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[Cdk-commits] SF.net SVN: cdk:[15471] cdk-taverna-paper/trunk/cdk-taverna
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From: <eg...@us...> - 2010-03-10 20:11:02
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Revision: 15471
http://cdk.svn.sourceforge.net/cdk/?rev=15471&view=rev
Author: egonw
Date: 2010-03-10 20:10:51 +0000 (Wed, 10 Mar 2010)
Log Message:
-----------
Replaced image with one that actually matches workflow 555 and updated the Figure caption
Modified Paths:
--------------
cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex
cdk-taverna-paper/trunk/cdk-taverna/pics/databaseSubstructureSearch.png
Added Paths:
-----------
cdk-taverna-paper/trunk/cdk-taverna/pics_src/substructure_search_on_database.svg.xml
Modified: cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex
===================================================================
--- cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex 2010-03-10 19:54:30 UTC (rev 15470)
+++ cdk-taverna-paper/trunk/cdk-taverna/bmc_article.tex 2010-03-10 20:10:51 UTC (rev 15471)
@@ -78,8 +78,8 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\def\includegraphic{}
-\def\includegraphics{}
+%\def\includegraphic{}
+%\def\includegraphics{}
@@ -278,7 +278,7 @@
In 2005 we started to integrate our open source cheminformatics
library, the Chemistry Development Kit (CDK)~\cite{Steinbeck2004a,Steinbeck2003a}
-with Taverna~\cite{Chemblaics2005,CDKTaverna2005,TomOinn2004}}, a
+with Taverna~\cite{Chemblaics2005,CDKTaverna2005,TomOinn2004}, a
workflow environment with an extensible architecture, to produce CDK-Taverna,
the first completely free~\cite{free-software-foundation} workflow solution for
cheminformatics, which we present here. It makes additional use of other
@@ -657,11 +657,11 @@
\begin{figure*}[h!]
\centering
- \includegraphics[angle=0,clip=false,scale=.4]{pics/databaseSubstructureSearch.png}
+ \includegraphics[angle=0,clip=false,scale=.2]{pics/databaseSubstructureSearch.png}
\caption{Workflow performing a substructure search (Scenario~1)
in a database~\cite{MyExperiementWFSubstructureDB}.
- The substructure is loaded from a MDL SDfile. The output is a PDF
- file containing a tabular view of the molecules containing the
+ The substructure is defined with a SMILES. The output is a PDF
+ file with a tabular view of the molecules from the database containing the
substructure.}
\label{fig:database_substructure_search}
\end{figure*}
Modified: cdk-taverna-paper/trunk/cdk-taverna/pics/databaseSubstructureSearch.png
===================================================================
(Binary files differ)
Added: cdk-taverna-paper/trunk/cdk-taverna/pics_src/substructure_search_on_database.svg.xml
===================================================================
--- cdk-taverna-paper/trunk/cdk-taverna/pics_src/substructure_search_on_database.svg.xml (rev 0)
+++ cdk-taverna-paper/trunk/cdk-taverna/pics_src/substructure_search_on_database.svg.xml 2010-03-10 20:10:51 UTC (rev 15471)
@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.0//EN"
+ "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd" [
+ <!ATTLIST svg xmlns:xlink CDATA #FIXED "http://www.w3.org/1999/xlink">
+]>
+<!-- Generated by Graphviz version 2.14.1 (Fri Sep 7 12:22:15 UTC 2007)
+ For user: (myexperiment) myExperiment User -->
+<!-- Title: scufl_graph Pages: 1 -->
+<svg width="276pt" height="189pt"
+ viewBox="0.00 0.00 276.00 189.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 185)">
+<title>scufl_graph</title>
+<polygon style="fill:white;stroke:white;" points="-4,4 -4,-185 272,-185 272,4 -4,4"/>
+<g id="cluster2" class="cluster"><title>cluster_sources</title>
+<polygon style="fill:none;stroke:black;stroke-dasharray:1,5;" points="91,-114 91,-173 195,-173 195,-114 91,-114"/>
+<text text-anchor="middle" x="135" y="-160" style="font-family:Arial;font-size:10.00;">Workflow Inputs</text>
+</g>
+<!-- Substructure_Search_of_molecules_on_the_database -->
+<g id="node1" class="node"><title>Substructure_Search_of_molecules_on_the_database</title>
+<polygon style="fill:white;stroke:black;" points="268,-67.5 1.13687e-13,-67.5 0,-46.5 268,-46.5 268,-67.5"/>
+<text text-anchor="middle" x="134" y="-54" style="font-family:Arial;font-size:10.00;">Substructure_Search_of_molecules_on_the_database</text>
+</g>
+<!-- Create_PDF_File_with_2D_Structures -->
+<g id="node2" class="node"><title>Create_PDF_File_with_2D_Structures</title>
+<polygon style="fill:white;stroke:black;" points="231,-29.5 37,-29.5 37,-8.5 231,-8.5 231,-29.5"/>
+<text text-anchor="middle" x="134" y="-16" style="font-family:Arial;font-size:10.00;">Create_PDF_File_with_2D_Structures</text>
+</g>
+<!-- Substructure_Search_of_molecules_on_the_database->Create_PDF_File_with_2D_Structures -->
+<g id="edge5" class="edge"><title>Substructure_Search_of_molecules_on_the_database->Create_PDF_File_with_2D_Structures</title>
+<path style="fill:none;stroke:black;" d="M134,-46C134,-44 134,-42 134,-40"/>
+<polygon style="fill:black;stroke:black;" points="137.5,-40 134,-30 130.5,-40 137.5,-40"/>
+</g>
+<!-- Parse_SMILES -->
+<g id="node3" class="node"><title>Parse_SMILES</title>
+<polygon style="fill:white;stroke:black;" points="177,-105.5 91,-105.5 91,-84.5 177,-84.5 177,-105.5"/>
+<text text-anchor="middle" x="134" y="-92" style="font-family:Arial;font-size:10.00;">Parse_SMILES</text>
+</g>
+<!-- Parse_SMILES->Substructure_Search_of_molecules_on_the_database -->
+<g id="edge3" class="edge"><title>Parse_SMILES->Substructure_Search_of_molecules_on_the_database</title>
+<path style="fill:none;stroke:black;" d="M134,-84C134,-82 134,-80 134,-78"/>
+<polygon style="fill:black;stroke:black;" points="137.5,-78 134,-68 130.5,-78 137.5,-78"/>
+</g>
+<!-- WORKFLOWINTERNALSOURCECONTROL -->
+<g id="node5" class="node"><title>WORKFLOWINTERNALSOURCECONTROL</title>
+<polygon style="fill:#ff4040;stroke:black;" points="180,-140 173,-129.5 187,-129.5 180,-140"/>
+</g>
+<!-- WORKFLOWINTERNALSOURCE_in_SMILES -->
+<g id="node6" class="node"><title>WORKFLOWINTERNALSOURCE_in_SMILES</title>
+<polygon style="fill:skyblue;stroke:black;" points="169,-143.5 99,-143.5 99,-122.5 169,-122.5 169,-143.5"/>
+<text text-anchor="middle" x="134" y="-130" style="font-family:Arial;font-size:10.00;">in_SMILES</text>
+</g>
+<!-- WORKFLOWINTERNALSOURCE_in_SMILES->Parse_SMILES -->
+<g id="edge7" class="edge"><title>WORKFLOWINTERNALSOURCE_in_SMILES->Parse_SMILES</title>
+<path style="fill:none;stroke:black;" d="M134,-122C134,-120 134,-118 134,-116"/>
+<polygon style="fill:black;stroke:black;" points="137.5,-116 134,-106 130.5,-116 137.5,-116"/>
+</g>
+</g>
+</svg>
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