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Chemistry made mobile – the expanding world of chemistry in the hand


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Mobile devices are now mainstream handheld computers providing access to computational power and storage that a decade ago was available only on desktop computers. In terms of chemistry informatics the majority of capabilities that were previously found only on desktop computers is fast migrating to mobile devices making use of the combination of powerful visualization capabilities, fast cloud-based calculations, websites optimized for the mobile platforms, and delivering “apps”. This presentation will provide an overview of how access to chemistry continues to be made increasingly mobile and specifically on how the Royal Society of Chemistry is contributing to this computing environment.

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Chemistry made mobile – the expanding world of chemistry in the hand

  1. 1. Chemistry made mobile – the expanding world of chemistry in the hand Antony J Williams ACS San Diego March 2012
  2. 2. Mobilizing Chemistry We live in the time of “Generation App” Mobile devices, apps, cloud-based services and databases provide “Chemistry in the Hand” Hundreds of apps for multiple mobile devices are appearing: iPhone, iPads, Android, Blackberry etc. It’s not just Chemistry…Science has gone Mobile..
  3. 3. Increasing Mobility… For this audience…how mobile are we?  Smartphone?  Tablet?  Apple iOS?  Android?  Who does NOT have a tablet or smartphone?
  4. 4. Mobile Chemistry is not new
  5. 5. Now Mobile Chemistry is different.. Chemistry is made mobile as  Websites  Apps  Podcasts  eBooks  And then…
  6. 6. What’s Important on iTunes AppStore
  7. 7. What’s Important on iTunes AppStore Is there Science? Is thereChemistry?
  8. 8. Now Mobile Chemistry is different.. Chemistry is made mobile as  Websites  Apps  Podcasts  eBooks  And then…
  9. 9. iTunes Episodes
  10. 10. iTunes Materials
  11. 11. Free and Expensive
  12. 12. This Presentation….segregates Publisher apps Accessing publications eBooks Theoretical chemistry Data and chemical dictionaries Chemical calculators Safety and Hazards Chemical Reactions Structure drawing apps Analytical chemistry Biomolecules
  13. 13. Scientific Publishers Apps Scientific publishers release apps to:  Provide mobile access to content  Search and deliver content to its registered users and engage other possible users  Greater accessibility means greater readership  Revenue generation from the content, not the app
  14. 14. Increase in Scientific Publisher Apps
  15. 15. Do YOU read “mobile” scientific papers? I am a browser of papers on my iPhone… I will read PDF files on my tablet But I read my “Nook books” on my Nook, my computer, iPhone and iPad…
  16. 16. Accessing Publications Various apps are available for accessing and searching across the literature  CAS’ Scifinder Mobile  Accessing PubMed Apps are available for managing your own publication library – integrated to desktop applications  Mendeley  Papers
  17. 17. SciFinder Mobile
  18. 18. PubMed on TapiPhone and iPad:
  19. 19. PubMed on TapiPhone and iPad:
  20. 20. Managing Papers
  21. 21. Papers
  22. 22. Mendeley on iPhone
  23. 23. eBooksiPad: Mobile devices can deliver “books” as “apps” An ideal example in Chemistry is Theodore Gray’s “The Elements” An eBook with rotatable objects, 3D stereoscopic images, videos, linked to the Wolfram Alpha computational engine and even a song…
  24. 24. Wikipedia Chemistry
  25. 25. The Future of Chemistry eBooks What will we see?  eBooks already link to computational engines  3D rotating molecules are expected – stereoscopic viewing will become standard?  Kinect type interface for a tablet?  Interactive graphing – data mine public websites to include data  Direct model generation and prediction  But doesn’t this sound like an ELN set of tools???
  26. 26. Theoretical Chemistry Only a small number of theoretical chemistry apps are available Theoretical chemistry means so much math so chemistry integrated to math functions would make sense….Think Wolfram Alpha and Mathematica
  27. 27. Atom in a BoxiPod, iPhone and iPad:
  28. 28. MolsimiPod, iPhone and iPad:
  29. 29. Data and Chemical Dictionaries Apps are ideal for delivering reference data Public domain data has been assembled into small collections and delivered via app interfaces Data collections include  Elements  Lists of chemicals  Drugs and Medications
  30. 30. Wikipedia Chemistry
  31. 31. EleMints
  32. 32. Chemistry DictionaryiOS:
  33. 33. Organic Compound BibleiPhone and iPad:
  34. 34. Drugs & Medications (A-Z)iOS:
  35. 35. Epocrates
  36. 36. Chemical Calculators Basic chemical calculations are simple to deliver  Mass calculations  Molarity  Volume  pH
  37. 37. LabCalProiPhone:
  38. 38. DailyCalcs
  39. 39. Buffers
  40. 40. Chemical Safety and Hazards Chemical safety data is simply data tables Most safety/hazard data are public domain and simply rewrapped for app-based delivery
  41. 41. NIOSH Chemical HazardsiPhone and iPad:
  42. 42. NIOSH Chemical HazardsiPhone and iPad:
  43. 43. Structure Drawing as an entry point Structure entry as an entry point to:  Calculations (formula, mass)  Predictions (local or server-based)  Systematic name generation, logP, pKa, NMR prediction, etc.  Database lookup  On device dictionaries (because space doesn’t matter!)  Internet-hosted databases (because the latest content does matter)
  44. 44. Chemical Structure Drawing
  45. 45. Chemical Structure Drawing
  46. 46. Structure drawing on Mobile Personal experiences…I don’t work in a lab now  I mostly draw structures to show the capability  If I draw it’s to search a database but mostly I search by name  Structure drawing to “publish”? I don’t write papers on a tablet yet? Who does? Do you draw structures on a tablet to publish?
  47. 47. Structure Lookup of ChemSpider
  48. 48. Structure Lookup of ChemSpider
  49. 49. Structure Searching ChemSpiderRight platform, Right partner ChemSpider Mobile app – don’t reinvent the wheel Choose the best partners - Alex Clark MMDS app, Yield101, Reaction 101, etc… Three days from tweet to Green Solvent app on iTunes:
  50. 50. ChemSpider Mobile
  51. 51. Open in Browser  Substructure searching  Similarity searching  Depends on responsive services and infrastructure
  52. 52. Infrastructure
  53. 53. Infrastructure Architecture
  54. 54. Chemical Reactions Chemical reactions are very amenable to serving up on mobile applications What is available now?  Teaching basics of chemical reactions  Look-ups against reaction databases  Reaction mechanisms
  55. 55. Named Reactions
  56. 56. Organic Named Reactions
  57. 57. ReactionFlash
  58. 58. Reaction101
  59. 59. Yield 101
  60. 60. Reaction Database Look-up
  61. 61. Reaction Database Look-up
  62. 62. Analytical Chemistry Various type of analytical science can be served:  General capabilities  Spectral display  Tables of constants  NMR  Active nuclei, frequencies  Chemical shift prediction  Mass Spectrometry  Mass calculation:  Infrared  Others….
  63. 63. NMR IsotopesiPhone, iPod & iPad:
  64. 64. Mass Spectrometry: IsotopiaiPhone, iPod & iPad:
  65. 65. Accurate Mass TooliPhone, iPod & iPad:
  66. 66. LabCalPlusIpad:
  67. 67. Spectra in the hand Future (maybe it’s done?) – spectra processed and sent to your phone for viewing Search spectra against an online database for structure identification “Handheld spectrometers” with ChemDoodle Widgets database lookup in the cloud
  68. 68. SpectraSchool and Spectroscopy Tutorials
  69. 69. Spectroscopy in a Suitcase
  70. 70. “App-Based Spectroscopy” What could be possible for spectra?  Process  View  Predict  Analyse Already available  Do we need to process?  View  Predict  Analyse
  71. 71. Spectra on ChemSpider
  72. 72. Spectral Display Mobile devices with Java support can use JSpecView iOS devices require Javascript widgets/HTML5 components
  73. 73. ChemDoodle Web Components An open-source and free HTML5 toolkit. For desktop and mobile browsers.
  74. 74. SpectralGame in the hand
  75. 75. BioScience is Becoming Mobile…GenomePad:
  76. 76. Large Molecules
  77. 77. iKinase for iPad
  78. 78. iKinase for iPhone
  79. 79. Other Scientific Apps There are an abundance of other scientific apps..  Physics  Biology  Medicine  Mathematics  Geology
  80. 80. Mobile Tools in Drug Discovery
  81. 81. Mobile Tools in Drug Discovery
  82. 82. It is so difficult to navigate… IP? What’s the structure? Are they in our file? What’s similar? What’s the Pharmacology target? data? Known Pathways? Competitors? Working On Connections Now? to disease? Expressed in right cell type?
  83. 83. Open PHACTS Project Develop a set of robust standards… Implement the standards in a semantic integration hub Deliver services to support drug discovery programs in pharma and public domain 22 partners, 8 pharmaceutical companies, 3 biotechs 36 months project Guiding principle is open access, open usage, open source - Key to standards adoption -
  84. 84. Already Mobilizing Open PHACTS Javascript widgets
  85. 85. Mobile Annotation and Nanopubs Since we read papers, look at databases, make judgments…and so much on mobile devices…we should annotate! Mobile will be an enabler.. An assertion can be a “nanopublication”.  Scientist X asserts  This relationship is false…  A new relationship exists…  This data suggests…  This work is related to…  And commonly Twitter is an assertion interface!
  86. 86. Open Drug Discovery Teams
  87. 87. Tapping into the Larger Network…
  88. 88. Creating communities around disease
  89. 89. Sourcing information about SciApps Lots of Science Apps Different platforms, different versions How do you find them? Where can developers post information about their apps? NOT Wikipedia!
  90. 90. Conflict of Interest on Wikipedia Wikipedia is an encyclopedia so Where is a good place to centralize App details?
  91. 91. There’s a lot of Mobile Chemistry! Categorization of chemistry apps. More later…
  92. 92. Sourcing information about SciApps Where can developers post information about their apps? NOT Wikipedia! iTunes does not segregate based on science SciMobileApps Wiki…
  93. 93. SciMobileApps Wiki
  94. 94. SciMobileApps Wiki
  95. 95. SciMobile Apps Wiki
  96. 96. SciMobile Apps Wiki Request account: Click for Link Content depends on contributors!
  97. 97. Next in the world of Mobile?
  98. 98. Next in the world of Mobile? 2003!
  99. 99. QR Codes (Quick Response)
  100. 100. Periodic Table of QR Codes
  101. 101. Are we there yet???  Vendor QR codes could link directly to:  Vendor website to reorder  Safety/Toxicity data  Reference data (spectra)  ChemSpider/PubChem
  102. 102. Conclusions “Mobile” is far from novel…it’s mainstream Every ACS there is more mobile adoption – and regular sessions on Mobile! Chemistry apps are now commonplace From here it will be:  Federated data access  More creative tools for collaboration  Hopefully more crowdsourced participation in mobile-enabled curation, annotation and “nanopublication” generation.
  103. 103. ACS Philadelphia 2012 Harry Pence and Antony Williams session Mobile devices, augmentedreality, and the mobile classroom. Abstracts Welcome
  104. 104. Acknowledgments Sean Ekins – SciMobileApps wiki Alex Clark – ChemSpider Mobile RSC Cheminformatics team – Mobile ChemSpider and ChemSpider SyntheticPages JC Bradley and Andy Lang – SpectralGame Kevin Thiesen – ChemDoodle James Jack – ChemMobi
  105. 105. Other Resources Smart Phones – A Powerful Tool in the Classroom Mobile chemistry - chemistry in your hands and in your face Mobile apps for chemistry in the world of drug discovery Slideshare presentations  Chemistry in the hand the delivery of structure databases and spectroscopy gaming on mobile devices  Chemistry in your hand using mobile devices to access public chemistry compound data
  106. 106. Thank youEmail: williamsa@rsc.orgTwitter: ChemConnectorPersonal Blog: www.chemconnector.comSLIDES: