Vizbi Takeaway 2012 Visualising biological data - highlights
Vizbi Takeaway 2012 - visualising biological data
Photo: avlxyz - http://www.flickr.com/photos/avlxyz/3786955645/
Monday, 2 April 2012
Vizbi Takeaway 2012 - visualising biological data
Visualising biological data
Photos: francisrowland / SéanO / Siemar | Flickr
6 - 8 March 2012 EMBL Heidelberg
300 participants, 80 posters, 25 talks, 12 tutorials
Monday, 2 April 2012
Vizbi Takeaway 2012 - visualising biological data
Takeaway menu
• Juri Pärn - The curse of n-dimensions
• Ingvar Lagerstedt - The power of images
• Martijn van Iersel - Pathway visualisation & WikiPathways
• Glen van Ginkel - Principles of data visualisation
• Francis Rowland - UX design for data visualisation
• Benedetta Baldi - Data visualisation technology for biologists
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Vizbi Takeaway 2012 - visualising biological data
The curse of n-dimensionsJuri Pärn EMBL-EBI External Services
One dimension...
1
2
3
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Vizbi Takeaway 2012 - visualising biological data
The curse of n-dimensions
Two dimensions...
1 2
3 4
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Vizbi Takeaway 2012 - visualising biological data
The curse ofn-dimensions...
Three dimensions...
Monday, 2 April 2012
Vizbi Takeaway 2012 - visualising biological data
The curse ofn-dimensions...
Three dimensions...
Monday, 2 April 2012
Vizbi Takeaway 2012 - visualising biological data
The curse ofn-dimensions...
Three dimensions...
Monday, 2 April 2012
Vizbi Takeaway 2012 - visualising biological data
The curse ofn-dimensions...
Three dimensions...
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Vizbi Takeaway 2012 - visualising biological data
• With every new dimension, it gets worse
• The diagonal grows slowly but steadily with
• For dimension = 100 the diagonal is
• Important to keep in mind for clustering, as many clustering algorithms use euclidian distance
• Points tend to cluster along dimensions, not across dimensions
• Possible solution for clustering
- dimension reduction
- using another distant function, e.g.
The curse of n-dimensions
Monday, 2 April 2012
Vizbi Takeaway 2012 - visualising biological data
an example...
The curse of n-dimensions
Monday, 2 April 2012
Vizbi Takeaway 2012 - visualising biological data
The power of imagesIngvar Lagerstedt PDBe
How do you read a paper?
• Title
• Author
• Abstract
• Images/Tables
• Legends for images/table
• Conclusions
• Methods/Body of text
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Vizbi Takeaway 2012 - visualising biological data
Using images effectively
• What do you want to show?
• Highlight/simplify
- remove details that are not relevant to the point you want to make
• We are not all layout designers
- use professional help
- I tend to cram in far to much detail
• Publishers often charge per image
- encourages composite images
Monday, 2 April 2012
Vizbi Takeaway 2012 - visualising biological data
Example from Nature Structural& Molecular Biology
Monday, 2 April 2012
Vizbi Takeaway 2012 - visualising biological data
Colouring
• Use limited number of colours
- Horror example with 250+ colour based keys
- Think hard if you really need more than say 5-6 colours
• Use soft colours for large areas
- It is fine to use strong colours for features/lines etc., but they tend to be tiring if used excessively
• Think about the colour blind
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Vizbi Takeaway 2012 - visualising biological data
Designing a new file format (RNA)
• Many existing competing compact formats
• Wanted a new community based
• Everyone likes XML
• parsers are free
• Except
• There was 30 X bloat
• Details were left ambiguous
• Each group produced slightly different versions
• Hardly anyone can cope with reading other groups version
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Vizbi Takeaway 2012 - visualising biological data
Pathway Visualization & WikiPathwaysMartijn van Iersel Saez-Rodriguez Group
http://www.wikipathways.org
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Vizbi Takeaway 2012 - visualising biological data
Editing pathways
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Vizbi Takeaway 2012 - visualising biological data
26
90
1
5
26
90
15
Pathways
Genes
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Vizbi Takeaway 2012 - visualising biological data
Simple Macro
moleculeCatalysis
Clone
Systems Biology Graphical Notation (SBGN)
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Vizbi Takeaway 2012 - visualising biological data
LibSBGN
ReferencePathVisio
Rend. Ext.SBGN-ED
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Vizbi Takeaway 2012 - visualising biological data
Principles & Resource sharingGlen van Ginkel PDBe
Cross-Origin Resource Sharing (CORS)
http://www.w3.org/TR/cors/
https://developer.mozilla.org/en/HTTP_access_control
Domain A http://domaina.example
Domain B http://domainb.foo
XMLHttpRequest
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Vizbi Takeaway 2012 - visualising biological data
Graphics & visualisation
• Graphics used to form a sign system:
- Each mark (point, line, or area) represents a data element
- Visualisation is about choosing visual variables to encode relationships between data elements
- difference, similarity, order, proportion
- only position supports all relationships • Huge range of alternative visual encodings for
data
- find images that express and effectively convey the information
Prof Jessie Kennedy (Institute for Informatics & Digital Innovation)
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Vizbi Takeaway 2012 - visualising biological data
Encoding schemes
Adapted from Mackinlay J (1986) Automating the design of graphical presentations of relational information.
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Vizbi Takeaway 2012 - visualising biological data
Accuracy of Quantitative Perceptual Tasks
Cleveland, W.S. & McGill, R. Science 229, 828–833 (1985).
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Vizbi Takeaway 2012 - visualising biological data
Mapping data types to encoding
Mackinlay J (1986) Automating the design of graphical presentations of relational information.
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Vizbi Takeaway 2012 - visualising biological data
Colour
• “Above all, do no harm”
• colour can cause the wrong information to stand out and
• make meaningful information difficult to see.
“Colour used poorly is worse than no colour at all”- Edward Tufte
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Vizbi Takeaway 2012 - visualising biological data
Brewer Palettes
Brewer palettes (colorbrewer.org) provide a range of palettes based on HSV model which make life easier for us….
Avoid the use of hue to encode quantitative variables
QUALITATIVE SEQUENTIAL DIVERGING
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Vizbi Takeaway 2012 - visualising biological data
UX design for data visualisation
Data vizexpertsBiologists
Designers
Francis Rowland EMBL-EBI External Services
Data visualisationsweet spot
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Vizbi Takeaway 2012 - visualising biological data
Tell the story of your research through data visualisation
Biologists
Data visualisation experts
Integrate analysis & visualisation
Designers
Apply design principles and expertise
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Vizbi Takeaway 2012 - visualising biological data
Data visualisation technology for biologistsBenedetta Baldi Computational Neurobiology
autoFill
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Vizbi Takeaway 2012 - visualising biological data
Simulation Animation
Eric Keller
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Vizbi Takeaway 2012 - visualising biological data
autoFill http://autofill.grahamj.com/
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Vizbi Takeaway 2012 - visualising biological data
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Vizbi Takeaway 2012 - visualising biological data
Drew Berry
Questions?
Monday, 2 April 2012
Vizbi Takeaway 2012 - visualising biological data
Thanks to...
Scientific Organisers:
Seán O’Donoghue CSIRO and Garvan Institute, Australia
James Procter University of Dundee, UK
Conference Organiser:
Anja Maria Kröffges EMBL Heidelberg, Germany
Continue the discussion on the EBI Interfaces mailing list:
http://listserver.ebi.ac.uk/mailman/listinfo/interfaces
Monday, 2 April 2012
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