Vizbi 2012 Takeaway

Vizbi Takeaway 2012 - visualising biological data

Vizbi Takeaway 2012
Visualising biological data - highlights

Photo: avlxyz - http://www.flickr.com/photos/avlxyz/3786955645/
Monday, 2 April 2012


Visualising biological data
6 - 8 March 2012 EMBL Heidelberg

300 participants, 80 posters, 25 talks, 12 tutorials

Photos: francisrowland / SéanO / Siemar | Flickr


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



The curse of n-dimensions
Juri Pärn EMBL-EBI External Services

One dimension...

1

2

3



Two dimensions...

1 2

3 4



The curse of
n-dimensions...
Three 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.



an example...



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



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



Example from Nature Structural
& Molecular Biology



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



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



Pathway Visualization & WikiPathways
Martijn van Iersel Saez-Rodriguez Group

http://www.wikipathways.org



Editing pathways



Pathways
Genes 90
90
5

26
26
15
1



Systems Biology Graphical Notation (SBGN)

Macro
Simple Catalysis
molecule

Clone



LibSBGN
Reference Rend. Ext.
PathVisio SBGN-ED



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



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)



Encoding schemes

Adapted from Mackinlay J (1986) Automating the design of graphical presentations of relational information.



Accuracy of Quantitative Perceptual Tasks

Cleveland, W.S. & McGill, R. Science 229, 828–833
(1985).



Mapping data types to encoding

Mackinlay J (1986) Automating the design of graphical presentations of relational information.



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.



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



UX design for data visualisation
Francis Rowland EMBL-EBI External Services

Biologists Data viz
experts

Data visualisation
sweet spot

Designers



Biologists
Tell the story of your research
through data visualisation

Data visualisation experts
Integrate analysis & visualisation

Designers
Apply design principles and expertise



Data visualisation technology for biologists
Benedetta Baldi Computational Neurobiology

autoFill



Simulation Animation

Eric
Keller



autoFill http://autofill.grahamj.com/



Questions?

Drew Berry


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


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