1. Pipelining ChemAxon Moises Hassan, Ton van Daelen, Rob Brown ChemAxon Users Group Meeting Budapest, June 6-7 2006

2. …ask more of your data Pipelining ChemAxon ChemAxon components Pipeline Pilot architecture Implementation Timings Future Work

3. …ask more of your data ChemAxon Components Viewers – ChemAxon Molecular Table Viewer Calculators – ChemAxon Calculator Manipulators – ChemAxon Ionize Molecule at pH – ChemAxon MicroSpecies – ChemAxon Standardize Filters – ChemAxon Chemical Terms JChem Base – Connection – CTAB from DB table – Insert – JChem Search JChem Cartridge (under development)

4. …ask more of your data ChemAxon Molecular Table Viewer

5. …ask more of your data ChemAxon Molecular Table Viewer

6. …ask more of your data ChemAxon Calculator

7. …ask more of your data ChemAxon Micro Species

8. …ask more of your data ChemAxon Micro Species Report

9. …ask more of your data ChemAxon Standardize

10. …ask more of your data ChemAxon Chemical Terms

11. …ask more of your data ChemAxon JChem Database Search

12. …ask more of your data ChemAxon Ionize at pH subprotocol

13. …ask more of your data Platform Integration Options Web services SciTegic Enterprise Server Perl API Java API Cmd Line Telnet / FTP SOAP ODBCJDBC OracleISISAccord Application Services Application integration layer Data access layer IBM II Data Sources JavaScript SDK.NET SDK Java SDK Native and Java ClientsBrowser Clients Apache SOAP SDK Various Clients Client side Server side

14. …ask more of your data 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) (v6.0)

15. …ask more of your data Integration of SOAP Web Services 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)

16. …ask more of your data 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 Commercially released in PP 5.0

17. …ask more of your data Java Molecular Weight Example private static final double HYDROGEN_WEIGHT = Hydrogen.atomicWeight(); // get molecule and properties, skip data record if molecule is not found Molecule mol = Molecule.findMolecule(data); if (mol == null) return Component.State.ReadyForInputData; PropertyCollection props = mol.getProperties(); // calculate mol weight and exact weight (most common isotopes) double mw = 0.0; for (Atom atom : mol.getAtoms()) { int numImplH = atom.getNumImplicitHydrogens(); mw += atom.getAtomicWeight(); mw += numImplH*HYDROGEN_WEIGHT; } props.define("Java_MW", mw);

18. …ask more of your data ChemAxon Ionize Java Class OnInitialize() Method

19. …ask more of your data ChemAxon Ionize Java Class OnProcess() Method continue…

20. …ask more of your data ChemAxon Ionize Java Class OnProcess() Method

21. …ask more of your data Clustering and Visualization with ChemAxon BCUT Values

22. …ask more of your data Clustering and Visualization with ChemAxon BCUT Values Equation "BCUT_PC1" Constant: 1.454383 + -0.367600 * "ChemAxon_BCUTBurden[1]" + -0.417106 * "ChemAxon_BCUTBurden[2]" + 0.021342 * "ChemAxon_BCUTBurden[3]" + 0.005342 * "ChemAxon_BCUTBurden[4]" + -0.530599 * "ChemAxon_BCUTCharge[1]" + -0.811792 * "ChemAxon_BCUTCharge[2]" + 0.825596 * "ChemAxon_BCUTCharge[3]" + 0.525619 * "ChemAxon_BCUTCharge[4]" + -0.535487 * "ChemAxon_BCUTHBond[1]" + -0.838793 * "ChemAxon_BCUTHBond[2]" + 0.281795 * "ChemAxon_BCUTHBond[3]" + 0.280152 * "ChemAxon_BCUTHBond[4]" Equation "BCUT_PC2" Constant: -2.434596 + -0.107767 * "ChemAxon_BCUTBurden[1]" + 0.524903 * "ChemAxon_BCUTBurden[2]" + -0.052277 * "ChemAxon_BCUTBurden[3]" + -0.023233 * "ChemAxon_BCUTBurden[4]" + -0.482553 * "ChemAxon_BCUTCharge[1]" + 0.770592 * "ChemAxon_BCUTCharge[2]" + -0.789049 * "ChemAxon_BCUTCharge[3]" + 0.468833 * "ChemAxon_BCUTCharge[4]" + -0.511670 * "ChemAxon_BCUTHBond[1]" + 0.929707 * "ChemAxon_BCUTHBond[2]" + -0.006878 * "ChemAxon_BCUTHBond[3]" + 0.496791 * "ChemAxon_BCUTHBond[4]"

23. …ask more of your data Clustering and Visualization with ChemAxon BCUT Values

24. …ask more of your data Clustering and Visualization with ChemAxon BCUT Values

25. …ask more of your data Preliminary Execution Times Command-line vs. Pipeline Pilot Components (Asinex dataset, IBM IntelliStation 3.2 GHz, 1GB RAM)

26. …ask more of your data Preliminary Execution Times Command-line vs. Pipeline Pilot Components (Asinex dataset, IBM IntelliStation 3.2 GHz, 1GB RAM)

27. …ask more of your data Preliminary Execution Times Command-line vs. Pipeline Pilot Components (Asinex dataset, IBM IntelliStation 3.2 GHz, 1GB RAM)

28. …ask more of your data Conclusions Compatible architectures Pipeline Pilot good prototyping environment for ChemAxons advanced science Multiple deployment options

29. …ask more of your data Future Work Integrate more ChemAxon functionality Let us know what your priorities are Contact –Alex Allardyce: aa@chemaxon.comaa@chemaxon.com –Ton van Daelen: tvd@scitegic.comtvd@scitegic.com

30. …ask more of your data Acknowledgements Moises Hassan Szilard Dorant Beta testers –Robert Feinstein, Kelaroo –Christine Clayton, Takeda –Frank Yan, GNF