A handful of lightning talks with the aim of communicating some takeaway points from the Vizbi 2012 data visualisation conference. Speakers: Juri Pärn, Ingvar Lagerstedt, Martijn van Iersel, Glen van Ginkel, Francis Rowland and Benedetta Baldi (EMBL-EBI). The problem with a presentation about data viz is... BIG IMAGES! I had to save this as a PDF and compress it a lot. I'm afraid that means that the [helpful] speaker notes have been lost.

1. Vizbi Takeaway 2012 - visualising biological data
Vizbi Takeaway 2012
Visualising biological data - highlights
Photo: avlxyz - http://www.flickr.com/photos/avlxyz/3786955645/
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2. Vizbi Takeaway 2012 - visualising biological data
Visualising biological data
6 - 8 March 2012 EMBL Heidelberg
300 participants, 80 posters, 25 talks, 12 tutorials
Photos: francisrowland / SéanO / Siemar | Flickr
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3. 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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4. Vizbi Takeaway 2012 - visualising biological data
The curse of n-dimensions
Juri Pärn EMBL-EBI External Services
One dimension...
1
2
3
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5. Vizbi Takeaway 2012 - visualising biological data
The curse of n-dimensions
Two dimensions...
1 2
3 4
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6. Vizbi Takeaway 2012 - visualising biological data
The curse of
n-dimensions...
Three dimensions...
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7. Vizbi Takeaway 2012 - visualising biological data
The curse of
n-dimensions...
Three dimensions...
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8. Vizbi Takeaway 2012 - visualising biological data
The curse of
n-dimensions...
Three dimensions...
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9. Vizbi Takeaway 2012 - visualising biological data
The curse of
n-dimensions...
Three dimensions...
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10. Vizbi Takeaway 2012 - visualising biological data
The curse of n-dimensions
• 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.
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11. Vizbi Takeaway 2012 - visualising biological data
The curse of n-dimensions
an example...
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12. Vizbi Takeaway 2012 - visualising biological data
The power of images
Ingvar 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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13. 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
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14. Vizbi Takeaway 2012 - visualising biological data
Example from Nature Structural
& Molecular Biology
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15. 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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16. 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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17. Vizbi Takeaway 2012 - visualising biological data
Pathway Visualization & WikiPathways
Martijn van Iersel Saez-Rodriguez Group
http://www.wikipathways.org
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18. Vizbi Takeaway 2012 - visualising biological data
Editing pathways
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19. Vizbi Takeaway 2012 - visualising biological data
Pathways
Genes 90
90
5
26
26
15
1
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20. Vizbi Takeaway 2012 - visualising biological data
Systems Biology Graphical Notation (SBGN)
Macro
Simple Catalysis
molecule
Clone
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21. Vizbi Takeaway 2012 - visualising biological data
LibSBGN
Reference Rend. Ext.
PathVisio SBGN-ED
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22. Vizbi Takeaway 2012 - visualising biological data
Principles & Resource sharing
Glen van Ginkel PDBe
Cross-Origin Resource Sharing (CORS)
Domain A XMLHttpRequest Domain B
http://domaina.example http://domainb.foo
http://www.w3.org/TR/cors/
https://developer.mozilla.org/en/HTTP_access_control
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23. 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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24. 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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25. 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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26. 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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27. Vizbi Takeaway 2012 - visualising biological data
Colour
“Colour used poorly is worse than no colour at all”
- Edward Tufte
• “Above all, do no harm”
• colour can cause the wrong information to stand
out and
• make meaningful information difficult to see.
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28. 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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29. Vizbi Takeaway 2012 - visualising biological data
UX design for data visualisation
Francis Rowland EMBL-EBI External Services
Biologists Data viz
experts
Data visualisation
sweet spot
Designers
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30. Vizbi Takeaway 2012 - visualising biological data
Biologists
Tell the story of your research
through data visualisation
Data visualisation experts
Integrate analysis & visualisation
Designers
Apply design principles and expertise
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31. Vizbi Takeaway 2012 - visualising biological data
Data visualisation technology for biologists
Benedetta Baldi Computational Neurobiology
autoFill
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32. Vizbi Takeaway 2012 - visualising biological data
Simulation Animation
Eric
Keller
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33. Vizbi Takeaway 2012 - visualising biological data
autoFill http://autofill.grahamj.com/
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34. Vizbi Takeaway 2012 - visualising biological data
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35. Vizbi Takeaway 2012 - visualising biological data
Questions?
Drew Berry
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36. 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