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MCM Website

MCM Website. The underlying technology Dr Stephen Pascoe British Atmospheric Data Centre. Evolving use of the Web. Use of the web has changed a lot since 1995. Websites are increasingly interfaces to dynamic applications Database driven backends. 2 Tier design. MCM Server. Update.

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MCM Website

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  1. MCM Website The underlying technology Dr Stephen Pascoe British Atmospheric Data Centre

  2. Evolving use of the Web • Use of the web has changed a lot since 1995. • Websites are increasingly interfaces to dynamic applications • Database driven backends.

  3. 2 Tier design MCM Server Update MySQL Database Query Query Response Developer Web Server HTML URL Web Browser

  4. Requirements • Find reactions of a species quickly. • Search for species by SMILES string. • Extract sub-mechanisms. • Depict (draw) structures. • Attach context (metadata) to reactions. • Interact easily with current developers tools (Accord) Indexing Coordinates Database design

  5. Indexing • What can we index? • MCM name:Unique NOT Systematic • SMILES string: Systematic NOT Unique • We need a Unique Systematic Identifier. • Unique linear representation: USMILES, IChI • Canonical number. Accord, ICAMS.

  6. Searching Accord can do this BUT not on the web server Web form Calculate Canonical No. C(O)CC 7438297 Search: Database Lookup

  7. Finding Reactions Relational approach MySQL Full Text Search Indexed words Accord DB

  8. Developer interaction

  9. Depicting • The hard part is generating the 2D coordinates. • We need a connection table. • MDL Mol file Accord can do this BUT not on the web server MCM Server MySQL Database Connection Table Insert Export Accord Chemistry MDL Molfile Render PNG image

  10. Developer interaction Export Mol Calc canon.

  11. Context • Every reaction belongs to a category. • Categories are web template URL. • General categories can be refined into more specific ones. • Rate parameters also have a context URL. • By explicitly parameterising SAR rates we could provide full context for rates.

  12. Future • Context for rate coefficients • Know the source of a rate. • Evaluate uncertainty • We would need to redo all SAR calculations. • New developments in Cheminformatics • CML: Could replace Mol files • IChI: The new SMILES? • OpenSource development tools • CDK: Depiction & uninque id. Generation. Integrated species editor.

  13. The End Thanks.

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