Pipelining ChemAxon

Moises Hassan, Ton van Daelen, Rob Brown

ChemAxon User’s Group Meeting

Budapest, June 6-7 2006

…ask more of your data

Pipelining ChemAxon

• ChemAxon components

• Pipeline Pilot architecture

• Implementation

• Timings

• Future Work

…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)

…ask more of your data

ChemAxon Molecular Table Viewer

…ask more of your data

ChemAxon Molecular Table Viewer

…ask more of your data

ChemAxon Calculator

…ask more of your data

ChemAxon Micro Species

…ask more of your data

ChemAxon Micro Species Report

…ask more of your data

ChemAxon Standardize

…ask more of your data

ChemAxon Chemical Terms

…ask more of your data

ChemAxon JChem Database Search

…ask more of your data

ChemAxon Ionize at pH

subprotocol

…ask more of your data

Platform Integration Options

Web services

SciTegic Enterprise Server

PerlAPI

JavaAPI

Cmd Line

Telnet /FTP

SOAP ODBC JDBC

Oracle ISIS Accord

Application Services

Application integration layer Data access layer

IBM II

Data Sources

JavaScriptSDK

.NETSDK

JavaSDK

Native and Java ClientsBrowser Clients

ApacheApache

SOAPSDK

Various Clients

“Client side”

“Server side”

…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)

…ask more of your data

Integration of SOAP Web Services

• Simple method examplepublic 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”)

…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

…ask more of your data

ChemAxon Ionize Java ClassOnInitialize() Method

…ask more of your data

ChemAxon Ionize Java ClassOnProcess() Method

continue…

…ask more of your data

ChemAxon Ionize Java ClassOnProcess() Method

…ask more of your data

Clustering and Visualization with ChemAxon BCUT Values

…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]"

…ask more of your data

Clustering and Visualization with ChemAxon BCUT Values

…ask more of your data

Clustering and Visualization with ChemAxon BCUT Values

…ask more of your data

Preliminary Execution TimesCommand-line vs. Pipeline Pilot Components

(Asinex dataset, IBM IntelliStation 3.2 GHz, 1GB RAM)

…ask more of your data

Preliminary Execution TimesCommand-line vs. Pipeline Pilot Components

(Asinex dataset, IBM IntelliStation 3.2 GHz, 1GB RAM)

…ask more of your data

Preliminary Execution TimesCommand-line vs. Pipeline Pilot Components

(Asinex dataset, IBM IntelliStation 3.2 GHz, 1GB RAM)

…ask more of your data

Conclusions

• Compatible architectures

• Pipeline Pilot good prototyping environment for ChemAxon’s advanced science

• Multiple deployment options

…ask more of your data

Future Work

• Integrate more ChemAxon functionality

• Let us know what your priorities are

• Contact– Alex Allardyce: aa@chemaxon.com– Ton van Daelen: tvd@scitegic.com

…ask more of your data

Acknowledgements

• Moises Hassan

• Szilard Dorant

• Beta testers– Robert Feinstein, Kelaroo– Christine Clayton, Takeda– Frank Yan, GNF