interfacing the jchem suite outside of java
DESCRIPTION
Interfacing the JChem Suite outside of Java. Jonathan Lee. Solutions for Cheminformatics. Outline. JChem Interfaces Situational Factors SQL .NET Web Services Details Demo Workflow Integrations. Interfaces to JChem Suite of Tools. Java Direct POJO and Server-side JSP SQL - PowerPoint PPT PresentationTRANSCRIPT
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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