Chem Axon — Pipeline Pilot Integration Ton van

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Chem. Axon - Pipeline Pilot Integration Ton van Daelen Accelrys, Inc. Chem. Axon - Pipeline Pilot Integration Ton van Daelen Accelrys, Inc.

Outline • Pipeline Pilot • Chem. Axon components • Integration technologies Outline • Pipeline Pilot • Chem. Axon components • Integration technologies

Pipeline Pilot Pipeline Pilot

Aggregate and Disseminate Information… An Example of How To Step Forward In The Informatics 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

Release history - major changes • Version 1. 6, August 2009 – New component: Release history - major changes • Version 1. 6, August 2009 – New component: "Chem. Axon 3 D Conformers" • Version 1. 5, May 2009 – New components: "Chem. Axon Mol. Converter", "Chem. Axon Tautomerization", "Chem. Axon Markush Enumeration" • Version 1. 4, November 2008 – New components: "Lib. MCS Clustering", "Molecule to IUPAC Name", "Molecule from IUPAC Name“ – Major upgrade of "Chem. Axon Reactor" component • Version 1. 3, July 2008 – New component: “Chemical Terms Calculator” • Version 1. 2, March 2008 – New components: “Chem. Axon Reactor”, “Drop JChem Base Table”, “Create JChem Base Table” – Several components upgraded

Calculator Easy access for the most important calculations Calculator Easy access for the most important calculations

Chemical Terms Calculator Maximum freedom trough Chemical Terms Expressions for the expert user • Chemical Terms Calculator Maximum freedom trough Chemical Terms Expressions for the expert user • Use arbitrary Chemical Terms expressions • Results stored to arbitrary properties • A wide range of Chem. Axon functionality can be accessed as Chemical Terms functions New in 1. 3

Clustering with Lib. MCS Maximum Common Substructure (MCS) based clustering Options: • Size of Clustering with Lib. MCS Maximum Common Substructure (MCS) based clustering 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) New in 1. 4

Markush Enumeration of generic structures • File input • Enumeration type: – Sequential – Markush Enumeration of generic structures • 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) New in 1. 5

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

Telnet/FTP Component • Execute command line applications on remote server (any platform) • No 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)

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

Java on Server component • Create new PP components – Filters, calculators, readers, writers Java on Server component • Create new PP components – Filters, calculators, readers, writers • Single class with three methods – on. Initialize – on. Process – on. Finalize • Referencing Java classes on server • Interact with Molecular Toolkit

New Java class: Chem. Axon. Component • Parent class for component classes, implements com. New Java class: Chem. Axon. Component • Parent class for component classes, implements com. scitegic. pilot. Component • Error reporting: all exceptions thrown in on. Initialize. Body(), on. Process. Body(), on. Finalize. Body() 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. : find. String. Parameter(String name) • Reduced code redundancy, better readability

Conclusions • Compatible architectures • Pipeline Pilot good prototyping environment for Chem. Axon’s advanced Conclusions • Compatible architectures • Pipeline Pilot good prototyping environment for Chem. Axon’s advanced science • Multiple deployment options

Future Work • Integrate more Chem. Axon functionality • Let us know what your Future Work • Integrate more Chem. Axon functionality • Let us know what your priorities are • Acknowledgements – Szilard Dorant – Moises Hassan – Keith Burdick • Contact – Alex Allardyce: [email protected] com – Ton van Daelen: [email protected] com




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