[Cdk-commits] SF.net SVN: cdk:[14701] cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex

[<ste...@us...>]

Revision: 14701
          http://cdk.svn.sourceforge.net/cdk/?rev=14701&view=rev
Author:   steinbeck
Date:     2009-08-07 15:24:11 +0000 (Fri, 07 Aug 2009)

Log Message:
-----------
Addition of a proper trademark symbol and cleanup of the Taverna extension points section.

Modified Paths:
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    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	2009-08-07 14:42:56 UTC (rev 14700)
+++ cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex	2009-08-07 15:24:11 UTC (rev 14701)
@@ -252,14 +252,14 @@
 workflow engine for cheminformatics, where numerous recurring tasks can be automated, including
 tasks for  
 \begin{itemize}
-  \item Chemical data filtering, transformation, curation and migration workflows
-  \item Chemical documentation and information retrieval related workflows (structures, reactions, pharmacophores, object relational data etc.)
-  \item Data analysis workflows (statistics and clustering/machine learning for QSAR, diversity analysis etc.)
+  \item chemical data filtering, transformation, curation and migration workflows
+  \item chemical documentation and information retrieval related workflows (structures, reactions, pharmacophores, object relational data etc.)
+  \item data analysis workflows (statistics and clustering/machine learning for QSAR, diversity analysis etc.)
 \end{itemize}
 
 The workflow paradigm allows scientists to flexibly create generic
 workflows using different kinds of data sources, filters and algorithms, which can later be adapted to changing needs.
-In order to achieve this, library methods are encapsulated in Lego(TM)-like building blocks
+In order to achieve this, library methods are encapsulated in Lego\texttrademark-like building blocks
 which can be manipulated with a mouse or any pointing device in a graphical environment, 
 relieving the scientist from the need to learn a programming language. 
 Building blocks are connected by data pipelines to enable data flow between them, which is why 
@@ -285,29 +285,28 @@
 \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. 
+Like Taverna itself the plug-in uses Maven 2 \cite{MavenWeb} as a 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} \remark{this is a verbose copy of 
-some text from taverna people and needs a citation TK: Done}. For the integration of these
-different kind of resources Taverna provides various interfaces and
-protocols for its extension. It allows for an easy integration
-of webservices which use the WSDL \cite{WSDLWeb} or SOAP \cite{SOAPWeb}
-protocol. \remark{CS: Thomas, how much of the surrounding text is copied verbally from someone else? TK: As far as I remember only the frist part is a citation. the other part is my composition.} 
-The CDK-Taverna plug-in uses a local extension of Taverna. For the
-local extension Taverna provides a list of different Service Provider Interfaces (SPI).
-The CDK-Taverna project implements some of these extensions: This leads to an
-integration of the CDK functionality as so called Local Workers which run on the 
-same machine as the CDK taverna installation.
-All workers provided from the CDK-Taverna plug-in implement the
-``CDKLocalWorker`` interface. This interface is used for the detection of each
-worker, performed within the implementation of the
-``CDKScavenger`` which itself implements the Taverna SPI
-``org.embl.ebi.escience.scuflui.workbench.Scavenger``.
+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. 
+The CDK-Taverna plug-in, on the other side, 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.
+All workers in CDK-Taverna implement the
+\texttt{CDKLocalWorker} interface. It is used for the detection of 
+workers by the \texttt{CDKScavenger} class which itself implements the Taverna SPI
+\texttt{org.embl.ebi.escience.scuflui.workbench.Scavenger} interface.
 Adding user interfaces for some of the workers requires an extension of the
-``AbstractCDKProcessorAction`` which itself implements the Taverna SPI
-``org.embl.ebi.escience.scuflui.spi.ProcessorActionSPI``. The use of this SPI
+\texttt{AbstractCDKProcessorAction} which again implements the Taverna SPI
+\texttt{org.embl.ebi.escience.scuflui.spi.ProcessorActionSPI}. The use of this SPI
 allows the addition of, for example, file chooser dialogs for workers like file
 reader or writer. 
 


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