From: <eg...@us...> - 2009-11-11 21:21:05
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Revision: 15062 http://cdk.svn.sourceforge.net/cdk/?rev=15062&view=rev Author: egonw Date: 2009-11-11 21:20:49 +0000 (Wed, 11 Nov 2009) Log Message: ----------- Removed to use of 'so' here and there, in favor of more formal writing English. Also consist spelling of plug-in. Modified Paths: -------------- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex Modified: cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex =================================================================== --- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex 2009-11-11 21:09:36 UTC (rev 15061) +++ cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex 2009-11-11 21:20:49 UTC (rev 15062) @@ -329,9 +329,10 @@ \subsubsection*{Iteration over large data sets} Cheminformatics by definition deals with the discovery of chemical knowledge from large data collections. -These data sources are usually too large to be loaded into memory as a whole so one needs to loop over the data sets to process them -piece by piece. Unfortunately the architecture of Taverna's current stable version does not support such loops. -CDK-Taverna therefore provides workers which act like FOR or WHILE loops,making use of Taverna's iteration and retry mechanism to allow workflows +Because these data sources are usually too large to be loaded into memory as a whole, it is needed to +loop over all data entries to process them one by one. Unfortunately, the architecture of Taverna's +current stable version (1.7) does not support such loops. CDK-Taverna, therefore, provides workers which +act like FOR or WHILE loops, making use of Taverna's iteration-and-retry mechanism to allow workflows to process large data sets. %see section iterative qsar workflow @@ -537,24 +538,22 @@ \section*{Methods} The CDK-Taverna plug-in written in Java is published under the GNU Lesser -General Public License (LGPL). -Like Taverna itself the plug-in uses Maven 2~\cite{MavenWeb} as a build system. +General Public License (LGPL). Version 0.5.1 uses CDK revision 12084. +Like Taverna itself the CDK-Taverna plug-in uses Maven 2~\cite{MavenWeb} as build system. \subsection*{Taverna's extension points} Taverna allows the execution of workflows linking together heterogeneous -open services, applications or databases (remote or local, private or public, third-party or home-grown)\cite{Taylor2007}. -For the integration of these +open services, applications or databases (remote or local, private or public, third-party or +home-grown)~\cite{Taylor2007}. For the integration of these different resource types Taverna provides various interfaces and protocols for its extension. For example, it allows for easy use -of webservices through the WSDL~\cite{WSDLWeb} or SOAP~\cite{SOAPWeb} -protocol. +of webservices through the WSDL~\cite{WSDLWeb} and SOAP~\cite{SOAPWeb}. -The CDK-Taverna plug-in, on the other hand, uses a local extension of Taverna. For the -local extension Taverna provides a list of different Service Provider Interfaces (SPI), so -of which we implement in CDK-Taverna, which leads to an -integration of the CDK functionality as so called Local Workers running on the -same machine as the CDK-Taverna installation. The CDK-Taverna plug-in Version 0.5.1 uses the CDK revision 12084. -Full JavaDoc documentation of the plugin's source code is +The CDK-Taverna plug-in, on the other hand, uses Taverna's local extension mechanism. For +local extensions, Taverna provides a list of different Service Provider Interfaces (SPI). +CDK-Taverna implements several of these, integrating CDK functionality as so-called Local Workers +which run on the same machine as the Taverna installation. +Full JavaDoc documentation of the plug-in's source code is available at \url{http://cdk.sourceforge.net/cdk-taverna/api/}. All workers in CDK-Taverna implement the @@ -569,12 +568,12 @@ \subsection*{Plug-in installation} The CDK-Taverna project employs the plug-in detection manager of Taverna -for its installation. The detection manager requires a plugin description XML file containing a plugin name, +for its installation. The detection manager requires a plug-in description XML file containing a plug-in name, a version number, a target Taverna version number, a repository location and a Maven-like Java package description. After adding the plug-in installation URL (http://www.cdk-taverna.de/plugin/) to the plug-in manager all available plug-in versions will be graphically accessible to the user. -In order to install the CDK-Taverna plugin the user selects the desired version after which +In order to install the CDK-Taverna plug-in the user selects the desired version after which all necessary Java libraries are installed on-the-fly from the given repository location. This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |