Commit a12fc66c by Jerome Mariette

### add new cover letter and take into account reviewers

parent a6f8e2b1
 ... @@ -294,7 +294,7 @@ providing an insight on the similarities between the lists. ... @@ -294,7 +294,7 @@ providing an insight on the similarities between the lists. In a Venn diagram each list is figured by a transparent shape. Shape overlaps In a Venn diagram each list is figured by a transparent shape. Shape overlaps contain the elements shared between lists or more often the corresponding counts. contain the elements shared between lists or more often the corresponding counts. In proportional Venn diagrams the size of a shape depends on the number of In proportional Venn diagrams the size of a shape depends on the number of elements of the corresponding list intersection. Venn diagram with up to four elements of the corresponding list intersection. Venn diagrams with up to four lists are easy to read and understand, but they become difficult to interpret lists are easy to read and understand, but they become difficult to interpret with more lists. To solve this problem, the Edwards-Venn \cite{Edwards2004} with more lists. To solve this problem, the Edwards-Venn \cite{Edwards2004} representation introduces new shapes providing a clearer view (Fig. 2). representation introduces new shapes providing a clearer view (Fig. 2). ... @@ -323,17 +323,17 @@ RNAbrowse \cite{Mariette} and WallProtDB \cite{SanClemente}. ... @@ -323,17 +323,17 @@ RNAbrowse \cite{Mariette} and WallProtDB \cite{SanClemente}. \subsection*{Inputs} \subsection*{Inputs} The library accepts three different input formats : lists, intersection counts The library accepts three different input formats : Lists'', Intersection and count lists. All are JSON objects. Examples are presented in Table 1. counts'' and Count lists''. Examples are presented in Table 1. Lists'' contain Lists'' contain for each input a label and an identifier table. Intersection for each input a label and an identifier table. Intersection counts'' contain a counts'' contain a correspondence table between labels and letters [A..F] and a correspondence table between labels and letters [A..F] and a table linking the table linking the intersection names formed by the successions of letters and intersection names formed by the successions of letters and the counts. Count the counts. Count lists'' are organized as Lists'' in which identifiers are lists'' are organized as Lists'' in which identifiers are replaced by their replaced by their unique occurrences and their counts. With Count lists'' the unique occurrences and their counts. With Count lists'' the figures presented figures presented in the diagram correspond to the sums of counts of all in the diagram correspond to the sums of counts of all identifiers shared identifiers shared between lists. This has been used in diversity studies to between lists. This has been used in diversity studies to present OTU present OTU (Operational Taxonomic Unit) read counts. For lists'' and count (Operational Taxonomic Unit) read counts. For Lists'' and Count lists'', lists'', jvenn computes the intersection counts and displays the chart. For jvenn computes the intersection counts and displays the chart. For intersection counts'', it only displays the graphic. intersection counts'', it only displays the graphic. \subsection*{Display features} \subsection*{Display features} ... @@ -343,8 +343,8 @@ representation. But then, the intersection areas are often too small to display ... @@ -343,8 +343,8 @@ representation. But then, the intersection areas are often too small to display the figures. the figures. To present, in a user-friendly manner, five or six list diagrams, jvenn implements To present, in a user-friendly manner, five or six list diagrams, jvenn implements (Fig. 1) several functionalities. First, the display can be switched to Edwards-Venn several functionalities (Fig. 1). First, the display can be switched to (Fig. 2) which gives a clearer graphical representation for six list diagrams. To Edwards-Venn (Fig. 2) which gives a clearer graphical representation for six list diagrams. To enhance the figure's readability on the classical six lists Venn graphic, it was enhance the figure's readability on the classical six lists Venn graphic, it was decided not to present all the values and to link some areas to their figures decided not to present all the values and to link some areas to their figures using lines. This still did not permit to show all figures, therefore the switch using lines. This still did not permit to show all figures, therefore the switch ... @@ -451,10 +451,10 @@ Multiple layouts ... @@ -451,10 +451,10 @@ Multiple layouts \section*{Conclusions} \section*{Conclusions} jvenn allows whoever is familiar with the jquery library and has some JavaScript jvenn allows programers, with moderate JavaScript experiences to embed Venn programming skills to embed Venn diagrams in a Web page without dependency. It diagrams in a Web page without dependency. It has been designed following the has been designed following the examples of jbrowse \cite{Westesson01032013}, examples of jbrowse \cite{Westesson01032013}, Cytoscape-Web \cite{Lopes2010}, Cytoscape-Web \cite{Lopes2010}, and jHeatmap \cite{DeuPons2014}. and jHeatmap \cite{DeuPons2014}. \section*{Availability and requirements} \section*{Availability and requirements} ... @@ -586,7 +586,7 @@ reviewers for their insightful and constructive comments. ... @@ -586,7 +586,7 @@ reviewers for their insightful and constructive comments. \\ \\ & & and Edwards & and JavaScript & & intersection & diagram, \\ & & and Edwards & and JavaScript & & intersection & diagram, \\ & & & library & & counts and & PNG and CSV \\ & & & library & & counts and & PNG and CSV \\ & & & & & count lists & & & & & & Count lists & \end{tabular} \end{tabular} \end{table} \end{table} ... @@ -595,8 +595,8 @@ reviewers for their insightful and constructive comments. ... @@ -595,8 +595,8 @@ reviewers for their insightful and constructive comments. \caption{Available formats and example for the \textit{series} option.} \caption{Available formats and example for the \textit{series} option.} \begin{tabular}{cccc} \begin{tabular}{cccc} \hline \hline format & example\\ \hline Format & Example\\ \hline lists & Lists & \begin{lstlisting} \begin{lstlisting} series: [{ series: [{ name: 'sample1', name: 'sample1', ... @@ -606,7 +606,7 @@ series: [{ ... @@ -606,7 +606,7 @@ series: [{ data: ["Otu1", "Otu2", "Otu5", "Otu7", "Otu8", "Otu9"] data: ["Otu1", "Otu2", "Otu5", "Otu7", "Otu8", "Otu9"] }] }] \end{lstlisting}\\ \hline \end{lstlisting}\\ \hline intersection counts & Intersection counts & \begin{lstlisting} \begin{lstlisting} series: [{ series: [{ name: {A: 'sample 1', B: 'sample 2'}, name: {A: 'sample 1', B: 'sample 2'}, ... @@ -614,7 +614,7 @@ series: [{ ... @@ -614,7 +614,7 @@ series: [{ "Otu2", "Otu5", "Otu7"]} }], "Otu2", "Otu5", "Otu7"]} }], values: {A: 3, B: 2, AB: 4} values: {A: 3, B: 2, AB: 4} \end{lstlisting}\\ \hline \end{lstlisting}\\ \hline count lists & Count lists & \begin{lstlisting} \begin{lstlisting} series: [{ series: [{ name: 'sample1', name: 'sample1', ... ...
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % Long Lined Cover Letter % LaTeX Template % Version 1.0 (1/6/13) % % This template has been downloaded from: % http://www.LaTeXTemplates.com % % Original author: % Matthew J. Miller % http://www.matthewjmiller.net/howtos/customized-cover-letter-scripts/ % % License: % CC BY-NC-SA 3.0 (http://creativecommons.org/licenses/by-nc-sa/3.0/) % %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %---------------------------------------------------------------------------------------- % PACKAGES AND OTHER DOCUMENT CONFIGURATIONS %---------------------------------------------------------------------------------------- \documentclass[10pt,stdletter,dateno,sigleft]{newlfm} % Extra options: 'sigleft' for a left-aligned signature, 'stdletternofrom' to remove the from address, 'letterpaper' for US letter paper - consult the newlfm class manual for more options \usepackage{charter} % Use the Charter font for the document text \newlfmP{sigsize=30pt} % Slightly decrease the height of the signature field %---------------------------------------------------------------------------------------- % YOUR NAME AND CONTACT INFORMATION %---------------------------------------------------------------------------------------- \namefrom{Jerome Mariette} % Name %---------------------------------------------------------------------------------------- % ADDRESSEE AND GREETING/CLOSING %---------------------------------------------------------------------------------------- \greetto{BMC bioinformatics editorial board,} % Greeting text \closeline{Sincerely yours,} % Closing text %---------------------------------------------------------------------------------------- \begin{document} \begin{newlfm} %---------------------------------------------------------------------------------------- % LETTER CONTENT %---------------------------------------------------------------------------------------- The present cover letter is pertaining to the paper "jvenn: an interactive venn diagram viewer". Hereafter are our answers to the reviewers. \textbf{-- REVIEWER 1 --} \textbf{1. The authors do a comprehensive job of describing other Venn diagram viewers. The bulleted list could be turned into a paragraph summarizing the benefits and limitations. However, they fail to clearly explain the benefits of jvenn that overcome limitations of other methods. The table provides this information, but it should go in the last paragraph of the Background.} The bulleted list has been removed and replaced by a paragraph, concluded by a sentence summarizing the benefits of jvenn. \textbf{2. In the first round of revisions, Reviewer 1 noted that the manuscript is written like a set of features, with relatively little depth. The user-interaction and web developer details make parts of the paper sound more like an API than an article. Explaining different variable names in the paper such as shortNumber & fnClickCallback are not important; what's important is that the library supports the intersection of large lists by modifying the information displayed, and allows developers to customize the callback function for selecting an intersection.} All parameters and options descriptions have been removed. All sentences explaining the configuration have been deleted from the manuscript. \textbf{3. The authors should carefully consider the organization of the paper, namely, the Implementation, Results & Discussion, and Conclusions. There are implementation details described in the Results & Discussion section, which de-emphasizes the major points of the section. Further, the Conclusions section is not concluding the main points of the article; instead it introduces other minor details of jvenn that have not be adequately described.} The organisation of the paper has been modified. The section implementation'' is now described by 5 sub sections: Inputs'', Display features'', Outputs'', Web application'' and Performances''. The Results & Discussions'' section has been splited into 2 distincts sections. \textbf{4. Some sentences are still awkwardly-phrased; instead of run-on sentences, there are many sentences that are too short / sentence fragments. Some examples include:\newline - "All are JSON objects."\newline - "jvenn intersection computing algorithm is based on venny."\newline - "This is true for up to four lists."\newline - "The value pops up on mouse-over."} Taken into account. \textbf{- First paragraph of Background: "Venn diagram[s] with up to four lists are easy to read and understand..."\newline - Capitalization consistency for "Count" and "Lists" when describing the inputs.\newline - Second paragraph of Results & Discussion: "jvenn implements (Fig. 1) several functionalities" - move figure reference to end of sentence.\newline - Conclusion: "whoever has some JavaScript programming" is too informal. Refer to comment from Reviewer 1 in first round of reviews\newline} Taken into account. \textbf{-- REVIEWER 2 --} \textbf{The paragraph that starts with "The Web application developer can de#ne the diagram display by setting the display Type option to edwards or classic..." - sounds like something that should go on a webpage for the project. You can keep information about what the system is able to do, what features it has, but I think you can skip on some of the low level details about how it is achieved. Readers will want to know what can be done and that it can be done in an easy way. State this and skip the details.} All options and parameters descriptions have been removed from the manuscript. \textbf{For me, a lot of the information in results and discussion sound like features and very much like the kind of information you have in your Implementation section. I encourage you to think hard about what the features are and what the results are and separate them. Results are things that couldn't be done before and can be done know with your system. There's a difference between a feature (method to do something) and what it can accomplish (result). Here are a few examples: "The extra charts presented under the Venn diagram simplify veri#cation and comparison of multiple diagrams." - this is the result (though you don't provide any proof that they do simplify...) "the display can be switched to Edwards-Venn" - method "gives a clearer graphical representation for six list diagrams" - result.} ok \textbf{"whoever has some" - this sounds very hand wavy! I know what you mean but try to make it sound more appropriate for a paper. "programers with moderate Javascript experience"?} Taken into account. \textbf{fix: "Venn diagramS with up to four lists are easy to read and understand,"} Taken into account. \textbf{in: "With “Count lists” the #gures presented in the diagram correspond to the sums of counts of all identi#ers shared between lists. This has been used in diversity studies to present OTU (Operational Taxonomic Unit) read counts" -- does "with cl" mean "when count lists are used?". Also, "this" at the beginning of the second sentence is a little ambiguous... qualify it "It includes, as well, search and intersection identi#ers export functions." - a little unclear what will be exported} \textbf{I'm not really satisfied with how the authors addressed my comments about this being a bag of features and lacking scientific depth. However, since this is a software component, that's probably fine and I'll let this pass as long as the authors put in the effort to make the writing more rigorous} All features description have been removed and a usage example has been added in the Results'' section. jvenn benefits are then presented in the Discussion'' section. \textbf{-- EDITOR'S COMMENTS --} \textbf{1. the Results section needs to contain an example case study for a biological problem, preferably following this template:\newline * a short description of the biological problem, \newline * a brief description of how the problem was approached using jvenn, \newline * any interesting/unusual findings facilitated by jvenn, \newline * any jvenn feedback on specific features used in this case, \newline * how long it took to solve the problem using jvenn, and \newline * a short description of how the problem would have been solved otherwise and how long it would have taken.\newline} \textbf{In contrast, the current Results section is a list of jvenn functionality; this list belongs in the system description (see reviewer comments), not in the Results section. See also both reviewer comments regarding this issue, in both review rounds.} \textbf{2. The Discussion section needs to iterate over the advantages of using jvenn, based on the Results above; then list limitations, assumptions in the approach, its relation to existing software etc. Mimi Zeiger's "Essentials of Writing Biomedical Research Papers" is an excellent resource in this respect.} \textbf{3. A short biological motivation should be added to the first paragraph of the Introduction, and also to the abstract; with specific examples of biological use of Venn diagrams. Many of the BMC Bioinformatics readers are biologists, and this is the audience that needs to be convinced to use the software. The current intro and abstract are too generic.} \textbf{4. The language should be further improved (see individual reviewer comments).} This paper is unpublished and has not been submitted for publication elsewhere. We would be grateful if you would consider it for publication in BMC bioinformatics. %---------------------------------------------------------------------------------------- \end{newlfm} \end{document} \ No newline at end of file
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