jMoby - BioMoby in Java (and Java in BioMoby)

• to access BioMoby registries, allowing all features provided by such registries, including but not limited to registering and deregistering of the BioMoby services and their parts, discovering them, and understanding their data in various formats (such as RDF),

• to create Java implementations of BioMoby services, especially to help service providers with creating BioMoby data containers (input and output data) without exposing providers to the complexity of the XML required and produced by BioMoby services, and finally

• to provide support for those writing Java clients accessing both BioMoby registries and BioMoby services.

To make the long story short: jMoby aims to develop BioMoby components and full applications in Java.

News...

February 20, 2008

Eddie Kawas released a new implementation (no API changes) of the org.biomoby.client.CentralCachedCallsImpl class - now getting the contents of the registry using the RDF files. When all bugs are fixed, it should significantly speed up cache update in Dashboard and elsewhere.

February 2008

Major changes in building and using jMoby were introduced during the BioHackathlon meeting in Japan. The changes, however, are not changes of the jMoby API - which means that your own code should continue to work without any changes.

The main issue is that jMoby uses now the 3rd-party libraries form the various Maven repositories. It fetches them when you compile jMoby, or when you use the new Ant's task install. There is an article about how it is done (coming from a different project but using the same principles as in jMoby).

Another issue is that the Ant itself is not anymore distributed with jMoby. You need to install it separately on your machine (see the requirement section).

Where to go now

• What license jMoby uses:
  Unless individual jMoby parts define it differently, the code is licensed under the Apache License.

• How to get jMoby

• How to use jMoby and how to develop with jMoby
  • General issues
    • Integration with Eclipse
    • Some issues with using jMoby on MS-Windows platform
    • The Twelve Commandments for jMoby developers (and some good advice)
    • Directories and packages names explained
    • Available APIs (see also a general description of package names)
    • How to change Ant's build.xml
    • RDF Agent
    • The Dashboard as Webstart
  There are more ways to develop clients and services using jMoby. The main two approaches are:
  • Using generated objects. It expresses all important BioMoby entities (data types and services) as pure Java objects. The main contact person for this approach is Martin Senger.

  • Using general methods. It allows to access the same BioMoby entities using non-object-specific ways/methods. The main contact person for this approach is Paul Gordon.

  Choose whatever you prefer, but probably mixing the main two approaches in the same project may be confusing. Therefore, the sections below try to separate the two approaches.

  • Using and developing jMoby clients
    • Command-line clients
    • How to use the BioMoby plugin in Taverna
    • The Feature Client (an extended MOBY client)

    • Using generated object (MoSeS)
      • Biomoby Dashboard
      • Developing MoSeS Clients
      • Client for creating Biomoby input XML data

    • Using general methods
      • Seahawk: An extensible, user-oriented MOBY client
      • How to develop a client talking to a BioMoby service (a Paul Gordon's simple client)
  • Developing jMoby services
    • Using generated object (MoSeS)
      • How to develop a BioMoby service
      • MoSeS - Moby Services Support
      • Biomoby Dashboard
      • An Alternative jMoby Step-by-Step Guide (with video guides how to set up JMoby with Eclipse and how to develop moby web services !)
      • Code Examples

    • Using general methods
      • How to develop a BioMoby service, an alternate mechanism for the Extremely Lazy, Complete Idiots, Dummies, etc. (a.k.a. "MobyServlet")
      • A note on using secondary articles with MobyServlet
      • How to wrap an EMBOSS/ACD program as a Moby service
      • How to wrap an existing Web Service as a Moby service (using SAWSDL)
      • A generic, customizable HTML SOAP Client (used as a base for Daggoo)
      • The org.biomoby.shared.data package "In Anger": creating data instances
      • How to setup and create secure BioMoby web services

• Links to other projects using jMoby
  • Checking services
  • BioMoby/BioCASE services
  • MoSeS for Perl developers

Acknowledgements

• myGrid, a multi-organisational project developing the infrastructural middleware for an e-Biologist's workbench, funded by EPSRC
• International Rice Research Institute
• Generation Challenge Programme

Other parts of jMoby are funded from the same sources as the BioMoby itself, i.e. Genome Canada, Genome British Columbia, and Genome Alberta.