2. “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
3. 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
4. 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
5. 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
18. 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
19. 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
20. 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
21. 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
22. 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
23. 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/
24. 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
26. 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/
27. 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
28. 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