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Building a mobile app ecosystem for chemistry collaboration
Dr. Alex M. Clark
March 2012
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© 2012 Molecular Materials Informatics, Inc. http://molmatinf.com
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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
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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
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Interprocess comms• Apps on
same device
• Share data:
- guided
- unguided
- clipboard
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Network comms• Many different transport
mechanisms
- file export
- web access
- cloud storage
- client-server RPC
• Heterogenerous platforms
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Story
• Illustrating a chemical workflow, involving collaboration between:
‣ 4 chemists...
‣ ... several devices...
‣ ... and lots of apps.
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MolPrime+
Draw publication-quality structure from scratch, using gestures and templates
bit.ly/GEGonX
Added to molecule collection
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Calculated Properties
• Access calculated properties
• Simple properties calculated within the app
• Complex properties use RPC call to web service (log P, MR)
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ChemSpider Mobile
Use Open With to send the structure to the ChemSpider Mobile app
Search and open the web page
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• Prepare an outgoing email
• Includes structure data, and prepared image
• Send to Person B
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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
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MMDS
Structure is prepended to scratch sheet
Can copy/paste into a datasheet of bromodomain inhibitors
Mobile Molecular DataSheet
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MolSync
• Communicate with MolSync• Upload to Dropbox• Create association
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MolSync
• Person C, an experimentalist, accesses shared folder from an iPad
• Opens datasheet with MMDS
• Creates shared association
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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
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MolSync
• Person B uses MolSync to view the datasheet in the shared folder
• Series is complete: open the datasheet with the SAR Table app...
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SAR Table
• Imported content has construct molecules
• Copy first molecule into Scaffold field
• Trim off substituents
• Use the Match feature...
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SAR Table
Initiate the match: calculation is done by remote procedure call
A variety of possibilities: select the preferred one
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SAR Table
• Scaffold has been decorated
• R1 and R2 columns defined
• Rinse and repeat
• Scaffold matching uses previous assignments to influence suggestions
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SAR Table• Can export the table via email as MS
Office documents (.docx, .xlsx)• Structures use vector graphics
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SPRESImobileWant to illustrate a representative synthesis: search for the common fragment using SPRESI
Open With Search
As Product
Search
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SPRESImobile
SearchAll content links to the scientific literature
Can access the journal article with one tap
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Reaction101
• Person D opens email with Reaction101
• Balance, add reagents, store
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Yield101• Opens Yield101 and accesses personal
reactions to obtain the balanced reaction template
• Fills in quantities, adds solvent, checks availability with Mobile Reagents
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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.
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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
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MolSync web
• Raw presentable data wrapped by HTML5 layer: can view, download, render, convert...
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Open Drug Discovery Teams (ODDT)
• Aggregates open data from Twitter
• Crowd-sourced curation
• Flipboard-like app interface
• Free. Current alpha testing
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ODDTfromMolSync
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Acknowledgments
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Steve Muskal, Maurizio Bronzetti
Eidogen-Sertanty
Peter Löw, Josef Eiblmaier, and others
InfoChem
Antony Williams
Royal Society of Chemistry
Sean Ekins
Collaborations in Chemistry
http://molmatinf.comhttp://molsync.comhttp://cheminf20.org
@aclarkxyz