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Chemistry in Your Pocket (Dr. Alex M. Clark)


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Shrinking cheminformatics applications for mobile devices

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Chemistry in Your Pocket (Dr. Alex M. Clark)

  1. 1. Chemistry in Your PocketShrinking cheminformatics applications for mobile devices Dr. Alex M. Clark Anaheim, March 2011 1
  2. 2. Mobile Molecular from Molecular Materials InformaticsSmartphones Tablets 2
  3. 3. Background• Cheminformatics domain is desktop and server software... with a bit of web thrown in• What about ultraportable devices?• Smartphones and tablets powerful enough...• ... but the user interface is very different. 3
  4. 4. Sketcher challenges• Many cheminformatics applications need the user to draw 2D structures• Normal sketchers need a mouse• A touchscreen is not the same! 4
  5. 5. Alternate approach• Need a technique that does not require an accurate pointing device: A.M. Clark, Basic primitives for molecular diagram sketching, Journal of Cheminformatics 2010, 2:8.• Primitives maximise information content from limited user input, by inference and automation• Publication quality results 5
  6. 6. Sketching primitives 1. Pick atoms/bond 2. Choose action 3. Confirm result no positioning required 6
  7. 7. Primitives 7
  8. 8. Geometry• Convenient sketching by guestimating geometry• Or specifying explicitly 8
  9. 9. Templates • Multiple grafting modes, multiple resultsunguidedguided 9
  10. 10. Clipboard• Clipboard is used as a transient template• Can avoid a lot of repetitive actions 10
  11. 11. Gestures• Primitives only require very limited input, e.g. trackpad... touchscreens can do more: Finger Crayon selection Context drawing 11 menus
  12. 12. Now what?• Have a sketcher that can draw publication quality diagrams quickly...• ... next step is to group molecules and data together into Molecular DataSheets: 12
  13. 13. Directory of DataSheets glyph:• Represent each row with a molecule 13
  14. 14. Detail view 14
  15. 15. Editing• Edit structures, scalar fields, table structure, etc.• Each task uses a full screen panel 15
  16. 16. Templates• Just like normal datasheets• Their content is used to compose the template groups: 16
  17. 17. Reactions• Devices too small for "freeform" editing, but separate components is viable: A B C D 17
  18. 18. Reaction editing • Dedicated editor • Stored as one row per reaction • ELN friendly format 18
  19. 19. On tablets • Landscape on iPad is ideal 19
  20. 20. Stoichiometry 20
  21. 21. Communication• Editing and arranging data doesnt happen in isolation• Mobile apps typically have access to: - Email attachments - HTTP connections - File transfer by cable - Other installed apps 21
  22. 22. Sending email• Include chemical data and an image: 22
  23. 23. Receiving email• Attachments include industry standard formats (MDL), file extensions and MIME types• Exchange data with other mobile users, or the outside world• Opens directly into app... 23
  24. 24. Web downloads• Same mechanism as attachments... 24
  25. 25. WebServices• Server protocol defines form-like interface... select emit service web form service submit return form data web service 25
  26. 26. Building services• WebServices use a simple, documented protocol• Easy to implement custom services with PHP• PubChem and ChEBI wrappers available• Special feature for URL opening... 26
  27. 27. File transfer• BlackBerry allows full access to SD card• iOS allows limited file exchange via iTunes 27
  28. 28. Clipboard and IPC• Can put chemical data or images onto clipboard, and paste into other apps• Can also launch other apps... 28
  29. 29. Embedded• The core tools necessary for a cheminformatics interface have been built...• ... and are available as a linkable library, for iOS devices.• Mobile Reagents and iProtein both use the embedded sketcher. 29
  30. 30. Reaction101• Specialised educational app built from MMDS components• Reaction editing, balancing, Mobile Reagents integration, email, image creation... 30
  31. 31. Future plans• The key user-facing cheminformatics components have been built, tested and are commercially available• Priority now is to integrate these tools into real workflows• e.g. custom web services, electronic lab notebook client, specialised tools... 31
  32. 32. Cloud data• MMDS makes key tools available in a mobile environment...• ... next step is to make the data available.• Work in progress: MolSync• Data synchronisation service 32
  33. 33. MolSync• MMDS front end, server API, web interface 33
  34. 34. Other devices• iOS, Android, BlackBerry, Windows, Symbian, WebOS, Qt... all incompatible• ... only common factor is HTML5. 34
  35. 35. Acknowledgements• Steve Muskal, Maurizio Bronzetti (Eidogen- Sertanty)• Greg Landrum, Johannes Maier, Alain Deschenes, Antony Williams, Christoph Steinbeck, Evan Bolton, David Thompson, Rich Apodaca, among others 35