina Fabrikant discusses how analysis of scientific data can be enhanced using information visualization, visual analytics, cognition principles, and graphical user interface design. She focuses on the use of evaluation to valid visualization approaches. This talk was presented at VIZBI...

Keywords: Information visualisation

Resource type: Video

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

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

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

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

EzMol and BioBlox: From Resources for Protein Modelling to Educational Computer Games

In this talk Michael Sternberg of Imperial reports how their research on protein modelling has led to the development of computer games with a role in scientific education. At Imperial, Chris Reynolds has developed a web-based molecular graphics resource EzMol which is a simple-to-use display of...

Keywords: Molecular

Resource type: Video

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

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