bmc_jvenn.tex 24.3 KB
 Jerome Mariette committed Mar 03, 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 %% BioMed_Central_Tex_Template_v1.06 %% % % bmc_article.tex ver: 1.06 % % % %%IMPORTANT: do not delete the first line of this template %%It must be present to enable the BMC Submission system to %%recognise this template!! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% LaTeX template for BioMed Central %% %% journal article submissions %% %% %% %% <8 June 2012> %% %% %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% For instructions on how to fill out this Tex template %% %% document please refer to Readme.html and the instructions for %% %% authors page on the biomed central website %% %% http://www.biomedcentral.com/info/authors/ %% %% %% %% Please do not use \input{...} to include other tex files. %% %% Submit your LaTeX manuscript as one .tex document. %% %% %% %% All additional figures and files should be attached %% %% separately and not embedded in the \TeX\ document itself. %% %% %% %% BioMed Central currently use the MikTex distribution of %% %% TeX for Windows) of TeX and LaTeX. This is available from %% %% http://www.miktex.org %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%% additional documentclass options: % [doublespacing] % [linenumbers] - put the line numbers on margins %%% loading packages, author definitions %\documentclass[twocolumn]{bmcart}% uncomment this for twocolumn layout and comment line below \documentclass{bmcart} %%% Load packages  Jerome Mariette committed Mar 20, 2014 50 51 52 53 54 55 56 57 58 59 60 61 62 \usepackage{listings} \usepackage{color} \definecolor{gray}{rgb}{0.5,0.5,0.5} \lstset{ language=Java, showstringspaces=false, columns=flexible, basicstyle={\scriptsize \ttfamily}, numbers=none, stringstyle=\color{gray}, breaklines=true, breakatwhitespace=true }  Jerome Mariette committed Mar 03, 2014 63 64 65 66 67 68 69 70 71 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 %\usepackage{amsthm,amsmath} %\RequirePackage{natbib} %\RequirePackage{hyperref} \usepackage[utf8]{inputenc} %unicode support %\usepackage[applemac]{inputenc} %applemac support if unicode package fails %\usepackage[latin1]{inputenc} %UNIX support if unicode package fails %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% If you wish to display your graphics for %% %% your own use using includegraphic or %% %% includegraphics, then comment out the %% %% following two lines of code. %% %% NB: These line *must* be included when %% %% submitting to BMC. %% %% All figure files must be submitted as %% %% separate graphics through the BMC %% %% submission process, not included in the %% %% submitted article. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \def\includegraphic{} \def\includegraphics{} %%% Put your definitions there: \startlocaldefs \endlocaldefs %%% Begin ... \begin{document} %%% Start of article front matter \begin{frontmatter} \begin{fmbox}  Jerome Mariette committed May 06, 2014 104 \dochead{Software}  Jerome Mariette committed Mar 03, 2014 105 106 107 108 109 110 111  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the title of your article here %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  Jerome Mariette committed May 05, 2014 112 \title{jvenn: an interactive Venn diagram viewer.}  Jerome Mariette committed Mar 03, 2014 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the authors here %% %% %% %% Specify information, if available, %% %% in the form: %% %% ={,} %% %% = %% %% Comment or delete the keys which are %% %% not used. Repeat \author command as much %% %% as required. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \author[  Jerome Mariette committed Mar 11, 2014 129 130 131 132 133 134  addressref={aff2}, % id's of addresses, e.g. {aff1,aff2} noteref={n1}, % id's of article notes, if any email={Philippe.Bardou@toulouse.inra.fr} % email address ]{\inits{PB}\fnm{Philippe} \snm{Bardou}} \author[ addressref={aff1},  Jerome Mariette committed Mar 03, 2014 135 136  corref={aff1}, % id of corresponding address, if any noteref={n1}, % id's of article notes, if any  Jerome Mariette committed Mar 11, 2014 137 138  email={Jerome.Mariette@toulouse.inra.fr} ]{\inits{JM}\fnm{J\'{e}r\^{o}me} \snm{Mariette}}  Jerome Mariette committed May 22, 2014 139 140 141 142 \author[ addressref={aff1}, email={Frederic.Escudie@toulouse.inra.fr} ]{\inits{FE}\fnm{Frederic} \snm{Escudie}}  Jerome Mariette committed Mar 11, 2014 143 144 145 146 \author[ addressref={aff1}, email={Christophe.Djemiel@toulouse.inra.fr} ]{\inits{CD}\fnm{Christophe} \snm{Djemiel}}  Jerome Mariette committed Mar 03, 2014 147 148 \author[ addressref={aff1,aff2},  Jerome Mariette committed Mar 11, 2014 149 150  email={Christophe.Klopp@toulouse.inra.fr} ]{\inits{CK}\fnm{Christophe} \snm{Klopp}}  Jerome Mariette committed Mar 03, 2014 151 152 153 154 155 156 157 158 159 160 161  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the authors' addresses here %% %% %% %% Repeat \address commands as much as %% %% required. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \address[id=aff1]{% % unique id  Jerome Mariette committed Mar 11, 2014 162 163 164 165 166  \orgname{Plate-forme bio-informatique Genotoul / MIA-T, INRA}, % university, etc \street{Borde Rouge}, % \postcode{31326} % post or zip code \city{Castanet-Tolosan}, % city \cny{France} % country  Jerome Mariette committed Mar 03, 2014 167 168 } \address[id=aff2]{%  Jerome Mariette committed Mar 11, 2014 169 170 171 172 173  \orgname{Plate-forme SIGENAE / GenPhySE, INRA}, % university, etc \street{Borde Rouge}, % \postcode{31326} % post or zip code \city{Castanet-Tolosan}, % city \cny{France} % country  Jerome Mariette committed Mar 03, 2014 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 } %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter short notes here %% %% %% %% Short notes will be after addresses %% %% on first page. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{artnotes} %\note{Sample of title note} % note to the article \note[id=n1]{Equal contributor} % note, connected to author \end{artnotes} \end{fmbox}% comment this for two column layout %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The Abstract begins here %% %% %% %% Please refer to the Instructions for %% %% authors on http://www.biomedcentral.com %% %% and include the section headings %% %% accordingly for your article type. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{abstractbox} \begin{abstract} % abstract  Jerome Mariette committed Mar 03, 2014 206 \parttitle{Background} %if any  Jerome Mariette committed May 22, 2014 207 208 The amount of rich Web applications allowing scientists to store, share and analyze data on-line is increasing. This enhances the need of embeddable  Jerome Mariette committed May 12, 2014 209 210 211 visualization tools. Scientists often produce lists of known identifiers corresponding to different experimental conditions. The Venn diagram is one of the most popular chart types used to present list comparison results.  Jerome Mariette committed Mar 04, 2014 212   Jerome Mariette committed Mar 03, 2014 213 \parttitle{Results} %if any  Jerome Mariette committed May 12, 2014 214 215 216 217 jvenn is a JavaScript library providing lists processing and Venn diagram displaying functions. It is able to handle up to six input lists presenting results as classical or Edwards-Venn diagrams. Using it, developers can easily embed dynamic Venn diagrams in Web pages. jvenn is fully configurable and  Jerome Mariette committed May 22, 2014 218 allows to control and customize user interactions.  Jerome Mariette committed Mar 07, 2014 219   Jerome Mariette committed Mar 03, 2014 220 \parttitle{Conclusions} %if any  Jerome Mariette committed May 12, 2014 221 222 223 We introduce jvenn, an open source component for Web environments helping scientists to analyze their data. The library package, which comes with full documentation and an integration example, is freely available at  Jerome Mariette committed May 06, 2014 224 http://bioinfo.genotoul.fr/jvenn.  Jerome Mariette committed Mar 20, 2014 225   Jerome Mariette committed Mar 03, 2014 226   Jerome Mariette committed Mar 03, 2014 227 228 229 230 231 232 233 234 235 236 237 \end{abstract} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The keywords begin here %% %% %% %% Put each keyword in separate \kwd{}. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{keyword}  Jerome Mariette committed Mar 11, 2014 238 239 240 \kwd{Venn} \kwd{Edward-Venn} \kwd{vizualisation}  Jerome Mariette committed Mar 03, 2014 241 \kwd{jquery}  Jerome Mariette committed May 05, 2014 242 \kwd{JavaScript}  Jerome Mariette committed Mar 03, 2014 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 \end{keyword} % MSC classifications codes, if any %\begin{keyword}[class=AMS] %\kwd[Primary ]{} %\kwd{} %\kwd[; secondary ]{} %\end{keyword} \end{abstractbox} % %\end{fmbox}% uncomment this for twcolumn layout \end{frontmatter} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The Main Body begins here %% %% %% %% Please refer to the instructions for %% %% authors on: %% %% http://www.biomedcentral.com/info/authors%% %% and include the section headings %% %% accordingly for your article type. %% %% %% %% See the Results and Discussion section %% %% for details on how to create sub-sections%% %% %% %% use \cite{...} to cite references %% %% \cite{koon} and %% %% \cite{oreg,khar,zvai,xjon,schn,pond} %% %% \nocite{smith,marg,hunn,advi,koha,mouse}%% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%% start of article main body % %%%%%%%%%%%%%%%% %% Background %% %%  Jerome Mariette committed Mar 03, 2014 285 \section*{Background}  Jerome Mariette committed Mar 04, 2014 286   Jerome Mariette committed May 23, 2014 287 288 289 290 291 292 293 294 Biological experiments are often based on sample or condition comparison. Thus, it is important to provide researchers with effective visualization tools to explore and extract relevant differences between data sets. Data analysis often leads to compare lists of biological identifiers (gene names, Operational Taxonomic Unit (OTU), ...). List intersection results are commonly visualized using Venn diagrams \cite{Venn1880} presenting shared and unshared identifier counts. They provide a simple way to extract similarities and differences between the lists.  Jerome Mariette committed May 16, 2014 295 296 297 298 299 300 301 302 303 304  Many Venn diagram software packages are already available. They can be classified using their type : stand-alone, library, Web applications, JavaScript library and their diagram layout: classical or Edwards. Edwards-Venn \cite{Edwards2004} representation provides a clearer view for diagrams having more than four lists (Fig. 2). VENNTURE \cite{Bronwen2012} is a stand-alone application able to generate this layout for up to six lists. VennDiagram \cite{RVennDiagram} is an R package including functions to draw classical diagrams from two to five lists. Venn diagrams are also often included in Web pages. BioVenn \cite{Hulsen2008} and venny \cite{venny} are Web applications with identifier input text areas. The  Jerome Mariette committed May 22, 2014 305 first one offers a three circles area-proportional diagram, the second one  Jerome Mariette committed May 16, 2014 306 307 outputs a non-proportional four lists diagram. Canvasxpress \cite{canvasxpress} and Google Chart API \cite{googleAPI} are  Jerome Mariette committed May 12, 2014 308 JavaScript libraries including Venn diagram features which can easily be  Jerome Mariette committed May 16, 2014 309 310 embedded in any Web page. They respectively produce diagrams with up to four and three lists. Both generate graphical outputs given the intersection counts but cannot calculate them.  Jerome Mariette committed Mar 05, 2014 311   Jerome Mariette committed May 12, 2014 312 313 314 315 We introduce jvenn, a JavaScript library helping scientists to present their data, in the same spirit as already existing tools such as jbrowse \cite{Westesson01032013}, Cytoscape-Web \cite{Lopes2010}, and jHeatmap \cite{DeuPons2014}. jvenn handles up to six input lists, can display classical  Jerome Mariette committed May 16, 2014 316 or Edwards-Venn diagrams, can easily be embedded in a Web  Jerome Mariette committed May 12, 2014 317 page, allows three different data formats (lists, intersection counts and count  Jerome Mariette committed May 22, 2014 318 lists), exports PNG or CSV files and permits to redefine the callback function  Jerome Mariette committed May 12, 2014 319 320 321 322 in order to control users interactions. jvenn has already been cited in two scientific publications \cite{Bianchia2013, Aravindraja2013} and is embedded within nG6 \cite{Mariette2012}, RNAbrowse \cite{Mariette} and WallProtDB \cite{SanClemente} Web applications.  Jerome Mariette committed Mar 03, 2014 323   Jerome Mariette committed Mar 03, 2014 324   Jerome Mariette committed Mar 05, 2014 325 \section*{Implementation}  Jerome Mariette committed Mar 04, 2014 326   Jerome Mariette committed May 16, 2014 327 328 329 330 jvenn is based on venny regarding the algorithm computing the lists intersections. The algorithm has been wrapped in a jQuery plug-in \cite{jquery}, extended with new features presented hereunder and the ability to use up to six lists. It can be embedded in an HTML page referencing the JavaScript file. For researchers  Jerome Mariette committed May 12, 2014 331 332 333 334 who want to produce a Venn diagram from their identifier lists, jvenn is also available as a Web application at http://bioinfo.genotoul.fr/jvenn/example.html. The installation documentation is included in the software package which can be downloaded from http://bioinfo.genotoul.fr/jvenn.  Jerome Mariette committed Mar 07, 2014 335   Jerome Mariette committed May 16, 2014 336 The library provides an option to define the input type : \textit{series}. It  Jerome Mariette committed May 23, 2014 337 338 339 accepts three different formats : lists, intersection counts and count lists. All are JSON objects. Lists'' contain for each input label and an identifiers table. Intersection counts'' contain a correspondence table  Jerome Mariette committed May 16, 2014 340 341 between labels and letters [A..F] and a table linking the intersection names formed by the successions of letters and the counts. Count lists'' are organized as Lists''  Jerome Mariette committed May 23, 2014 342 343 344 345 346 347 348 349 in which identifiers are replaced by their unique occurrence and their count. Examples are presented in Table 1. Venn diagrams show intersections between a collection of sets. However, in some cases it can be interested to display not just the sets but also their counts. As example, an OTU represents a species or a group of species given by a cluster leader of DNA sequences. Displaying such data with the lists'' format leads to produce intersections of shared and unshared OTUs between samples. However, using count lists'' allows to define the amount of sequences constituting each OTUs. Thus, the produced diagram  Jerome Mariette committed May 23, 2014 350 351 352 353 354 355 356 357 358 represents the species abondance between samples. For lists'' and count lists'' jvenn will first execute a function to compute the intersections and display the chart. For intersection counts'', the plug-in only displays graphic. The display is based on a JavaScript canvas object allowing to export it as a PNG file. The intersection table can also be downloaded as a CSV file. It contains a header line with the diagram area labels and, in column, the identifiers of the elements contained in the area. These features can be disabled by setting the \textit{exporting} option to \textit{false} hiding the exporting button.  Jerome Mariette committed May 22, 2014 359 360 361 362 363 364 365  The Web application developer can also define the diagram display setting the \textit{displayType} option to \textit{edwards} or \textit{classic}. Setting the \textit{shortNumber} option to \textit{false} will disable the default behaviour of the plugin to substitute the intersection count by a question mark if this one overflow its area. The callback function defining the click on an intersection count can be overloaded by defining the \textit{fnClickCallback} parameter.  Jerome Mariette committed May 23, 2014 366 367 This function gives access to the \textit{this.listnames} and \textit{this.list} variables allowing the developer to control the user interactions. This feature can be disabled by  Jerome Mariette committed May 12, 2014 368 setting the \textit{disableClick} option to \textit{true}. To customize the  Jerome Mariette committed May 23, 2014 369 diagram display, the developer can also set the \textit{colors} option.  Jerome Mariette committed Mar 27, 2014 370 371 372 373  \section*{Results and Discussion}  Jerome Mariette committed May 12, 2014 374 375 Venn diagrams are commonly used to display list intersections because they are simple to read and understand. This is true up to four lists but scientists are  Jerome Mariette committed May 23, 2014 376 interested in using it with more. This type of diagram is able to present up  Jerome Mariette committed May 16, 2014 377 378 to six lists in its classical representation. Reaching this number, the diagram can not a priori be proportional to the list counts and the intersection  Jerome Mariette committed May 12, 2014 379 380 areas are often too small to display the figures.  Jerome Mariette committed May 22, 2014 381 382 383 384 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 (Fig. 2) what gives a clearer graphical representation for six list diagrams. To enhance the figure's readability on the classical six lists Venn graphic, it was decided not  Jerome Mariette committed May 12, 2014 385 386 387 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 a switch button panel (Fig. 1) was added. This panel enables to switch on and off the different lists  Jerome Mariette committed May 23, 2014 388 and display the corresponding intersection counts. For all diagrams, when  Jerome Mariette committed May 12, 2014 389 the intersection count size exceeds the allowed space, the value is substituted  Jerome Mariette committed May 22, 2014 390 391 392 by a question mark. The real value pops-up on mouse over. Last, to show the lists taking part in an intersection, jvenn highlights the corresponding areas on mouse over, fading the others out.  Jerome Mariette committed May 12, 2014 393 394 395  Scientists are usually interested in extracting identifier lists from some of the intersections, therefore, jvenn implements an one-click function which  Jerome Mariette committed May 22, 2014 396 397 retrieves the names of the corresponding samples and the identifiers. Seeking an identifier can also be done using the plugin. The intersection with the  Jerome Mariette committed May 23, 2014 398 matching identifier is highlighted as well as the lists containing it.  Jerome Mariette committed Mar 27, 2014 399   Jerome Mariette committed May 12, 2014 400 401 402 Having an overview of the list size and comparing multiple diagrams can be difficult using a Venn diagram. Thus, jvenn provides two extra charts (Fig. 1) bellow the Venn. The first one represents the input lists size histogram. It  Jerome Mariette committed May 22, 2014 403 404 405 allows users to check the homogeneity of the lists size. The second one displays the number of elements located in intersections of a certain size. This feature can be used to compare the compactness of multiple Venn diagrams.  Jerome Mariette committed Mar 27, 2014 406   Jerome Mariette committed May 12, 2014 407 jvenn's performance depends on the client browser. Using the running version  Jerome Mariette committed May 22, 2014 408 on a standard Linux computer (1 cpu, 4GB of RAM), it displays a six lists diagram of  Jerome Mariette committed Mar 27, 2014 409 10 000 identifiers in two seconds.  Jerome Mariette committed Mar 27, 2014 410   Jerome Mariette committed May 12, 2014 411 412 413 As examples, 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  Jerome Mariette committed May 23, 2014 414 intersections between all of them using the classical Venn diagram display.  Jerome Mariette committed May 12, 2014 415 416 In Fig. 2, jvenn highlights the intersection between three samples out of six from an Edwards-Venn diagram.  Jerome Mariette committed Mar 07, 2014 417   Jerome Mariette committed Mar 03, 2014 418   Jerome Mariette committed Mar 03, 2014 419 420 \section*{Conclusions}  Jerome Mariette committed May 12, 2014 421 422 423 jvenn is an easy-to-use library which generates Venn and Edwards-Venn diagrams from lists of identifiers or from computed intersection counts. Its implementation as a library allows whoever has some JavaScript programming  Jerome Mariette committed May 16, 2014 424 skills to embed it in a Web page without any dependencies.  Jerome Mariette committed Mar 07, 2014 425   Jerome Mariette committed Mar 03, 2014 426 \section*{Availability and requirements}  Jerome Mariette committed Mar 03, 2014 427   Jerome Mariette committed May 12, 2014 428 429 430 431 jvenn is freely available under the GNU General Public License (GPL) and can be downloaded with an example and the full documentation at http://bioinfo.genotoul.fr/jvenn website. A running version is accessible at http://bioinfo.genotoul.fr/jvenn/example.html.  Jerome Mariette committed Mar 07, 2014 432   Jerome Mariette committed Mar 03, 2014 433 434 435 436 437 438 439 440 441 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Backmatter begins here %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{backmatter} \section*{Competing interests}  Jerome Mariette committed Mar 11, 2014 442 The authors declare that they have no competing interests.  Jerome Mariette committed Mar 03, 2014 443 444  \section*{Author's contributions}  Jerome Mariette committed May 22, 2014 445 JM conceived and designed the project. JM, PB, FE and CD implemented the project.  Jerome Mariette committed May 12, 2014 446 447 CK evaluated software capabilities, and provided feedback on implementation. JM and CK wrote the manuscript. All authors read and approved the final manuscript.  Jerome Mariette committed Mar 03, 2014 448 449  \section*{Acknowledgements}  Jerome Mariette committed Mar 03, 2014 450 451 452 We would like to acknowledge all our users for providing us useful feedback on the system and for pointing out features worth developing.  Jerome Mariette committed Mar 03, 2014 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% The Bibliography %% %% %% %% Bmc_mathpys.bst will be used to %% %% create a .BBL file for submission. %% %% After submission of the .TEX file, %% %% you will be prompted to submit your .BBL file. %% %% %% %% %% %% Note that the displayed Bibliography will not %% %% necessarily be rendered by Latex exactly as specified %% %% in the online Instructions for Authors. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % if your bibliography is in bibtex format, use those commands: \bibliographystyle{bmc-mathphys} % Style BST file  Jerome Mariette committed Mar 05, 2014 470 \bibliography{bmc_jvenn} % Bibliography file (usually '*.bib' )  Jerome Mariette committed Mar 03, 2014 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492  % or include bibliography directly: % \begin{thebibliography} % \bibitem{b1} % \end{thebibliography} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Figures %% %% %% %% NB: this is for captions and %% %% Titles. All graphics must be %% %% submitted separately and NOT %% %% included in the Tex document %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% Do not use \listoffigures as most will included as separate files \section*{Figures} \begin{figure}[h!]  Jerome Mariette committed Mar 25, 2014 493  \caption{\csentence{A six lists classic Venn diagram.}  Jerome Mariette committed May 12, 2014 494 495 496 497 498 499 500  This Venn diagram displays overlaps between six different biological samples. When the user clicks on a figure, it calls the developer defined function. The icon located on the top-right, allows users to download the diagram as a PNG file. On the bottom-right of the chart, a switch button panel allowing to activate or dis-activate lists to access a specific intersection count. The charts showing the lists size repartition and the number of common and specific elements are located underneath the  Jerome Mariette committed Mar 27, 2014 501  diagram.}  Jerome Mariette committed Mar 03, 2014 502 503 504  \end{figure} \begin{figure}[h!]  Jerome Mariette committed Mar 05, 2014 505  \caption{\csentence{A six lists Edwards-Venn diagram.}  Jerome Mariette committed May 12, 2014 506 507 508 509  On mouse over a figure, the shape corresponding to the list involved in the intersection are highlighted and the other ones faded out. In this example, the user points the intersection between samples SRR068049, SRR068051 and SRR068052 which contains eight different items.}  Jerome Mariette committed Mar 03, 2014 510 511  \end{figure}  Jerome Mariette committed Mar 20, 2014 512 513 514 515 516 517 518 519 520 521 522 523 524 525 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Tables %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% Use of \listoftables is discouraged. %% \section*{Tables} \begin{table}[h!] \caption{Available formats and example for the \textit{series} option.} \begin{tabular}{cccc} \hline format & example\\ \hline  Jerome Mariette committed Mar 24, 2014 526  lists &  Jerome Mariette committed Mar 20, 2014 527 528 529 530 531 532 533 534 535 \begin{lstlisting} series: [{ name: 'sample1', data: ["Otu1", "Otu2", "Otu3", "Otu4", "Otu5", "Otu6", "Otu7"] }, { name: 'sample2', data: ["Otu1", "Otu2", "Otu5", "Otu7", "Otu8", "Otu9"] }] \end{lstlisting}\\ \hline  Jerome Mariette committed Mar 24, 2014 536  intersection counts &  Jerome Mariette committed Mar 20, 2014 537 538 539 540 541 542 \begin{lstlisting} series: [{ name: {A: 'sample 1', B: 'sample 2', C: 'sample 3'}, data: {A: 340, B: 562, C: 620, AB: 639, AC: 456, BC: 915, ABC: 552} }] \end{lstlisting}\\ \hline  Jerome Mariette committed Mar 24, 2014 543  count lists &  Jerome Mariette committed Mar 20, 2014 544 545 546 547 548 549 550 551 552 553 554 555 556 557 \begin{lstlisting} series: [{ name: 'sample1', data: ["Otu1", "Otu2", "Otu3", "Otu4", "Otu5", "Otu6", "Otu7"], values: [5, 15, 250, 20, 23, 58, 89] }, { name: 'sample2', data: ["Otu1", "Otu2", "Otu5", "Otu7", "Otu8", "Otu9"], values: [90, 300, 10, 2, 45, 9] }] \end{lstlisting}\\ \hline \end{tabular} \end{table}  Jerome Mariette committed Mar 03, 2014 558 \end{backmatter}  Jerome Mariette committed Mar 24, 2014 559 \end{document}