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
Browsing 3D Genomes
https://bivi.co/presentation/browsing-3d-genomes
https://tess.elixir-europe.org/materials/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 3D. This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Genome, Molecular
2017-01-31
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: Database management, Pathway or network
Keywords: Pathway, Databases
Resource type: Slideshow
Reactome
https://bivi.co/presentation/reactome
https://tess.elixir-europe.org/materials/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.
Dr. Konstantinos Sidiropoulos
Database management
Pathway or network
Pathway, Databases
2017-02-03
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
GeneProf Visualisations
https://bivi.co/presentation/geneprof-visualisations
https://tess.elixir-europe.org/materials/geneprof-visualisations
Dr Simon Tomlinson discusses the GeneProf visualisation system at 1st BiVi in 2014.
Created at: 1st BiVi Annual Meeting.
Dr. Simon Tomlinson
Genome, Molecular
2017-02-02
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
https://bivi.co/presentation/biological-networks
https://tess.elixir-europe.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
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
Non-coding RNA
https://bivi.co/presentation/non-coding-rna
https://tess.elixir-europe.org/materials/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 robust and reliable, low abundance transcripts can be difficult to account for and the variations in experimental as well as computational conditions can lead to vastly different data.This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Genome, Molecular
2017-01-31
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
BiVi theme: Anatomy, Physiology and Atlases 2015
https://bivi.co/presentation/bivi-theme-anatomy-physiology-and-atlases-2015
https://tess.elixir-europe.org/materials/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.
Prof. Richard Baldock
Anatomy Physiology and Atlases
2017-02-03
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
Pathway visualization in the Reactome pathway database
https://bivi.co/presentation/pathway-visualization-reactome-pathway-database
https://tess.elixir-europe.org/materials/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 represented in both Pathway Diagrams and Overview as coloured overlays.
Created at: 3rd BiVi Annual Meeting (2017).
Dr. Steve Jupe
Pathway or network
Pathway
2017-05-15
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
Geographic & Evolutionary Visualization
https://bivi.co/presentation/geographic-evolutionary-visualization
https://tess.elixir-europe.org/materials/geographic-amp-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.
Phylogenetics
Phylogenetics, Populations
2017-01-31
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
Comparison and assemblies
https://bivi.co/presentation/comparison-and-assemblies
https://tess.elixir-europe.org/materials/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 conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Prof. Thomas Ferrin
Molecular
2017-01-31
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
RNA-Seq
https://bivi.co/presentation/rna-seq
https://tess.elixir-europe.org/materials/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 highlights the inherent challenges associated with the analysis of isoform-resolution data and proposes several different areas that are open for improvement.This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Genome
2017-01-31
Poster presentation given at 1st BiVi in 2014
Created at: 1st BiVi Annual Meeting.
OME Bio-Formats and OMERO
https://bivi.co/presentation/ome-bio-formats-and-omero
https://tess.elixir-europe.org/materials/ome-bio-formats-and-omero
Poster presentation given at 1st BiVi in 2014
Created at: 1st BiVi Annual Meeting.
Dr. Simon Li
2017-02-01
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
ApiNATOMY visualisation of multiscale physiology circuitboards
https://bivi.co/presentation/apinatomy-visualisation-multiscale-physiology-circuitboards
https://tess.elixir-europe.org/materials/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).
Dr. Bernard de Bono
Anatomy Physiology and Atlases
2017-05-12
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
EzMol and BioBlox: From Resources for Protein Modelling to Educational Computer Games
https://bivi.co/presentation/ezmol-and-bioblox-resources-protein-modelling-educational-computer-games
https://tess.elixir-europe.org/materials/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 protein structures. In collaboration with Frederic Fol Leymarie, William Latham and their team at Goldsmiths, we have developed the BioBlox suite of scientific-based computer games based around protein docking. BioBox3D is a serious crowd-sourced game for predicting protein/protein docking. BioBlox2D is a fun-to-play game with scientific content for phone/tablet inspired by the recognition between proteins and small molecules. Finally, BioBloxVR is a virtual reality environment for protein docking inspired by BioBlox3D. We are exploring the opportunities for EzMol and BioBlox as educational resources. The projects were supported by the BBSRC.
Created at: 3rd BiVi Annual Meeting (2017).
Prof. Michael J E Sternberg
Molecular
2017-05-15
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
Foldsynth: From proteins to DNA
https://bivi.co/presentation/foldsynth-proteins-dna
https://tess.elixir-europe.org/materials/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.
Prof. Frederic Fol Leymarie
Ph.D.
Molecular
2017-02-03
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
https://bivi.co/presentation/art-and-science-partnership-catalyzing-discovery-biomedicine
https://tess.elixir-europe.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
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://bivi.co/presentation/visualization-approaches-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
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://bivi.co/presentation/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
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
Visualization of Epigenetic Data
https://bivi.co/presentation/visualization-epigenetic-data
https://tess.elixir-europe.org/materials/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 (http://www.broadinstitute.org/igv/), the Roadmap Epigenomics Project (http://www.roadmapepigenomics.org/) and ECODE project (http://genome.ucsc.edu/encode/). This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Genome, Molecular
2017-01-31
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
Evaluation of Helium: Visualisation of Large Scale Plant Pedigrees
https://bivi.co/presentation/evaluation-helium-visualisation-large-scale-plant-pedigrees
https://tess.elixir-europe.org/materials/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.
Dr. Paul Shaw
Genome, Populations, HCI
2017-02-02
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://bivi.co/presentation/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
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
Joint visualisation and analysis of large sequence data with Alvis and Sequence Bundles
https://bivi.co/presentation/joint-visualisation-and-analysis-large-sequence-data-alvis-and-sequence-bundles
https://tess.elixir-europe.org/materials/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.
Dr. Roland Schwarz
Phylogenetics
Genome, Phylogenetics
2017-02-03
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://bivi.co/presentation/visualization-biomolecular-structures-state-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
Yo Yehudi describes Intermine, an open source data warehouse and analysis system at 2nd BiVi in 2015
Created at: 2nd BiVi Annual Meeting.
Scientific topics: Database management
Keywords: Databases
Resource type: Slideshow
Intermine 2.0
https://bivi.co/presentation/intermine-20
https://tess.elixir-europe.org/materials/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.
Ms. Yo Yehudi
Database management
Databases
2017-02-03
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
Revise and Redraw—Visual Design Principles for Scientific Data
https://bivi.co/presentation/revise-and-redraw%E2%80%94visual-design-principles-scientific-data
https://tess.elixir-europe.org/materials/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 with graphical elements, combine them into phrases, and package them into a complete figure, the visual equivalent of a paragraph. We show how effective designs for this composition are underpinned by conclusions from studies in visual perception and awareness.
Created at: 1st BiVi Annual Meeting.
Martin Krzywinski
HCI, Communication
2017-02-02
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
Visualizing Protein Structures and Features
https://bivi.co/presentation/visualizing-protein-structures-and-features
https://tess.elixir-europe.org/materials/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 Aquaria (http://aquaria.ws), a web-based 3D molecular structure visualization tool that combines data from various databases and allows investigators to easily view and explore proteins and protein-protein interactions.This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Dr. Sean I O’Donoghue
Molecular
2017-01-31
Poster presentation at 3rd BiVi in April 2017.
Created at: 3rd BiVi Annual Meeting (2017).
Keywords: Molecular
Resource type: Poster
XiGUI- Visual Interface to Cross-Linking Mass Spectrometry Data
https://bivi.co/presentation/xigui-visual-interface-cross-linking-mass-spectrometry-data
https://tess.elixir-europe.org/materials/xigui-visual-interface-to-cross-linking-mass-spectrometry-data
Poster presentation at 3rd BiVi in April 2017.
Created at: 3rd BiVi Annual Meeting (2017).
Dr. Martin Graham
Molecular
2017-05-30
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
Genomic Visualisations at TGAC
https://bivi.co/presentation/genomic-visualisations-tgac
https://tess.elixir-europe.org/materials/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.
Anil S. Thanki
Genome
2017-02-02
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
BiVi theme: Anatomy, Physiology and Atlases
https://bivi.co/presentation/bivi-theme-anatomy-physiology-and-atlases
https://tess.elixir-europe.org/materials/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.
Prof. Richard Baldock
Anatomy Physiology and Atlases
2017-02-01
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
Making Science Beautiful
https://bivi.co/presentation/making-science-beautiful
https://tess.elixir-europe.org/materials/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 Associate Professor of Molecular Biology at the Scripps Institute, California Campus.
Created at: VIZBI 2014.
Molecular, Communication
2017-01-31
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://bivi.co/content/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
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
BiVi theme: Molecular - Structural molecular graphics
https://bivi.co/presentation/bivi-theme-molecular-structural-molecular-graphics
https://tess.elixir-europe.org/materials/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.
Prof. Michael J E Sternberg
Molecular
2017-02-03
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
Keynote on Communicating Science Visually
https://bivi.co/presentation/keynote-communicating-science-visually
https://tess.elixir-europe.org/materials/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.
Communication
2017-01-31
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
Interacting with large biomolecules using haptic feedback
https://bivi.co/presentation/interacting-large-biomolecules-using-haptic-feedback
https://tess.elixir-europe.org/materials/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.
Dr. Stephen David Laycock
Molecular
2017-02-03
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
https://bivi.co/presentation/zegami-image-visualisation-annotation-and-searching
https://tess.elixir-europe.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
Andy Yates introduces the Genomes session at 2nd BiVi in 2015.
Created at: 2nd BiVi Annual Meeting.
Keywords: Genome
Resource type: Slideshow
BiVi theme: Genomes
https://bivi.co/presentation/bivi-theme-genomes
https://tess.elixir-europe.org/materials/bivi-theme-genomes
Andy Yates introduces the Genomes session at 2nd BiVi in 2015.
Created at: 2nd BiVi Annual Meeting.
Mr. Andy Yates
Genome
2017-02-03
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
Developmental Anatomy
https://bivi.co/presentation/developmental-anatomy
https://tess.elixir-europe.org/materials/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 (https://wiki.med.harvard.edu/SysBio/Megason/ACME). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Anatomy Physiology and Atlases
2017-01-31
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
Leeds Virtual Microscope and Orchestral
https://bivi.co/presentation/leeds-virtual-microscope-and-orchestral
https://tess.elixir-europe.org/materials/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.
Dr. Roy Ruddle
Genome
2017-02-02
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
Visualisation of cross-linking/mass spectrometry data
https://bivi.co/presentation/visualisation-cross-linkingmass-spectrometry-data
https://tess.elixir-europe.org/materials/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.
Dr. Colin Combe
Molecular
2017-02-01
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
https://bivi.co/presentation/cell-lineage-visualisation
https://tess.elixir-europe.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
Poster presentation at 3rd BiVi in April 2017.
Created at: 3rd BiVi Annual Meeting (2017).
Scientific topics: Phylogenetics
Keywords: Phylogenetics
Resource type: Poster
ViCTree-Virus Taxonomy Classification Framework
https://bivi.co/presentation/victree-virus-taxonomy-classification-framework
https://tess.elixir-europe.org/materials/victree-virus-taxonomy-classification-framework
Poster presentation at 3rd BiVi in April 2017.
Created at: 3rd BiVi Annual Meeting (2017).
Ms. Sejal Modha
Phylogenetics
Phylogenetics
2017-05-30
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
MARender: A Simple JavaScript Library for Biomedical Visualisation
https://bivi.co/presentation/marender-simple-javascript-library-biomedical-visualisation
https://tess.elixir-europe.org/materials/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.
Mr. William Edward Hill
Anatomy Physiology and Atlases, Information visualisation
2017-02-03
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
Visualizing odors with insect brains
https://bivi.co/presentation/visualizing-odors-insect-brains
https://tess.elixir-europe.org/materials/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.
Martin Strauch
Anatomy Physiology and Atlases
2017-01-31
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
SeqMonk: Using visualisation to identify errors and biases in genome scale sequencing data
https://bivi.co/presentation/seqmonk-using-visualisation-identify-errors-and-biases-genome-scale-sequencing-data
https://tess.elixir-europe.org/materials/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 approach to analysis can identify problems which would otherwise go undetected by standard pipelines.
Created at: 3rd BiVi Annual Meeting (2017).
Dr. Simon Andrews
Genome
2017-05-15
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
enRoute: BioVis Best Paper
https://bivi.co/presentation/enroute-biovis-best-paper
https://tess.elixir-europe.org/materials/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 same topography. enRoute tool allows the investigator to select defined sections of the pathway and display them in a linear fashion to allow for easier navigation of collated data. This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Dr. Alexander Lex
Pathway or network
Pathway
2017-01-31
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
Keynote on Visual Analytics & Human/Computer Interfaces
https://bivi.co/presentation/keynote-visual-analytics-humancomputer-interfaces
https://tess.elixir-europe.org/materials/keynote-on-visual-analytics-amp-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 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Information visualisation
2017-01-31
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
https://bivi.co/content/introducing-bivico
https://tess.elixir-europe.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
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
Aequatus-vis
https://bivi.co/presentation/aequatus-vis
https://tess.elixir-europe.org/materials/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 tree .
Created at: 2nd BiVi Annual Meeting.
Anil S. Thanki
Phylogenetics
Genome, Phylogenetics
2017-02-03
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
BiVi theme: Phylogenetics
https://bivi.co/presentation/bivi-theme-phylogenetics
https://tess.elixir-europe.org/materials/bivi-theme-phylogenetics
Prof Rod Page discusses bio-visualisation and the Phylogenetics theme at 1st BiVi in 2014.
Created at: 1st BiVi Annual Meeting.
Prof. Rod Page
Phylogenetics
Phylogenetics
2017-02-02
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
https://bivi.co/presentation/zegami-tool-image-data-exploration
https://tess.elixir-europe.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
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
Metagenomics
https://bivi.co/presentation/metagenomics
https://tess.elixir-europe.org/materials/metagenomics-6625dde2-a7da-4cc2-a51d-14c1c31b51b2
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 analysis and visualisation solutions are required at the microbial community and ecosystem level.This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Phylogenetics
Genome, Phylogenetics, Populations
2017-01-31
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
Foldsynth
https://bivi.co/presentation/foldsynth
https://tess.elixir-europe.org/materials/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.
Prof. Frederic Fol Leymarie
Ph.D.
Molecular
2017-02-01
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
Physiology & Function
https://bivi.co/presentation/physiology-function
https://tess.elixir-europe.org/materials/physiology-amp-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.
Anatomy Physiology and Atlases
2017-01-31
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
https://bivi.co/presentation/cellular-image-data
https://tess.elixir-europe.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
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
Web-based Tools for Integrative Analysis of Pancreatic Cancer Data
https://bivi.co/presentation/web-based-tools-integrative-analysis-pancreatic-cancer-data
https://tess.elixir-europe.org/materials/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 survival.
Created at: 3rd BiVi Annual Meeting (2017).
Derek Wright
Pathway or network
Genome, Pathway
2017-05-30
Poster presentation from 1st BiVi in 2014
Created at: 1st BiVi Annual Meeting.
Keywords: Genome
Resource type: Poster
Graphical applica ons for visualiza on and analysis of genotype data sets
https://bivi.co/presentation/graphical-applica-ons-visualiza-and-analysis-genotype-data-sets
https://tess.elixir-europe.org/materials/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.
Dr. Iain Milne
Genome
2017-02-02
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
Keynote on Visual Design Principles
https://bivi.co/presentation/keynote-visual-design-principles
https://tess.elixir-europe.org/materials/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 design.This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Martin Krzywinski
Genome, HCI, Information visualisation, Communication
2017-01-31
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://bivi.co/presentation/visual-exploration-biomedical-data-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
Poster presentation at 1st BiVi in 2014.
Created at: 1st BiVi Annual Meeting.
Keywords: Molecular
Resource type: Poster
XiNET: A molecular interaction viewer
https://bivi.co/presentation/xinet-molecular-interaction-viewer
https://tess.elixir-europe.org/materials/xinet-a-molecular-interaction-viewer
Poster presentation at 1st BiVi in 2014.
Created at: 1st BiVi Annual Meeting.
Dr. Colin Combe
Molecular
2017-02-01
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
Genes into Geometry
https://bivi.co/presentation/genes-geometry
https://tess.elixir-europe.org/materials/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.
Anatomy Physiology and Atlases
2017-01-31
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
BiVi theme: Molecular
https://bivi.co/presentation/bivi-theme-molecular
https://tess.elixir-europe.org/materials/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.
Prof. Michael J E Sternberg
Molecular
2017-02-01
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
Evolution of Protein Structure and Function
https://bivi.co/presentation/evolution-protein-structure-and-function
https://tess.elixir-europe.org/materials/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 license.
Created at: VIZBI 2013.
Molecular
2017-01-31
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
Visualising dynamic genetics in human populations
https://bivi.co/presentation/visualising-dynamic-genetics-human-populations
https://tess.elixir-europe.org/materials/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 that the relationship between genotype and phenotype can change across a lifetime or in different environments. For example, some genetic variants may have larger effects in adulthood or in the centre of cities. Data visualisation plays a vital role in bringing researchers together across disciplines to understand these dynamic patterns of gene-environment interaction.
Created at: 3rd BiVi Annual Meeting (2017).
Oliver Davis
Populations
2017-05-15
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...
Scientific topics: Database management
Keywords: Cells and Organisms, Databases
Resource type: Video
Zegami: Digital Data Integration, Visualisation and Management
https://bivi.co/presentation/zegami-digital-data-integration-visualisation-and-management
https://tess.elixir-europe.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
Database management
Cells and Organisms, Databases
2017-05-12
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
Data visualization in proteomics
https://bivi.co/presentation/data-visualization-proteomics
https://tess.elixir-europe.org/materials/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 the onset of targeted and shot-gun mass spectrometry, there is an increasing amount of proteomics data which will need to be classified, integrated and available for analysis in a meaningful and accessible manner.This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Molecular
2017-01-31
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
Infectious Disease Host/Pathogen Relationships
https://bivi.co/presentation/infectious-disease-hostpathogen-relationships
https://tess.elixir-europe.org/materials/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 of human-computer interface professionals in the design process.This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Populations, HCI
2017-01-31
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
Visualizing RNA Structures and Alignments
https://bivi.co/presentation/visualizing-rna-structures-and-alignments
https://tess.elixir-europe.org/materials/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 RNAs. This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Genome, Molecular
2017-01-31
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
Epigenome Browser
https://bivi.co/presentation/epigenome-browser
https://tess.elixir-europe.org/materials/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 multiple tracks, upload their own data as well as explore long-range interactions. He also highlights the need for the genome browsers to act as community resources and bioinformatics engines with the ability to analyse the mined data. This talk was presented at VIZBI 2013, an international conference series on visualizing biological data (http://vizbi.org). This video was filmed and distributed with permission under a Creative Commons license.
Created at: VIZBI 2013.
Dr. Ting Wang
Genome, Molecular
2017-01-31
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
https://bivi.co/presentation/biolayout-express-3d
https://tess.elixir-europe.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
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
BiVi Genomes theme
https://bivi.co/content/bivi-genomes-theme
https://tess.elixir-europe.org/materials/bivi-genomes-theme
Prof David Burt introduces the Genomes theme in bio-visualisation.
Created at: 1st BiVi Annual Meeting.
Prof. David Willaim Burt
PhD BSc FSB
Phylogenetics
Genome, Phylogenetics
2016-12-08
Poster presentation by Dr Maya Topf at 1st BiVi Annual Meeting in 2014
Created at: 1st BiVi Annual Meeting.
Validation and Visualisation of Electron Microscopy Density Fits
https://bivi.co/content/validation-and-visualisation-electron-microscopy-density-fits
https://tess.elixir-europe.org/materials/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.
Prof. Maya Topf
2016-12-08
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
https://bivi.co/presentation/model-organism-analysis-using-intermine
https://tess.elixir-europe.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
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
BioJS
https://bivi.co/presentation/biojs
https://tess.elixir-europe.org/materials/biojs-6f4125d4-aca1-407d-b0c7-02345f3b3900
Dr Manuel Corpas discusses the BioJS Javascript component library at the 1st BiVi Annual Meeting in 2014.
Created at: 1st BiVi Annual Meeting.
Dr. Manuel Corpas
Phylogenetics
Pathway or network
Anatomy Physiology and Atlases, Genome, Molecular, Pathway, Phylogenetics
2016-12-08
