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 User Groups 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/vizb

i2013-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 Structure and 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

cell's 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 Cellular response 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/Megason/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