interfacing the jchem suite outside of java jonathan lee solutions for cheminformatics
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Interfacing the JChem Suite outside of Java
Jonathan Lee
Solutions for Cheminformatics
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Outline• JChem Interfaces
• Situational Factors
• SQL
• .NET
• Web Services– Details– Demo
• Workflow Integrations
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Interfaces to JChem Suite of ToolsJava
• Direct POJO and Server-side JSP
SQL
• JChem Cartridge for environments with Oracle
.NET
• Interoperability with .NET framework
Web Services
• Platform and Language-Independent
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Situational Factors
Language Strength
• Does Java, .NET, SQL, or other Web language figure prominently?
Data Environment
• Is Oracle the target structure database?
End User Environment
• Will the user have a Desktop Client or a Web Client?
Overall Technical Architecture
• Do you use a Service Oriented Architecture?
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JChem Cartridge• Leverage Oracle Database Advantages
• Stored procedures quickly handle database work
• External communication with JChem Server for process intensive work
Supports•SQL•Most JChem Modules (Searching, Standardization, Reactor, Chemical Terms, Calculator Plugins, …)
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.NET• Pure .NET solution for all non-GUI elements
• Marvin .NET GUI components (Marvin 5.3)
• New no cost native .dll is simpler, faster, than earlier JNBridge solution
Supports•All .NET languages (C#, VB.NET, …)•All of JChem Suite (except Cartridge and Marvin Beans classes)
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JChem Web Services• WS-I, SOAP, and WSDL standards
• Reusable and accessible to other services
• Automated client-side code generation
Supports•Web Languages: AJAX/JavaScript, Perl, Python, Ruby, …•App languages: Java, C#, …•Growing list of JChem Modules (Searching, Standardization, Chemical Terms, Molecule Conversion)
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Unlocking the Scripting Menagerie
<soap:Body> <evaluateReturnNum xmlns="http://webservice.jchem.chemaxon">
<target>CC=CC</target> <expression>logp</expression>
</evaluateReturnNum> </soap:Body>
loc = ChemicalTermsWS_client.ChemicalTermsWSLocator()evaluator = loc.getChemicalTermsWSHttpSoap11Endpoint()req = ChemicalTermsWS_client.evaluateReturnNumRequest()req.Target = ‘CC=CC’req.Expression = ‘logp’resp = evaluator.evaluateReturnNum(req)
var xhr = new XMLHttpRequest();xhr.open(method, url, async);xhr.setRequestHeader('Content-Type', 'text/xml; charset=utf-8');xhr.send(createEvaluateReturnNumRequest(“CC=CC”, “logp”);
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JChem WS Server Architecture
Apache Open Source Components
•Axis2 Web Service Engine and Tomcat Web Container
Image here
OS List
•Windows
•Unix
•Linux (SUSE, Red Hat, Ubuntu, Gentoo)
•Mac OS X
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Current and Future Services• JChem Search Service
• Standardization Service
• Molecular Conversion Service
• Chemical Terms Evaluation ServiceFuture Enhancements•SQL Execution•Database Connection and Structure Manipulation•Batch Processing•Future JChem Enhancements and Refactorings
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AJAX Demo of JChem Web Services
JChemSearch Web Service - www.chemaxon.com/ajax
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Workflow Integrations
ChemAxon components exist for several workflow software vendors
- Pipeline Pilot
- KNIME (by Infocom)
- Inforsense
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Find out more about JChem Cartridge
• Product descriptions & linkswww.chemaxon.com/product/jc_cart.html
• Forumwww.chemaxon.com/forum/forum7.html
• Presentations and posterswww.chemaxon.com/conf/JChem_Cartridge.ppt
• Download
www.chemaxon.com/jchem/download.html
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Find out more about .NET integration
• Product descriptions & linkswww.chemaxon.com/NET_support_land.html
• Forumwww.chemaxon.com/forum/forum7.html
• Presentations and posterswww.chemaxon.com/conf
• Download
www.chemaxon.com/jchem/download.html
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Find out more about JChem Web Services
• Product descriptions & linkswww.chemaxon.com/product/jc_webservices.html
• Forumwww.chemaxon.com/forum/forum93.html
• Presentations and posterswww.chemaxon.com/conf
• Download
www.chemaxon.com/webservices/
download.html