srs2acd.jar | Updated 13/09/06

This executable jar file allows one to automatically generate ACD files for each databank which has been indexed by a given Sequence Retrieval System (SRS). These ACD files contain metadata about a SRS repository and can be used by Soaplab for deploying a web service interface to the SRS databank. Currently, only version 7.1.3.2 Sequence Retrieval Systems have been tested against this version of Srs2acd.

This JAR file has an entry point set to a main method allowing the tool to be executed in the following manner:

java -jar srs2acd.jar [OPTION]... URL to a Sequence Retrieval System

The following options are applicable to the tool:

-h, -help Displays this help file.

-d, -default Runs this tool using the default Sequence Retrieval System URL, http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?

ebi_srs_acd.zip | Updated 13/09/06

This zip file contains the ACD files describing the databanks indexed by the Sequence Retrieval System hosted by the European Bioinformatics Institute which have been generated by the above Srs2acd tool. Soaplab can use these ACD files to deploy each of the SRS databanks as a Soaplab web service. See the Soaplab web site for information about using these ACD files for deployment of SRS databank services.

A Soaplab server providing services to the databanks indexed by the SRS hosted by the European Bioinformatics Institute that have been deployed using these ACD files is available here.

soaplab_ncbi_blast.zip | Updated 13/09/06

This zip file contains the ACD files which can be used for deploying a Soaplab service interface to the Blast tool hosted by the NCBI. In addition, this zip file contains a plugin jar file which is required by Soaplab for interacting with the NCBI Blast service.

Information about using these ACD files to deploy the NCBI Blast tools as Soaplab services is available on the Soaplab website. The ncbi plugin jar should be placed in the Axis WEB-INF/lib directory that is used by your Soaplab server.

analysis-interfaces-2006-08-31.tar.gz | Updated 13/09/06

This is a build of Soaplab containing all the above files which can be used to deploy SRS@EBI and NCBI Blast services. Instructions for installing Soaplab using this file is available on the Soaplab website.

Soaplab @ http://dbk-ed.mib.man.ac.uk:8080/axis/services/ | Updated 13/09/06

A Soaplab server providing the above NCBI Blast services and SRS databank services is available at http://dbk-ed.mib.man.ac.uk:8080/axis/services/. The reccommended method for calling these services is to use the Taverna workflow editor and enactment tool.

The Taverna user manual provides instructions for making Soaplab services available for use by this workflow editor. When requested, "http://dbk-ed.mib.man.ac.uk:8080/axis/services/" should be entered as the root URL of this soaplab server.

A workflow demonstrating the use of these Soaplab services is available here.