Vizbi Takeaway 2012 - visualising biological data Vizbi Takeaway 2012   Visualising biological data - highlights      Phot...
Vizbi Takeaway 2012 - visualising biological data                         Visualising biological data                     ...
Vizbi Takeaway 2012 - visualising biological data                                        Takeaway menu                    ...
Vizbi Takeaway 2012 - visualising biological data                             The curse of n-dimensions                   ...
Vizbi Takeaway 2012 - visualising biological data                             The curse of n-dimensions                   ...
Vizbi Takeaway 2012 - visualising biological data        The curse of        n-dimensions...        Three dimensions...Mon...
Vizbi Takeaway 2012 - visualising biological data        The curse of        n-dimensions...        Three dimensions...Mon...
Vizbi Takeaway 2012 - visualising biological data        The curse of        n-dimensions...        Three dimensions...Mon...
Vizbi Takeaway 2012 - visualising biological data        The curse of        n-dimensions...        Three dimensions...Mon...
Vizbi Takeaway 2012 - visualising biological data                              The curse of n-dimensions                  ...
Vizbi Takeaway 2012 - visualising biological data                             The curse of n-dimensions                   ...
Vizbi Takeaway 2012 - visualising biological data                                   The power of images                   ...
Vizbi Takeaway 2012 - visualising biological data                               Using images effectively                  ...
Vizbi Takeaway 2012 - visualising biological data                        Example from Nature Structural                   ...
Vizbi Takeaway 2012 - visualising biological data                                              Colouring                  ...
Vizbi Takeaway 2012 - visualising biological data                       Designing a new file format (RNA)                 ...
Vizbi Takeaway 2012 - visualising biological data                       Pathway Visualization & WikiPathways              ...
Vizbi Takeaway 2012 - visualising biological data                                      Editing pathwaysMonday, 2 April 2012
Vizbi Takeaway 2012 - visualising biological data                                        Pathways                         ...
Vizbi Takeaway 2012 - visualising biological data                   Systems Biology Graphical Notation (SBGN)             ...
Vizbi Takeaway 2012 - visualising biological data                                               LibSBGN                   ...
Vizbi Takeaway 2012 - visualising biological data                           Principles & Resource sharing                 ...
Vizbi Takeaway 2012 - visualising biological data                                 Graphics & visualisation                ...
Vizbi Takeaway 2012 - visualising biological data                                                     Encoding schemes    ...
Vizbi Takeaway 2012 - visualising biological data                       Accuracy of Quantitative Perceptual Tasks         ...
Vizbi Takeaway 2012 - visualising biological data                        Mapping data types to encoding                   ...
Vizbi Takeaway 2012 - visualising biological data                                                    Colour               ...
Vizbi Takeaway 2012 - visualising biological data                                             Brewer Palettes             ...
Vizbi Takeaway 2012 - visualising biological data                        UX design for data visualisation                 ...
Vizbi Takeaway 2012 - visualising biological data                           Biologists                       Tell the stor...
Vizbi Takeaway 2012 - visualising biological data                       Data visualisation technology for biologists      ...
Vizbi Takeaway 2012 - visualising biological data                  Simulation                                 Animation   ...
Vizbi Takeaway 2012 - visualising biological data                   autoFill                 http://autofill.grahamj.com/M...
Vizbi Takeaway 2012 - visualising biological dataMonday, 2 April 2012
Vizbi Takeaway 2012 - visualising biological data                                             Questions?                  ...
Vizbi Takeaway 2012 - visualising biological data                                                       Thanks to...      ...
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Vizbi 2012 Takeaway

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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.

Published in: Design, Technology, Business
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Vizbi 2012 Takeaway

  1. 1. 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
  2. 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 | FlickrMonday, 2 April 2012
  3. 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 biologistsMonday, 2 April 2012
  4. 4. Vizbi Takeaway 2012 - visualising biological data The curse of n-dimensions Juri Pärn EMBL-EBI External Services One dimension... 1 2 3Monday, 2 April 2012
  5. 5. Vizbi Takeaway 2012 - visualising biological data The curse of n-dimensions Two dimensions... 1 2 3 4Monday, 2 April 2012
  6. 6. Vizbi Takeaway 2012 - visualising biological data The curse of n-dimensions... Three dimensions...Monday, 2 April 2012
  7. 7. Vizbi Takeaway 2012 - visualising biological data The curse of n-dimensions... Three dimensions...Monday, 2 April 2012
  8. 8. Vizbi Takeaway 2012 - visualising biological data The curse of n-dimensions... Three dimensions...Monday, 2 April 2012
  9. 9. Vizbi Takeaway 2012 - visualising biological data The curse of n-dimensions... Three dimensions...Monday, 2 April 2012
  10. 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.Monday, 2 April 2012
  11. 11. Vizbi Takeaway 2012 - visualising biological data The curse of n-dimensions an example...Monday, 2 April 2012
  12. 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 textMonday, 2 April 2012
  13. 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 imagesMonday, 2 April 2012
  14. 14. Vizbi Takeaway 2012 - visualising biological data Example from Nature Structural & Molecular BiologyMonday, 2 April 2012
  15. 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 blindMonday, 2 April 2012
  16. 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 versionMonday, 2 April 2012
  17. 17. Vizbi Takeaway 2012 - visualising biological data Pathway Visualization & WikiPathways Martijn van Iersel Saez-Rodriguez Group http://www.wikipathways.orgMonday, 2 April 2012
  18. 18. Vizbi Takeaway 2012 - visualising biological data Editing pathwaysMonday, 2 April 2012
  19. 19. Vizbi Takeaway 2012 - visualising biological data Pathways Genes 90 90 5 26 26 15 1Monday, 2 April 2012
  20. 20. Vizbi Takeaway 2012 - visualising biological data Systems Biology Graphical Notation (SBGN) Macro Simple Catalysis molecule CloneMonday, 2 April 2012
  21. 21. Vizbi Takeaway 2012 - visualising biological data LibSBGN Reference Rend. Ext. PathVisio SBGN-EDMonday, 2 April 2012
  22. 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_controlMonday, 2 April 2012
  23. 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)Monday, 2 April 2012
  24. 24. Vizbi Takeaway 2012 - visualising biological data Encoding schemes Adapted from Mackinlay J (1986) Automating the design of graphical presentations of relational information.Monday, 2 April 2012
  25. 25. Vizbi Takeaway 2012 - visualising biological data Accuracy of Quantitative Perceptual Tasks Cleveland, W.S. & McGill, R. Science 229, 828–833 (1985).Monday, 2 April 2012
  26. 26. Vizbi Takeaway 2012 - visualising biological data Mapping data types to encoding Mackinlay J (1986) Automating the design of graphical presentations of relational information.Monday, 2 April 2012
  27. 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.Monday, 2 April 2012
  28. 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 DIVERGINGMonday, 2 April 2012
  29. 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 DesignersMonday, 2 April 2012
  30. 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 expertiseMonday, 2 April 2012
  31. 31. Vizbi Takeaway 2012 - visualising biological data Data visualisation technology for biologists Benedetta Baldi Computational Neurobiology autoFillMonday, 2 April 2012
  32. 32. Vizbi Takeaway 2012 - visualising biological data Simulation Animation Eric KellerMonday, 2 April 2012
  33. 33. Vizbi Takeaway 2012 - visualising biological data autoFill http://autofill.grahamj.com/Monday, 2 April 2012
  34. 34. Vizbi Takeaway 2012 - visualising biological dataMonday, 2 April 2012
  35. 35. Vizbi Takeaway 2012 - visualising biological data Questions? Drew BerryMonday, 2 April 2012
  36. 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/interfacesMonday, 2 April 2012
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