Visualization of Biological Data for Understanding and Analysis

1. Visualization

2. Visualisation The process of representing abstract data to aid in understanding the meaning of the data. Not to be confused with rendering data (drawing pictures) Typically though, we render data in such a way to visualize the information within that data.

3. Introduction Biological data comes from & is of interest to: Chemists : reaction mechanism, drug design Biologists : sequence, expression, homology, function. Structure biologists : atomic structure, fold, classification, function. Medicine : clinical effect Education : Media : Presentation of diverse information to a diverse audience. Each has there own point of view (context). Expert = scientist working within their own field of expertise Non-expert = scientist using data/information outside their field Novice = Non-scientist

4. Web pages These are notoriously badly designed often resulting in the information on that site being unusable. The front page should load quickly The main point should appear on the first full screen Clutter – not logically laid out Too busy – cannot find the salient point 8% men & 0.5% women are colour blind Bad text/fonts Too often it doesn’t work User will go somewhere else The latest wiz-bang stuff only works on the latest browsers Only works in one browser – they only tested on one. Does not conform to standard HTML Not just presentation of results Google is a good design

5. Asking questions • Asking questions • Biological data is very complex • Chemistry, Biology, Physics, Statistics, Medicine.. • Most users will be from a different field • Asking the right question is difficult. • The user cannot use the correct terminology • Too many things to query (2000 attributes in MSD) • SQL : not suitable for most users • Interface too complex • Too many check boxes, widgets etc • Trying to be too clever • The “Go” button is buried somewhere

6. Result presentation • Results • Biological data is complex • Chemistry, physics, biology, statistics, medicine… • Experts users want all the detail • Ie : want to use a specific method • They want all the details • The want (I hope) the statistical validity of the results • The non-expert wants the best practice answer returned within their own context. • The want comparative analysis with other fields • The want to know the results are valid

7. Query design Suitable for text queries Only one logic AND or OR Predefined Easy to use Limited scope 2000 attributes -> 2000 check-boxes ! • The simple text box design is very common

8. Query design Graphical interface Multiple logic AND/OR/NOT Under users control Slower Steep learning curve Some users just cannot get it Intuitive once mastered Pretty

9. Query design Figurative 2D sketch for 3D query (Active sites) Informative – presents meaning for the question Slower Less error prone select distinct entry_id, ligand_id from contact_search sel where neighbour_code_3_letter in ('SER','HIS') and DISTANCE <= 2.0 and type_id = 1 and neighbour_substruct_code = 'side' and MACROMOL_SEC_STRUCT_TYPE = 1 intersect select distinct entry_id, ligand_id from contact_search sel where neighbour_code_3_letter = 'HIS' and ( NEIGHBOUR_ATOM_NAME = 'NE2' and type_id = 1 and distance <= 2.0 or NEIGHBOUR_SYMBOL = 'N' and type_id = 1 and distance <= 2.0) and TYPE_ID != 0 group by entry_id, ligand_id having count(distinct neighbour_residue_id) >= 2 intersect select distinct entry_id, ligand_id from contact_search sel where neighbour_code_3_letter = 'HIS' and NEIGHBOUR_ATOM_NAME = 'NE2' and DISTANCE <= 2.0 and type_id = 1 and neighbour_substruct_code = 'side' and MACROMOL_SEC_STRUCT_TYPE = 2 intersect select distinct entry_id, ligand_id from contact_search sel where neighbour_code_3_letter = 'HIS' and NEIGHBOUR_SYMBOL = 'N' and DISTANCE <= 2.0 and type_id = 1 and neighbour_substruct_code = 'side' and MACROMOL_SEC_STRUCT_TYPE = 3 intersect select distinct entry_id, ligand_id from residue_contact sel where neighbour_code_3_letter in ('HIS','SER','HIS') and BOND_STRENGTH != 10 group by entry_id, ligand_id having count(*) >= 3; HIS|SER:S/H>C2.0 HIS.ne2:S/S>C2.0 HIS.[n]:S/T>C2.0

10. YAMGP (yet another molecular graphics program) • Many different programs are available VMD AstexViewer@MSD-EBI LigPlot Quanta InsightII Bobscript WebMol Frodo iMol Chime Grasp Pymol POVRay Spock Rasmol Pymol Mage Raster3D Yasara Molscript Chimera O MolMol Whatif Frodo XtalView WebLab-viewer Swiss-PDBviewer

11. Result visualisation • Multiple types of biological data • Textual data • 3D structure • 2D chemical sketches • 1D sequence • Node linked • General/derived data • Web pages • Errors/Variance • Data provenance

12. MSD Atlas pages • ID code detail • Summary • Assembly • Sequence • Similarity • Ligands • Visualisation • Links • To other DB • Mapping to Uniprot

13. AstexViewer@MSD-EBI • Java 1.1 Applet • Should run under most browsers • Small footprint, high speed. • Structure • Line, stick, ball & stick, sphere, schematic, surface + texture map. • Written by Mike Hartshorn (Astex therapeutics Ltd). • Multiple structures supported

14. AstexViewer@MSD-EBI • Sequence • Multiple sequence alignment • Editing, • Annotation, colours… • Consensus alignment • Pick, Brushing & Magic lens

15. Chemistry • 2D flat representation • Annotation, colours… • Interaction types • Placement fn(contact distance) • Editable • Pick, Brush and magic lens

16. Graphs • Graphs • 2D, 2D grid and ND • Linkage plots • Annotation, colours… • Ramachandran, etc… • Pick, Brush Magic Len

17. AstexViewer@MSI-EBI Visualisation Lensing Linked views Brushing Picking Flying views Hyperbolic distortion Animation Solid rendering Depth cues Colour,lighting Highlighting Etc…

18. Visualisation : comparative analysis Similarity/Difference Data superposition Attribute display Colour, size… Correlation Attribute mapping Sequence colour by structure alignment

19. Animation Animation Time dependent display Reaction chemistry Visual clues. Expression data Shown as… Rotation Flash On/off Object Synchronization Size, Colour…. Sound NO : incredibly annoying Animation Example

20. Visualization- Summary Rendering data is not visualization Not just the display of results Hugh array of non-specific techniques – and entire scientific field ! Example