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Informatics Projects |
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If you are working within the ISB firewall then more complete documentation can be found on the main informatics group wiki.
Book Chapters
General help on programming, in particular the development of enterprise systems for the life sciences, can be found in:
Boyle J. (2008). "Programming Languages" in Edwards D, Hansen D and Stajich J (Eds), Bioinformatics Tools and Applications, Springer (forthcoming).
General information on Cytoscape, and how to contribute, can be found in:
Killcoyne S, Carter G, Smith J, Boyle J (2008). "Cytoscape: A community based framework for network modeling" Methods in Molecular Biology (forthcoming)
Tutorials
The following are step-by-step instructions for registering and testing a LSID data source and a Web Service, so that they function correctly with the ISB enterprise infrastructure.
Registering and testing a LSID data service
- Download LSID stack. Download the IBM LSID classes.
- Build the new authority/service. To add an authority of your own, create the necessary classes for the authority, metadata and data services (see the HelloWorld example from the above step) then add the corresponding mappings to the java/services/isb-services.xml file, rebuild and redeploy.
- Deploy the war file. Build the classes and deploy them to a web service container, such as Apache Tomcat.
- Install a sample client. Install the Firefox browser LSID extension.
- Configure the client. After installing the extension, you need to configure it use the IBM LSID classes. In Firefox, select "Add-Ons" from the "Tools" menu. You should see the LSID browser in the list. Select it and click the "Preferences" button. In the LSID Preferences window, select the "Network" tab and select "New". In the "authority" box type http:///authority (note that you may need the port number after your server name). In the "mapping" box type "systemsbiology.org"
- Test the client. Now that you have set up the correct mappings in the LSID browser, test it by typing (or copy-paste) the following LSID into your address bar: "lsidres:urn:lsid:systemsbiology.org:hello:21".You should see a link with the number "21" at the top and a message near the bottom "Hello metadata world".
Testing and Registering a Web Service
- Ensure your service is interoperable. Each language provided in our SOAP Interoperability example package has it's own methods for writing a WSDL. Generally you begin by creating a class with the method signatures you want the WSDL to handle. We have found that a Java or C# SOAP server provides for the best interoperability between different clients.
- In Java you can use Apache Axis to generate your WSDL from a class then use it again to generate the server and client stubs. Axis will create a service skeleton interface, after implementing that interface the server can be bundled and deployed under a servlet container (e.g. Apache Tomcat). Using the generated client stubs a client can be filled in and run against the deployed server
- Ruby provides similar functionality through the SOAP4R gem
- In Perl, use the SOAP::Lite library (available on the CPAN)
- A good page on C# web services can be found here
- Registering a Webservice If you are within the ISB firewall and wish to add a new or edit web service you should:
- go to http://specs.systemsbiology.net:3000/
- to add a new service select [Add New Service], alternatively select the service you wish to edit
- fill in the web form with the details about the web service.
- The information will be verified and the service will be registered.
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