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BMC_jvenn/bmc_jvenn.tex

@@ -516,12 +516,51 @@ reviewers for their insightful and constructive comments.
 %% Use of \listoftables is discouraged.
 %%
 \section*{Tables}
+
+\begin{table}[h!]
+\caption{Available formats and example for the \textit{series} option.}
+	\begin{tabular}{c|cccccc}
+		Application & Maximum & Layouts & Application &
+		Proportionality & Input data & Output\\ 
+		& number of & & type & & formats & formats \\
+		& input lists & & & & & \\ \hline
+		
+		VENNTURE \cite{Bronwen2012} &  6 & Edwards & Stand-alone & No & Lists &
+		Powerpoint,\\ 
+		& & & & & & Excel, CSV \\ \hline
+		
+		VennDiagram \cite{RVennDiagram} &  5 & Classical & R package & No & Lists
+		& R object, TIFF \\ \hline
+		
+		BioVenn \cite{Hulsen2008} &  3 & Classical & Web application & Yes &
+		Lists & SVG, PNG \\ \hline
+		
+		venny \cite{venny} &  4 & Classical & Web application & No &
+		Lists & PNG \\ \hline
+		 
+		Canvasxpress \cite{canvasxpress} &  4 & Classical & JavaScript library &
+		No & Intersection counts & JavaScript canvas \\ \hline
+		
+		Google & 3 & Classical & JavaScript library &
+		Yes & Lists & PNG \\ 
+		Chart API \cite{googleAPI} & & & & & & \\ \hline
+			
+		jvenn & 6 & Classical & Web application & No & Lists,
+		& Interactive 
+		\\
+		& & and Edwards & and JavaScript library & & intersection counts & diagram, \\
+		& & & & & and count lists & PNG, CSV
+	\end{tabular}
+\end{table}
+
+
+
 \begin{table}[h!]
 \caption{Available formats and example for the \textit{series} option.}
       \begin{tabular}{cccc}
         \hline
-        format & example\\ \hline
-        lists & 
+        Format & Example\\ \hline
+        Lists & 
 \begin{lstlisting}
 series: [{
 	name: 'sample1',
@@ -531,15 +570,16 @@ series: [{
 	data: ["Otu1", "Otu2", "Otu5", "Otu7", "Otu8", "Otu9"]
 }]
 \end{lstlisting}\\ \hline
-        intersection counts & 
+        Intersection counts & 
 \begin{lstlisting}
 series: [{
 	name: {A: 'sample 1', B: 'sample 2'},
 	data: {A: ["Otu3", "Otu4", "Otu6"], B: ["Otu8", "Otu9"], AB: ["Otu1",
-	"Otu2", "Otu5", "Otu7"]} }],
+	"Otu2", "Otu5", "Otu7"]},
 	values: {A: 3, B: 2, AB: 4}
+}]
 \end{lstlisting}\\ \hline
-        count lists  &
+        Count lists  &
 \begin{lstlisting}
 series: [{
 	name: 'sample1',

BMC_jvenn/jvenn_coverletter_bis.tex

@@ -51,7 +51,7 @@ The present cover letter is pertaining to the paper "jvenn: an interactive venn
 diagram viewer". This paper has already been submitted to BMC Bioinformatics 
 under the ID 1449643681123201. After the review process, we were asked to
 solve the concerns addressed. We made the requested modifications and we added 
-new features to jvenn presented in the manuscripts. Hereafter are our responses 
+new features to jvenn presented in the manuscript. Hereafter are our answers 
 to the reviewers.
 
 
@@ -68,6 +68,7 @@ The URL have been changed to fit the page size.
 
 \textbf{- run-on sentences}
 
+The organisation of the sections and paragraphs of the text has been modified.
 Many sentences have been rewritten.
 
 \textbf{- what is a standard linux computer?}
@@ -127,7 +128,7 @@ not directly embeddable in a webpage. Yet, the authors should note these
 libraries as well. Two that come to mind are: The VennDiagram R package, which 
 supports up to five lists. VENNTURE, which supports up to six lists Martin B, 
 Chadwick W, Yi T, Park SS, Lu D, Ni B, Gadkaree S, Farhang K, Becker KG,
-Maudsley  S. VENNTURE–A Novel Venn Diagram Investigational Tool for Multiple 
+Maudsley  S. VENNTURE Novel Venn Diagram Investigational Tool for Multiple 
 Pharmacological Dataset Analysis.}
 
 These 2 citations and the description of the tools have been added in the
@@ -139,7 +140,7 @@ diagrams with up to six lists; thus their statement is incorrect.}
 
 VENNTURE citation has been added to the manuscript. jvenn remains the only
 tools handling 6 lists as inputs written to be included in Web applications.
-Moreover it is the only software offering the classical Venn diagram displays
+Moreover it is the only software package offering classical Venn diagram displays
 for 6 input lists.
 
 \textbf{Also the authors point out that venny does not visualize the relative
@@ -147,7 +148,7 @@ areas of the intersecting sets; neither does jvenn, from what I can
 tell. Is this a current limitation of jvenn or an explicit decision?}
 
 This is right, all softwares displaying a relative areas Venn diagram handle up
-to 3 lists. Beyond that, displaying the graphic is a more complex problem.
+to 3 lists. Beyond that, displaying the graphic is a complex problem.
 
 \textbf{3. The jvenn library appears to be built upon the venny library;
 however this distinction is unclear. In the implementation section,
@@ -157,8 +158,8 @@ sets of items. A clear statement about the novel contributions (with
 respect to the library) will strengthen the paper.}
 
 jvenn is only using the venny algorithm to compute the lists intersection.
-The sentence ``jvenn is based on venny regarding the algorithm computing the
-lists intersections. The algorithm has been wrapped in a jQuery plug-in,
+The sentence ``jvenn intersection computing algorithm is based on venny.
+The algorithm has been wrapped in a jQuery plug-in,
 extended with new features presented hereunder and the ability to use up to six
 lists.'' has been added as introduction to the Implementation section.
 
@@ -296,4 +297,4 @@ bioinformatics.
 %----------------------------------------------------------------------------------------
 
 \end{newlfm}
-\end{document}
+\end{document}
\ No newline at end of file