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Chemistrify the Web

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Jean-Claude Bradley Memorial Symposium July 2014 Unilever Centre, Cambridge

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Chemistrify the Web

  1. 1. Chemistrifying the Web Noel M. O’Boyle Coupling Online Chemistry Resources for Education and Research NextMove Software, Cambridge, UK and Developer with Open Babel, GaussSum, Cinfony, cclib July 2014 Jean-Claude Bradley memorial symposium
  2. 2. http://usefulchem.wikispaces.com/Docking
  3. 3. http://usefulchem.wikispaces.com/First+100+Targets
  4. 4. http://usefulchem.wikispaces.com/D-EXP015
  5. 5. http://usefulchem.wikispaces.com/UClib005
  6. 6. Page History
  7. 7. Developing and deploying chemistry software • Choose a chemistry toolkit (e.g. CDK, Open Babel, RDKit) • Write a chemistry application using the toolkit • Make the application available for download • Users download the application, install and run it • Problems: – Requires certain level of expertise to develop – Difficulties installing (Administrator rights, conflicts with other software) – Supporting different platforms (Macs, Windows) – User interface design is difficult and slow, so command-line applications are common – Typically, users need to be familiar with SMILES strings, SDF files
  8. 8. Developing and deploying chemistry software • Choose a chemistry toolkit (e.g. CDK, Open Babel, RDKit) • Write a chemistry application using the toolkit • Make the application available for download • Users download the application, install and run it • Problems: – Requires certain level of expertise to develop – Difficulties installing (Administrator rights, conflicts with other software) – Supporting different platforms (Macs, Windows) – User interface design is difficult and slow, so command-line applications are common – Typically, users need to be familiar with SMILES strings, SDF files
  9. 9. CDK web services Chemical Identifier Resolver Existing web interface e.g. Google docs, Second Life, web page ONS web services Using online resources to develop software
  10. 10. http://onswebservices.wikispaces.c om/ http://onswebservices.wikispaces.com/
  11. 11. http://onswebservices.wikispaces.c om/ http://www.chemspider.com/aboutservices.aspx
  12. 12. http://onswebservices.wikispaces.c om/ http://cactus.nci.nih.gov/chemical/structure
  13. 13. http://onswebservices.wikispaces.c om/ CDK web services: http://rest.rguha.net/
  14. 14. Chemistrifying Google docs http://onswebservices.wikispaces.com/GoogleAppsScripts Work by Jean-Claude Bradley, Rich Apodaca, Andy Lang Uses ChemSpider, Chemical Identifier Resolver, ONS webservices
  15. 15. Chemistrifying web pages
  16. 16. Find PDB codes and add link to Jmol Before After
  17. 17. Annotate online journals with reviews Online abstract for BMC Bioinformatics article Adding discussions from blog posts
  18. 18. Add molecular depictions to web pages http://baoilleach.blogspot.co.uk/2009/11/ann-chemical-structure-resolver-with.html • TwirlyMol is a (basic) molecular viewer written in Javascript • The Chemical Identifier Resolver has support for conversion of chemical names to TwirlyMols • To add an interactive 3D structure to a web page, it just takes a single line of HTML
  19. 19. Combining web services to create a toolkit • Webel is a chemistry toolkit that runs entirely using web services – CDK webservices by Rajarshi Guha, hosted by Ola Spjuth at Uppsala University – NCI/CADD Chemical Identifier Resolver by Markus Sitzmann (uses Cactvs for much of backend) • Easy to install – no dependencies (a single Python file) • Can be used in environments where installing a traditional cheminformatics toolkit is not possible • Web services may provide additional services not available elsewhere • Webel is part of Cinfony (http://cinfony.googlecode.com) – N.M. O’Boyle and G.R. Hutchison. Chem. Cent. J. 2008, 2, 24.
  20. 20. Webel in the browser Available at http://tinyurl.com/cm7005-b
  21. 21. Chemistry in immersive environments
  22. 22. MineCraft as a Chemistry Platform
  23. 23. MineCraft as a Chemistry Platform • Raspberry Pi edition Feb 2013 – Runs on cheap hardware (£24) – Only single-user but… – Has API that allows the MineCraft world to be manipulated by software • getBlock, setBlock, getPos, setPos,… • Could write Python scripts to ‘inject’ chemistry into MineCraft – Develop games/quizzes, visualize molecules in 3D, … – Left as an exercise for your imagination
  24. 24. Chemistrifying the Web Coupling Online Chemistry Resources for Education and Research In memory of Jean-Claude Bradley
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Jean-Claude Bradley Memorial Symposium July 2014 Unilever Centre, Cambridge

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