Chemistry in Your    PocketShrinking cheminformatics applications          for mobile devices          Dr. Alex M. Clark  ...
Mobile Molecular    from Molecular Materials InformaticsSmartphones                               Tablets                 ...
Background• Cheminformatics domain is desktop and  server software... with a bit of web thrown in• What about ultraportabl...
Sketcher challenges• Many cheminformatics  applications need the user  to draw 2D structures• Normal sketchers need a  mou...
Alternate approach• Need a technique that does not require an  accurate pointing device:             A.M. Clark, Basic pri...
Sketching primitives      1. Pick atoms/bond      2. Choose action      3. Confirm result      no positioning required    ...
Primitives    7
Geometry• Convenient sketching by guestimating geometry• Or specifying explicitly                             8
Templates           • Multiple grafting modes, multiple resultsunguidedguided                                   9
Clipboard• Clipboard is used as a  transient template• Can avoid a lot of  repetitive actions                           10
Gestures• Primitives only require very limited input, e.g.  trackpad... touchscreens can do more:   Finger         Crayon ...
Now what?• Have a sketcher that can draw publication  quality diagrams quickly...• ... next step is to group molecules and...
Directory of          DataSheets glyph:• Represent each row with a molecule                  13
Detail view     14
Editing• Edit structures,  scalar fields,  table structure,  etc.• Each task uses  a full screen  panel                   ...
Templates• Just like normal datasheets• Their content is used to  compose the template  groups:                        16
Reactions• Devices too small for "freeform" editing, but  separate components is viable:    A                B          C ...
Reaction editing    • Dedicated      editor    • Stored as      one row per      reaction    • ELN friendly      format   ...
On tablets             • Landscape               on iPad is               ideal    19
Stoichiometry      20
Communication• Editing and arranging data doesnt happen in  isolation• Mobile apps typically have access to:   - Email att...
Sending email• Include chemical data and an image:                      22
Receiving email• Attachments include  industry standard formats  (MDL), file extensions and  MIME types• Exchange data wit...
Web downloads• Same mechanism as attachments...                     24
WebServices• Server protocol defines form-like interface...             select                emit            service    w...
Building services• WebServices use a simple,  documented protocol• Easy to implement custom services  with PHP• PubChem an...
File transfer• BlackBerry allows full  access to SD card• iOS allows limited file  exchange via iTunes             27
Clipboard and IPC• Can put chemical data or images onto  clipboard, and paste into other apps• Can also launch other apps....
Embedded• The core tools necessary for a  cheminformatics interface have  been built...• ... and are available as a  linka...
Reaction101• Specialised educational app built from MMDS  components• Reaction editing, balancing, Mobile Reagents  integr...
Future plans• The key user-facing cheminformatics  components have been built, tested and are  commercially available• Pri...
Cloud data• MMDS makes key tools available in a mobile  environment...• ... next step is to make the data available.• Work...
MolSync• MMDS front end, server API, web interface                       33
Other devices• iOS, Android, BlackBerry, Windows, Symbian,  WebOS, Qt... all incompatible• ... only common factor is HTML5...
Acknowledgements         http://molmatinf.com• Steve Muskal, Maurizio Bronzetti (Eidogen-  Sertanty)• Greg Landrum, Johann...
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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 http://molmatinf.com• 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

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