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BMC_jvenn/bmc_jvenn.tex

@@ -182,10 +182,11 @@
 
 \parttitle{Results} %if any
 
+...
+Currently there is no software that provides such features.
+
 \parttitle{Conclusions} %if any
-The software package is freely available under the GNU General Public License (GPL) at 
-https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil. Examples and the documentation 
-can be found on the sources directory and a running version is running at http://bioinfo.genotoul.fr/index.php?id=116.
+conclusions ....
 
 \end{abstract}
 
@@ -266,25 +267,64 @@ and cannot perform any calculations to otain them.
 We intruduce jvenn a javascript library aiming to be part of rich WEB environments helping scientists to analyse 
 their data, such does already existing tools as jbrowse \cite{Westesson01032013}, Cytoscape-Web \cite{Lopes2010}, 
 and jHeatmap \cite{DeuPons2014}. Jvenn handles up to 6 lists venn diagram, can display Edwards-Venn diagram
-\cite{Edwards2004}, can easily be embeded within any web site, allows to provide inputs data from three different ways 
-(list/number/list+number), provides a feature to export the diagram to png and allows to overload the callback 
+\cite{Edwards2004}, can easily be embeded within any web site, allows to provide inputs data in three different formats 
+(list/number/list+number), allows to export the diagram to png and permits to overload the callback 
 function to control users interactions. jvenn has already been used in several scientific publications to display 
 sets and their overlapping areas \cite{Bianchia2013, Aravindraja2013}. 
 
 
 \section*{Implementation}
 
-jvenn is a javascript library written as a jQuery plugin \cite{jquery}.
+jvenn is a javascript library written as a jQuery plugin \cite{jquery} and can be embeded within any WEB applications 
+by referencing the javascript file from an HTML page. For researchers who want to produce a Venn diagram from their 
+identifiers, jvenn is also available as a WEB application at http://bioinfo.genotoul.fr/index.php?id=116. A full 
+documentation to insert the plugin within a WEB application is included in the software package that can be downloaded 
+from https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil.
+
 
 \section*{Results and Discussion}
 
-jvenn is already embeded within nG6 \cite{Mariette2012}, RNAbrowse \cite{Mariette} and WallProtDB \cite{WallProtDB} 
-WEB applications.
+The jvenn output is a chart of two to six areas in which each area represents one of the identifiers set define as input. 
+The numbers of each overlaps are displayed and are clickable by the user to access the identifiers list belonging to the 
+intersection. In order to ease overlaps understanding, when the user is over an intersection number, jvenn overlights the 
+pointed classes and blurs the other ones.
+
+The library provides an option to define the data inputs: \textit{series}. The library accepts three different input formats. 
+In case the \textit{series} are a list of value, the plugin will compute itself the overlaps between lists. The \textit{series} 
+can also define the number to display for each intersections or can be defined as a mix of the first two formats. 
+The resulting display is created with the help of the javascript canvas object which allows to export the chart as a png file. 
+This last feature can be disabled in order to hide the exporting button from the user by setting the \textit{exporting} option 
+to \textit{false}.
+
+jvenn handles up to six classes, what leads to display sixty three overlap numbers. Displaying and interacting with such a chart
+can be bulky and difficult. In such a case, jvenn propose a switch button panel which allows to activate or disactivate classes. 
+The selected overlap number is then displayed and can be clicked just like the other ones. jvenn also provides the Edwards-Venn
+display (Fig. 2) available by setting the \textit{displayType} option to \textit{edwards}. This display gives a different 
+graphical representation of the classes which can be clearer whith a 6 classes diagram.
+The WEB application creator can also overload the callback function defining the click on an overlap number. This can be done 
+by defining the \textit{fnClickCallback} parameter. The overloading function has access to the \textit{this.listnames} and
+\textit{this.list} variables allowing the developer to control the users interactions with the jvenn plugin. This feature can
+be disabled by setting the \textit{disableClick} option to \textit{true}.
+
+As example, we produced two venn diagrams representing six samples SRR068049, SRR06805, SRR068051, SRR068052, SRR068053 and 
+SRR068054 corresponding to sets of Operational Taxonomic Units observed under different conditions. Fig. 1 shows intersections
+between five of them using the Venn diagram display. In Fig. 2, jvenn overlights the intersection between three samples of the 
+six ones used to create the Edwards-Venn diagram.
+
 
 \section*{Conclusions}
 
+jvenn is an easy-to-use library aiming to generate Venn and Edwards-Venn diagrams from lists of identifiers or from
+computed numbers. Its implementation as a javascript library allows whoever who have WEB programming skills to embed 
+it within its WEB application without any dependancies. jvenn is already embeded within nG6 \cite{Mariette2012}, 
+RNAbrowse \cite{Mariette} and WallProtDB \cite{WallProtDB} WEB applications.
+
 \section*{Availability and requirements}
 
+jvenn is freely available under the GNU General Public License (GPL) at 
+https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/venny/index.php/Accueil webcite. Some examples and a full documentation 
+can be found on the downloadable archive. A running version is accessible at http://bioinfo.genotoul.fr/index.php?id=116.
+
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