jvenn_coverletter_bis.tex 12.7 KB
 Jerome Mariette committed May 23, 2014 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % 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". 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  Jerome Mariette committed Jun 10, 2014 54 new features to jvenn presented in the manuscript. Hereafter are our answers  Jerome Mariette committed May 23, 2014 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 to the reviewers. \textbf{-- Reviewer 1 --} \textbf{1. The manuscript is sloppy / hand-wavy / not detailed enough in many ways. A few examples are listed below. The authors need to fix these before I can make a decision.} \textbf{- URL running off the page 3} The URL have been changed to fit the page size. \textbf{- run-on sentences}  Jerome Mariette committed Jun 10, 2014 71 The organisation of the sections and paragraphs of the text has been modified.  Jerome Mariette committed May 23, 2014 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 Many sentences have been rewritten. \textbf{- what is a standard linux computer?} The sentence Using the running version on a standard Linux computer (1 cpu, 4GB of RAM)'' has been added. \textbf{- "whoever has some WEB programming skills" is a very vague way of defining a user base} The sentences have been modified as following: whoever has some JavaScript programming skills'' \textbf{- I recommend rewording the first paragraph; I had a hard time following the logic in the way it is currently written. The point you are trying to make should be more clearly stated: diagrams are easy to read for up to four categories but more features are needed for 5 or 6.} The Background section has been fully rewritten. \textbf{- how many sets do [4] and [5] allow for?} They respectivly handle 3 and 4 lists. This has been added to the manuscript. \textbf{- there are many weird or poorly designed sentence structures (e.g.: "The library provides an option to de ne the data inputs: series.") and quite a few typos ("embeded", "overlights"?). I recommend the authors have the manuscript checked by an editor or at least an English speaker.} Many sentences have been rewritten as requested. \textbf{- the paper was submitted in the software category but at the top it says research? I was a little confused by this.} The section title of the manuscript has been changed for Software''. \textbf{2. The manuscript is more or less a list of features. I feel there needs to be a little more depth and insight in a scholarly article. For example, how do the features mentioned in paragraph two of the results and discussion alleviate the problem mentioned in the first paragraph? I have checked the two papers that cite the software (10,11) and both show only the venn diagram and not any of the other lists. How did the papers (10,11) use it and why couldn't they use another library? Perhaps a brief mention of other ways to look/visualize this data might be worth it:}  Jerome Mariette committed Jun 11, 2014 118 119 120 121 122 123 124 The organisation of the manuscript has been modified and several paragraph have been rewritten. The two papers citing jvenn used it to built a publishable diagram. They used jvenn because it is the only Web application available allowing users to provide 5 lists. To produce such a diagram they could have use VENNTURE as well, but this application is only available under MS-Windows and only produce Powerpoint outputs under the Edwards-Venn layout.  Jerome Mariette committed May 23, 2014 125 126 127 128 129 130 131 132 133 134 135 136  \textbf{-- Reviewer 2 --} \textbf{ -Major Compulsory Revisions For the manuscript: 1. In the Background section, the authors list a number of libraries designed for web applications such as BioVenn, venny, Canvasxpress, and the Google Chart API. However, there are number of other Venn diagram drawing libraries that are 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,  Jerome Mariette committed Jun 10, 2014 137 Maudsley S. VENNTURE Novel Venn Diagram Investigational Tool for Multiple  Jerome Mariette committed May 23, 2014 138 139 140 141 142 143 144 145 146 147 148 Pharmacological Dataset Analysis.} These 2 citations and the description of the tools have been added in the Background section. \textbf{2. The authors claim that jvenn is the only library to accommodate up to six input lists. VENNTURE (cited above) can produce Edwards-Venn 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.  Jerome Mariette committed Jun 10, 2014 149 Moreover it is the only software package offering classical Venn diagram displays  Jerome Mariette committed May 23, 2014 150 151 152 153 154 155 156 for 6 input lists. \textbf{Also the authors point out that venny does not visualize the relative 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  Jerome Mariette committed Jun 10, 2014 157 to 3 lists. Beyond that, displaying the graphic is a complex problem.  Jerome Mariette committed May 23, 2014 158 159 160 161 162 163 164 165 166  \textbf{3. The jvenn library appears to be built upon the venny library; however this distinction is unclear. In the implementation section, the authors should more clearly emphasize their contribution to the software, which appears to be modifying venny to handle more than 4 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.  Jerome Mariette committed Jun 11, 2014 167 168 The sentence jvenn intersection computing algorithm is based on venny.'' has been added to the Implementation section.  Jerome Mariette committed May 23, 2014 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291  \textbf{4. The authors should describe the three different data formats. Table 1 shows good examples of the inputs, but "count lists" is particularly unintuitive. This description could go in the Implementation section, where the authors reference the table.} A full explanation of the formats and a specific example of the "count lists" has been added in the Implementation section. \textbf{For the web application: 5. There is no help page on the web application. The wiki page is quite useful, however. At the very least, there should be a link to the wiki page to help answer user's questions. Adding a tutorial might increase usage as well.} The full documentation is now online and a user manuel has been written to help our Web application users. \textbf{6. The web application was down for a time between 4/12 and 4/13, which slowed the revision process. If this is a semi-regular occurrence, I advise moving the application to a more reliable server.} This was unfortunate, the server is reliable and monitored by our system administrator team. \textbf{7. The "on/off" switch buttons for the classic view and six lists are quite confusing. I expected the diagram to change when I clicked these. Perhaps a title or a box explaining their use would be better.} We made modifications on this feature. The "on/off" switch buttons now highlights the intersection figure. \textbf{Minor Essential Revisions Throughout: \newline - WEB -> web or Web \newline - javascript -> JavaScript \newline - developper -> developer \newline - Be consistent with six vs. 6 \newline Title and Abstract: \newline - venn should be capitalized in the title (though BMC Bioinformatics might make everything lower-case - disregard if this is true). \newline - embadable -> embeddable \newline - allows [users] to control and customize all user interaction \newline - awkward phrase: helping scientists to analyse their data \newline - The library package, [which comes] with [] full documentation \newline - vizualization -> visualization \newline Background: \newline - awkward phrase: Biological projects are increasingly multiplexing samples - what's a multiplexing sample? \newline - availble -> available \newline - These libraries generate [] graphical \newline - cannot perform [] calculations \newline - awkward phrase: permits to overload the callback function \newline} All these spelling and sentence errors have been taken into account. \textbf{Results and Discussion:\newline - In general, there are many sentences in this section that are more implementation details (such as the question mark, pop-ups, and mouse-over). If possible, try to describe these items in the Implementation section.} All parameters description were moved to the Implementation as recommended. \textbf{- Nowadays, this type of diagrams is able to present -> Nowadays, these types of diagrams are able to present\newline - "Nowadays" is incorrect - Venn diagrams have always been able to visualize multiple lists.\newline - diagrams are not proportional [to] the list counts\newline - functionnalities -> functionalities\newline - figures readibility -> figure's readability\newline - on click function -> one-click function\newline - awkward phrase: It allows users to check the list size homogeneity.\newline - The second one[] displays the number\newline - jvenn performances -> jvenn's performance\newline} All these spelling and sentence errors have been taken into account. \textbf{Conclusions and References:\newline - The fact that jvenn is already embedded within four web applications is impressive! I would add this fact in the Background section.} Taken into account. \textbf{- Venny is incorrectly cited - please provide the author and year} The citation has been modified to add the author and year. \textbf{- Some of the references have incorrect author names: last names are followed by a,b,c, etc , presumably from institution references. Please fix.} All the references were checked and standardized. \textbf{Discretionary Revisions For the manuscript: - In the background, "allows three different data formats (lists/intersection counts/count lists)" is misleading - looks like two fractions and an integer. I'd suggest (list, intersection counts, and count lists). - The reference to jvenn in citation [11] is a dead link.} Taken into account. \textbf{- The authors should describe the difference between a classical and Edwards-Venn diagrams. This description can be brief (1-2 sentences).} A description of Edwards-Venn diagrams has been added to the manuscript. \textbf{- The jvenn url goes off the page under 'Availability and requirements' For the web application:} The URL have been changed to fit the page size. \textbf{- The text box under "click on a number to show the corresponding elements" is writable, which was initially confusing.} This has been changed, the textarea is set as readonly, users are no longer able to edit it but can still copy its content. \textbf{- In the horizontal bar plot, labeling the numbers in the box and the numbers on the x-axis would clarify the plot.}  Jerome Mariette committed Jun 05, 2014 292 293 294 The graphic title has been changed for Number of elements: specific(1) or shared by 2, 3, \ldots lists''. This graphic is also explained in the user manual section.  Jerome Mariette committed May 23, 2014 295 296 297 298 299 300 301 302 303  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}  Jerome Mariette committed Jun 10, 2014 304 \end{document}