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Building a mobile appecosystem for chemistrycollaboration                                               Dr. Alex M. Clark ...
Mobile apps• Most action is for iOS• Chemistry feature set is becoming very  powerful: content consumption and creation• S...
So many apps• Should be limited in scope, narrow focus...• ... combine them and they become a toolchest• Apps can be a maj...
Interprocess comms• Apps on  same device• Share data: - guided - unguided - clipboard                4
Network comms• Many different transport  mechanisms    - email    - file export    - web access    - cloud storage    - cli...
Story• Illustrating a chemical  workflow, involving  collaboration between:   ‣ 4 chemists...   ‣ ... several devices...   ...
MolPrime+Draw publication-quality structurefrom scratch, usinggestures andtemplates  bit.ly/GEGonXAdded to moleculecollect...
Calculated Properties• Access calculated properties• Simple properties calculated  within the app• Complex properties use ...
ChemSpider  Mobile Use Open With to send the structure to the ChemSpider Mobile app Search and open the web page
Email• Prepare an outgoing  email• Includes structure data,  and prepared image• Send to Person B
MMDS• Email offers a list of apps that  can handle each attachment• Person B is a power user...• ... opens the structure fi...
MMDSMobile Molecular DataSheet     Structure is     prepended to     scratch sheet     Can copy/paste into     a datasheet...
MolSync• Communicate with MolSync• Upload to Dropbox• Create association
MolSync  • Person C, an    experimentalist, accesses    shared folder from an iPad  • Opens datasheet with    MMDS  • Crea...
MMDS• Runs the experiment,  measures the activity values• Enters the data fields using  MMDS• Resyncs the file via MolSync.....
MolSync• Person B uses MolSync to  view the datasheet in the  shared folder• Series is complete: open the  datasheet with ...
SAR Table• Imported content has construct  molecules• Copy first molecule into Scaffold  field• Trim off substituents• Use t...
SAR TableInitiate the match:calculation is done byremote procedurecallA variety ofpossibilities: selectthe preferred one
SAR Table• Scaffold has been decorated• R1 and R2 columns defined• Rinse and repeat• Scaffold matching uses previous assign...
SAR Table• Can export the table via email as MS  Office documents (.docx, .xlsx)• Structures use vector graphics
SPRESImobile Want to illustrate a representative synthesis: search for the common fragment using SPRESIOpen               ...
SPRESImobile  All content links to  the scientific  literature  Can access the  journal article with  one tap
Reaction101    • Person D      opens email      with      Reaction101    • Balance, add      reagents,      store
Yield101• Opens Yield101 and accesses personal  reactions to obtain the balanced reaction  template• Fills in quantities, ...
Yield101• Prepares a printable PDF  summary of the reaction• Takes a hard copy to the  lab...• ... performs the experiment...
MolSync• A number of chemical data files  have been created and shared  on a Dropbox account• Files in the Public folder ca...
MolSync web• Raw presentable data wrapped by HTML5 layer: can  view, download, render, convert...
Open Drug Discovery        Teams (ODDT)• Aggregates open  data from Twitter• Crowd-sourced  curation• Flipboard-like  app ...
fromMolSync   ODDT
AcknowledgmentsSteve Muskal, Maurizio Bronzetti     Eidogen-SertantyPeter Löw, Josef Eiblmaier, and others     InfoChemAnt...
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Building a mobile app ecosystem for chemistry collaboration

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Presentation by Alex M. Clark at the 2012 American Chemical Society meeting in San Diego, in the Chemical Information division.

Published in: Technology, Education
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Building a mobile app ecosystem for chemistry collaboration

  1. 1. Building a mobile appecosystem for chemistrycollaboration Dr. Alex M. Clark March 2012© 2012 Molecular Materials Informatics, Inc. http://molmatinf.com 1
  2. 2. Mobile apps• Most action is for iOS• Chemistry feature set is becoming very powerful: content consumption and creation• Structure drawing, reactions, datasheets• Access to webservices, calculations, graphics, RPC, social networking, cloud storage 2
  3. 3. So many apps• Should be limited in scope, narrow focus...• ... combine them and they become a toolchest• Apps can be a major part of a workflow 3
  4. 4. Interprocess comms• Apps on same device• Share data: - guided - unguided - clipboard 4
  5. 5. Network comms• Many different transport mechanisms - email - file export - web access - cloud storage - client-server RPC• Heterogenerous platforms 5
  6. 6. Story• Illustrating a chemical workflow, involving collaboration between: ‣ 4 chemists... ‣ ... several devices... ‣ ... and lots of apps.
  7. 7. MolPrime+Draw publication-quality structurefrom scratch, usinggestures andtemplates bit.ly/GEGonXAdded to moleculecollection
  8. 8. Calculated Properties• Access calculated properties• Simple properties calculated within the app• Complex properties use RPC call to web service (log P, MR)
  9. 9. ChemSpider Mobile Use Open With to send the structure to the ChemSpider Mobile app Search and open the web page
  10. 10. Email• Prepare an outgoing email• Includes structure data, and prepared image• Send to Person B
  11. 11. MMDS• Email offers a list of apps that can handle each attachment• Person B is a power user...• ... opens the structure file with the Mobile Molecular DataSheet
  12. 12. MMDSMobile Molecular DataSheet Structure is prepended to scratch sheet Can copy/paste into a datasheet of bromodomain inhibitors
  13. 13. MolSync• Communicate with MolSync• Upload to Dropbox• Create association
  14. 14. MolSync • Person C, an experimentalist, accesses shared folder from an iPad • Opens datasheet with MMDS • Creates shared association
  15. 15. MMDS• Runs the experiment, measures the activity values• Enters the data fields using MMDS• Resyncs the file via MolSync...• ... uploads modified version to Dropbox folder
  16. 16. MolSync• Person B uses MolSync to view the datasheet in the shared folder• Series is complete: open the datasheet with the SAR Table app...
  17. 17. SAR Table• Imported content has construct molecules• Copy first molecule into Scaffold field• Trim off substituents• Use the Match feature...
  18. 18. SAR TableInitiate the match:calculation is done byremote procedurecallA variety ofpossibilities: selectthe preferred one
  19. 19. SAR Table• Scaffold has been decorated• R1 and R2 columns defined• Rinse and repeat• Scaffold matching uses previous assignments to influence suggestions
  20. 20. SAR Table• Can export the table via email as MS Office documents (.docx, .xlsx)• Structures use vector graphics
  21. 21. SPRESImobile Want to illustrate a representative synthesis: search for the common fragment using SPRESIOpen As Search ProductWith
  22. 22. SPRESImobile All content links to the scientific literature Can access the journal article with one tap
  23. 23. Reaction101 • Person D opens email with Reaction101 • Balance, add reagents, store
  24. 24. Yield101• Opens Yield101 and accesses personal reactions to obtain the balanced reaction template• Fills in quantities, adds solvent, checks availability with Mobile Reagents
  25. 25. Yield101• Prepares a printable PDF summary of the reaction• Takes a hard copy to the lab...• ... performs the experiment. Enters the yield data, shares the scheme with MolSync.
  26. 26. MolSync• A number of chemical data files have been created and shared on a Dropbox account• Files in the Public folder can be shared on the web, or tweeted• Tweeting certain hash tags has interesting effects
  27. 27. MolSync web• Raw presentable data wrapped by HTML5 layer: can view, download, render, convert...
  28. 28. Open Drug Discovery Teams (ODDT)• Aggregates open data from Twitter• Crowd-sourced curation• Flipboard-like app interface• Free. Current alpha testing
  29. 29. fromMolSync ODDT
  30. 30. AcknowledgmentsSteve Muskal, Maurizio Bronzetti Eidogen-SertantyPeter Löw, Josef Eiblmaier, and others InfoChemAntony Williams Royal Society of Chemistry http://molmatinf.com http://molsync.comSean Ekins http://cheminf20.org Collaborations in Chemistry @aclarkxyz 30

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