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ChemAxon - Pipeline Pilot Integration

ChemAxon - Pipeline Pilot Integration. Ton van Daelen Accelrys, Inc. Outline. Pipeline Pilot ChemAxon components Integration technologies. Pipeline Pilot. Aggregate and Disseminate Information…. An Example of How To Step Forward In The Informatics Evolution. Easily Configurable Apps

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ChemAxon - Pipeline Pilot Integration

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  1. ChemAxon - Pipeline Pilot Integration Ton van Daelen Accelrys, Inc.

  2. Outline Pipeline Pilot ChemAxon components Integration technologies

  3. Pipeline Pilot

  4. Aggregate and Disseminate Information… An Example of How To Step Forward In The Informatics Evolution Easily Configurable Apps Into a Web Service Callable By Any Type Of Interface

  5. Release history - major changes • Version 1.6, August 2009 • New component: "ChemAxon 3D Conformers" • Version 1.5, May 2009 • New components: "ChemAxon MolConverter", "ChemAxon Tautomerization", "ChemAxon Markush Enumeration" • Version 1.4, November 2008 • New components: "LibMCS Clustering", "Molecule to IUPAC Name", "Molecule from IUPAC Name“ • Major upgrade of "ChemAxon Reactor" component • Version 1.3, July 2008 • New component: “Chemical Terms Calculator” • Version 1.2, March 2008 • New components: “ChemAxon Reactor”, “Drop JChem Base Table”, “Create JChem Base Table” • Several components upgraded

  6. Calculator Easy access for the most important calculations

  7. Chemical Terms Calculator New in 1.3 Maximum freedom trough Chemical Terms Expressions for the expert user • Use arbitrary Chemical Terms expressions • Results stored to arbitrary properties • A wide range of ChemAxon functionality can be accessed as Chemical Terms functions

  8. Clustering with LibMCS Maximum Common Substructure (MCS) based clustering New in 1.4 Options: • Size of smallest common substructure to consider • Three levels of heuristics: • Exact (no heuristics) • Fast • Very Fast • Bond type, atom type, charge can optionally be ignored • Disallow “breaking” rings (default)

  9. Markush Enumeration Enumeration of generic structures New in 1.5 • File input • Enumeration type: • Sequential • Random • Number of enumerated structures can be limited (per input structure) • Valence filter • Scaffold alignment • Markush code generation. The scaffold ID can be: • fetched from data field • generated (prefix + number)

  10. “Client side” “Server side” Pipeline Pilot Integration Browser Clients Native and Java Clients Various Clients JavaScript SDK .NET SDK Java SDK SOAP SDK Web services Pipeline Pilot Java API Perl API SOAP Cmd Line Telnet / FTP ODBC JDBC Data access layer Application integration layer Oracle ISIS Accord IBM II Application Services Data Sources

  11. Telnet/FTP Component Execute command line applications on remote server (any platform) No coding required Use files to pass input and output data Secure version (SSH)

  12. Simple method example public double GetCLogP(string SMILES) { // ... Do the calculation ... return clogp; } Configuring SOAP Component SOAP Endpoint - HTTP URL resource Method Name - Name of function (“GetCLogP”) Method Namespace - Found in WSDL (often http://tempuri.org/) SOAP Parameter Names - Name of function parameter (“Name”) Method Parameter Values - Pipeline Pilot property names Property Return Names - What to call the returned value (“Greeting”) Integration of SOAP Web Services

  13. Java on Server component • Create new PP components • Filters, calculators, readers, writers • Single class with three methods • onInitialize • onProcess • onFinalize • Referencing Java classes on server • Interact with Molecular Toolkit

  14. New Java class: ChemAxonComponent Parent class for component classes, implements com.scitegic.pilot.Component Error reporting: all exceptions thrown in onInitializeBody(), onProcessBody(), onFinalizeBody() are caught, logged and reported (re-thrown with added information) Parameters and context always readily available Utility functions for conveniently accessing parameters and properties, e.g.: findStringParameter(String name) Reduced code redundancy, better readability

  15. Conclusions Compatible architectures Pipeline Pilot good prototyping environment for ChemAxon’s advanced science Multiple deployment options

  16. Future Work • Integrate more ChemAxon functionality • Let us know what your priorities are • Acknowledgements • Szilard Dorant • Moises Hassan • Keith Burdick • Contact • Alex Allardyce: aa@chemaxon.com • Ton van Daelen: tvd@accelrys.com

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