BioMoby plugin

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Name: BioMoby plugin for Bioclipse
ID: net.bioclipse.biomoby

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BioMoby

The MOBY-S system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next.

For more information about BioMoby, see the BioMoby website.

The BioMoby plugin

BioMoby will allow for bioinformatic service discovery and invokation from within Bioclipse and hence will add a lot of online functionality that can be of use in analysis. Hopefully we can set up our own services for pharmacology, chemistry etc. The use of BioMoby simplifies UI generation as it standardizes input/output via an ontology of data types, which can be extended with new types as needed.


  • Browse categories and services in a TreeViewer DONE
  • Render dialog GUIs automatically from service description DONE
  • Invoke services with primary and secondary inputs from Wizard DONE
  • Allow to save results to file DONE
  • Restructure tree to look like dashboard DONE
  • Wrap long operations in jobs/runnables with progress DONE
  • Utilize Status from additional RDF to only show Active services DONE (Ping:ed not yet available)
  • Search for services in tree DONE
  • Handle different results Partly implemented
  • Allow to ask where file should be saved Not started
  • Search for services by text (findService) Not started
  • Caching of ontologies and namespaces Bug in BioJava
  • If multiple providers for a service, choose one from list Not started
  • Service lookup and invocation for IBioResources (e.g. right-click a sequence) Not started
  • Use BioMoby services within Bioclipse scripts Not started
  • Validation according to intelligent guessing Not started
  • If Length exists, make it optionally calculatable Not started

How to get and install the plugin

  • Download and install Bioclipse (see: XX)
  • Go to Help -> Add extensions. Select the Experimental category and install the BioMoby feature
  • After restarting Bioclipse, choose Window->Show View... Open the Service View. BioMoby will now refresh services from BioMoby registry. The first time this may take several minutes to download and pupolate the cache from the BioMoby registry. Following startups this is cached and is rather fast.

Usage

  • Double-click a service to get an invocation dialog
  • Right-click a sequence in the BioResource Navigator, select BioMoby->Look up services... This will find all services for accepting a Fasta sequence and simplesequence ??? as input.

Screenshots

See right side.