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VIZBI 2013 - Overview

VIZBI 2013 - Overview



Overview of presentations and posters at VIZBI 2013 - Visualizing Biological Data http://vizbi.org/2013/Program/

Overview of presentations and posters at VIZBI 2013 - Visualizing Biological Data http://vizbi.org/2013/Program/



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    VIZBI 2013 - Overview VIZBI 2013 - Overview Presentation Transcript

    • VIZBI 2013March 20-22The Broad Institute of MIT and Harvard
    • “How Can We Fix The Display?”Visual Analytics and HCI Visual variables  Colour, size, motion, luminance, shape etc. Change detection  Size > Colour > Orientation How much realism?  Too much requires inference Animation  New - longer knowledge of static design  Back button  Speed control – many animations too fast Sweet spot of complexity vs inference  Controls to add/remove information Training / domain knowledge important  Good visualization requires shorter training Studies – eye tracking, emotional response
    • Visual Design Principles Consistency, concise, no redundancy, clarity, focus/emphasis, truth/accuracy/detail Can’t compare network layouts side by side Optical illusions – problem for heat maps High contrast for legibility Visual weight  Don’t give different things same visual weight  Use gradient of visual weights instead of colour to show change e.g not obvious purple leads to red  Then use colour to delineate e.g. different cell populations using same weighting scheme
    • Communicating Science Visually A representation, not the thing  Photo, visualization etc.  Clarifies the work (to ourselves and others) Striking photo or model  Improve lighting, angle etc  Can make look too perfect Metaphor  e.g. pin art to illustrate rastering  Avoid factual errors Hand-drawing: a representation, a process Poster design  Panels in groups  More space  Delineate text – boxes, shadows  “Visual abstract”  See large images from far away
    • Designing for Different UserGroups Software designer’s idea of requirements is different from user’s Make requirements gathering part of research User registration – can group and store
    • Epigenetics Single genotype -> multiple phenotypes Malignant tumour analysis with IGV/cBio Portal  Network graphs from transcription factors  Red/blue edges: pos/neg regulation WASHU Epigenome Browser http://epigenomegateway.wustl.edu  Genome/metadata heatmaps Genome3D  http://genomebioinfo.musc.edu/Genome3D/  Structural, genomic, epigenetic data viewer
    • IGV/cBio Network Viewer
    • Caleydo / enRoute enRoute – extract pathway data from KEGG / WikiPathways Display pathway vertically Display experimental data horizontally in groups http://www.icg.tugraz.at/project/caleydo /projects-1/enroute
    • Caleydo / enRoute
    • Visualizing RNA http://www.slideshare.net/ppgardne/vizbi 2013-visualising-rna Rfam database  Sister to Pfam (protein)  Aim to annotate all ncRNA families  Analysis of C/D box snoRNA taxonomy  Sunbursts  Concentric pie charts  External ring contains child nodes of internal ring
    • Sunburst
    • Visualizing Transcript Data Non-coding RNA  Experimental/computational variation  Bowtie – parameters -> different results RNA-Seq  Transcriptome deep dequencing, levels, isoforms  Tuxedo suite of sequencing tools  Cufflinks/Cuffdiff2  Isoform resolution and splice variants  CummeRbund  Plots + heatmaps
    • Beyond the Hairball Network graphs don’t scale up - become “hairballs” Improvements  Clustering eg Cytoscape + clusterMaker  Collapsing nodes  Statistical analysis before visualisation  3D Alternatives  BioTapestry  Create submodels and drill down  BioFabric  Nodes are horizontal lines  Edges are vertical lines
    • BioTapestry
    • BioFabric
    • Structures & Features Protein structures  Crystallography  NMR “Sequence-Structure Gap”  Cost per genome sequence has fallen  Structure resolution difficult and expensive SRS 3D – integrate sequence, structure, gene features Aquaria WS (late 2013)  Scale to large screens  Hardware acceleration  Augmented reality navigation  Structure viewer – Java applet – to be redeveloped in WebGL  Sequence viewer – D3.js  Cross-highlighting between sequence and structure
    • Aquaria WS
    • Comparison and Assemblies UCSF Chimera Molecular structure visualization  Density maps, sequence alignment, docking Animation – create storyboard like iMovie Linear interpolation morphing between frames for smooth animation Autopack – packing algorithm Different types of transition between frames  Rock, rotate, morph etc. Interaction  3D glasses  Motion detection – hand gestures  Trackpad gestures Navigation – can clip through panes of the structure WebGL export of animation storyboard structureViz Cytoscape plugin
    • Evolution of Protein Structureand Function Protein superfamiles  Separated by billions of years  No sequence similarity  Structure conservation FunTree  Annotation of evolutionary branches ITOL  Circular graph with tree of life at centre CATH  Structure classification Genome3D  Predict structural domains from protein sequence Future  Develop library of JavaScript/HTML5 components using D3.js
    • Biological Networks Network Biology  Emerging field  Elements of systems biology, bioinformatics etc.  Nature Paper: Network biology: understanding the cells functional organization. (Barabási + Oltvai 2004) Networks an anchor for other visualizations Easy for biologist to understand Pathway – a type of network Similarity networks  E.g protein-protein, chemical-chemical, co-expression
    • Biological Networks: Opportunities Pathway automatic layout Hairball – cluster to provide structure and colour Clustering – mostly partitioning  Fuzzy, time-variant Network comparisons  Between states or species  Over time e.g. post-translational modification Connect structure information to nodes Large data  Progressive disclosure  Collapsing Stop reinventing  Integrate with existing platforms’ plugin architectures Google Summer of Code BioFabric – edges just as important as nodes
    • NIH LINCS Project http://www.lincsproject.org Cellularresponse to perturbation Catalogue changes in gene expression and cellular processes Cmap Data Explorer  Query up and down-regulated genes  Search for signatures
    • Physiology and Function 3D Slicer  Build up 3D model from 2D images  Load files on the fly so whole model not in memory  WebGL export – share with collaborators  Future – WebCL GPU computing, augmented reality interaction http://goxtk.com/  WebGL library for scientific visualization Entire presentation in WebGL! http://danielhaehn.com/p/vizbi2013/
    • Others Developmental Anatomy  GoFigure – time-lapse microscopyhttps://wiki.med.harvard.edu/SysBio/Megaso n/GoFigure Genes and Geometry  3D pheotyping http://www.mouseimaging.ca/  Average voxels to find true homologous points Supramap http://supramap.org  Integrate genetic/geospatial/temporal data e.g. spread of SARS Metagenomics  QIIME microbial community analysis http://qiime.org  Kbase – predictive systems biology
    • Posters BioTapestry – nodes are lines Shiny – Rstudio to web application Chimera – stucture modelling & animation Bombastic – clustering gene expression WASHU epigenome browser Visualizing molecules  Metalwork sculptures  WebGL application
    • Posters VIZBI Plus  Public engagement in Australia  Working with animators e.g. The Hungry Microbiome – intestinal flora animation OME/OMERO – Image data management BioVis contest  Predicting impact of mutations on proteins  http://biovis.net/contest/
    • Posters Connectivity Map – transcriptomics - LINCS genome-wide transcriptional expression data Clickme – Generate HTML from R 3D modelling of Streptomyces growth in WebGL OneZoom – fractal tree of life explorer Interactive Visualization of Biomolecular Simulations – GPU ray casting Aquaria – protein structure web app TRNDiff – multiple transcriptional regulatory networks visualized in D3.js
    • Posters InVeo  Network models of layers and connections  Layers for genome, transcriptome, proteome, metabolome CBioPortal.org – cancer genomics gateway Cell Signaling Pathways  HTML5 iPad app (ProMega) Streamgraphs  Temporal changes in gene expression in marine microbial communities
    • BioLayout Express3D Poster
    • BioLayout Feedback Alternative layout algorithms Navigation – gestures Plugin architecture – DB access, file formats etc. Pathway animation – input experimental values rather than simulation Align multiple networks 3D protein structures on nodes Pre-clustering