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+++ b/bmc_article.tex
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-\NeedsTeXFormat{LaTeX2e}[1995/12/01]
-\documentclass[10pt]{bmc_article}    
-
-% Load packages
-\usepackage{url}  % Formatting web addresses  
-\usepackage{ifthen}  % Conditional 
-\usepackage{multicol}   %Columns
-\usepackage[utf8]{inputenc} %unicode support
-%\usepackage[applemac]{inputenc} %applemac support if unicode package fails
-%\usepackage[latin1]{inputenc} %UNIX support if unicode package fails
-\urlstyle{rm}
-\usepackage[citestyle=numeric-comp]{biblatex}                                                                     
-\setlength{\bibitemsep}{0cm}                                                                                                                
-\renewbibmacro{in:}{%                                                                                                                       
-  \ifentrytype{article}{}{%                                                                                                                 
-  \printtext{\bibstring{in}\intitlepunct}}}                                                                                                 
-\addbibresource{bmc_article.bib}                                                                                                                    
- 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
-%%                                             %%
-%%  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{}
-
-\setlength{\topmargin}{0.0cm}
-\setlength{\textheight}{21.5cm}
-\setlength{\oddsidemargin}{0cm} 
-\setlength{\textwidth}{16.5cm}
-\setlength{\columnsep}{0.6cm}
-
-\newboolean{publ}
-
-%Review style settings
-\newenvironment{bmcformat}{\begin{raggedright}\baselineskip20pt\sloppy\setboolean{publ}{false}}{\end{raggedright}\baselineskip20pt\sloppy}
-
-%Publication style settings
-%\newenvironment{bmcformat}{\fussy\setboolean{publ}{true}}{\fussy}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%% RESEARCH PAPER %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\begin{document}
-\begin{bmcformat}
-
-\title{The Chemistry Development Kit (CDK). 3. Atom typing, Rendering, Molecular Formula, ...}
- 
-\author{
-  Egon L Willighagen$^{1}$% // FIXED FIRST AUTHOR
-  \email{Egon L Willighagen - egon.willighagen@ki.se}
-\and
-  Miguel Rojas Cherto$^2$%
-  \email{Miguel Rojas Cherto - steinbeck@ebi.ac.uk}
-\and
-  You C B Here$^3$%
-  \email{You C B Here - you.here@example.org}
-\and
-  C D K Project\correspondingauthor$^98$% // FIXED SECOND BUT LAST AUTHOR
-  \email{C D K Project - cdk-devel@lists.sourceforge.net}
-\and
-  Rajarshi Guha$^99$% // FIXED ONE BUT LAST AUTHOR
-  \email{Rajarshi Guha - steinbeck@ebi.ac.uk}
-\and
-  Christoph Steinbeck$^100$% // FIXED LAST AUTHOR
-  \email{Christoph Steinbeck - steinbeck@ebi.ac.uk}
-}
-      
-\address{
-    \iid(1)Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, SE-17177 Stockholm, Sweden\\
-    \iid(2)Division of Analytical Biosciences, Leiden/Amsterdam Center for Drug Research, Leiden, The Netherlands \\
-    \iid(3)Example Ltd., Glasgow, UK \\
-    \iid(98)\url{http://cdk.sourceforge.net/} \\
-    \iid(99)NIH Center for Translational Therapeutics, 9800 Medical Center Drive, Rockville, MD 20878, USA \\
-    \iid(100)Chemoinformatics and Metabolism team, European Bioinformatics Institute, Hinxton, UK 
-}
-
-\maketitle
-
-%% The Abstract begins here
-
-\begin{abstract}
-% Do not use inserted blank lines (ie \\) until main body of text.
-\paragraph*{Background:}
-Cheminformatics is a well-established field with many applications in chemistry,
-drug discovery, and the life sciences. Particularly in the latter field, however,
-molecular properties are not well-understood yet, and the interaction between
-molecules and larger systems remains a challenge to be modeled. Therefore, the
-development of new data mining and pattern recognition continues to be important
-and the need for access to a cheminformatics library that one can change remains.
-\paragraph*{Results:}
-We here report the 1.4 series of the Chemistry Development Kit and outline how
-it evolved since the previous report. We demonstrate the new APIs we introduced
-in this version and discuss the extensive quality control mechanism we have
-adopted. New APIs have been introduced for substructure searching, rendering of
-molecules, handling of molecular formulas, atom type perception, and InChI
-support. At a quality control side we have introduced automated building,
-extensive unit and use case testing, and adopted peer review.
-\paragraph*{Conclusions:}
-With this paper we have shown the continued effort to provide a free, Open Source
-cheminformatics library, and show that such colleborative projects can survive for
-a long period. We have taken advantage from the community support, and show
-that an open source cheminformatics project can act as a peer reviewed
-publishing platform for scientific computating software.
-\end{abstract}
-
-
-
-\ifthenelse{\boolean{publ}}{\begin{multicols}{2}}{}
-
-%%%%%%%%%%%%%%%%
-%% Background %%
-%%
-\section*{Background}
-
-Open Source cheminformatics state \ldots (EGON)
-
-Adoption of the CDK ... Cinfony~\cite{OBoyle2008}, and other bindings \ldots ...
-
-Recent prominent use cases of the CDK~\cite{Steinbeck2003,Steinbeck2006} \ldots (EGON)
-
- 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Results and Discussion %%
-%%
-\section*{Results and Discussion}
-
-\subsection*{New Functionality}
-
-Everyone is invited to contribute and write up the functionality they contributed;
-only requirement: the code must have been incorporated into the main CDK library by the
-time of submission of this paper.
-
-  \subsubsection*{Atom Typing}
-  
-  The CDK has adopted a new atom typing algorithm \ldots (EGON)
-
-  \subsubsection*{Rendering API}
-  
-  Initiated by ...
-  
-  \subsubsection*{Molecular Formula}
-  
-  ....
-
-  \subsubsection*{SMARTS parser}
-  
-  ....
-
-  \subsubsection*{Partial charges and Delocalization}
-  
-  ....
-
-  \subsubsection*{New Builders}
-  
-  ....
-
-  \subsubsection*{InChI integration}
-  
-  .... jni-inchi dep, atom numbering, tautomer generation
-  
-\subsection*{Improved Coding Standards}
-
-  \subsubsection*{Peer review}
-
-  \subsubsection*{Modularization}
-
-  \subsubsection*{Documentation}
-
-  Initially done with DocCheck, replaced by OpenJavaDocCheck ...
-  
-  \subsubsection*{Unit testing}
-  
-  \subsubsection*{Code Quality}
-
-  PMD ...
-
-  \subsubsection*{Git, branching, and patches}
-
-%%%%%%%%%%%%%%%%%%%%%%
-\section*{Conclusions}
-  Text for this section \ldots
-  
-%%%%%%%%%%%%%%%%%%
-\section*{Methods}
-  \subsection*{Peer Review: Automated}
-    \subsubsection*{PMD}
-    \subsubsection*{JavaDoc Checks}
-  \subsection*{Peer Review: Manual}
-  \subsection*{Unit Testing}
-    
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section*{Authors contributions}
-    Text for this section \ldots
-
-    
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%
-\section*{Acknowledgements}
-  \ifthenelse{\boolean{publ}}{\small}{}
-  Text for this section \ldots
-
-
-{\ifthenelse{\boolean{publ}}{\footnotesize}{\small}
-\printbibliography
-}
-
-%%%%%%%%%%%
-
-\ifthenelse{\boolean{publ}}{\end{multicols}}{}
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Figures                       %%
-
-%% Do not use \listoffigures as most will included as separate files
-
-%\section*{Figures}
-%  \subsection*{Figure 1 - Sample figure title}
-%      A short description of the figure content
-%      should go here.
-%
-%  \subsection*{Figure 2 - Sample figure title}
-%      Figure legend text.
-
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Tables                        %%
-
-%% Use of \listoftables is discouraged.
-%%
-%\section*{Tables}
-%  \subsection*{Table 1 - Sample table title}
-%    Here is an example of a \emph{small} table in \LaTeX\ using  
-%    \verb|\tabular{...}|. This is where the description of the table 
-%    should go. \par \mbox{}
-%    \par
-%    \mbox{
-%      \begin{tabular}{|c|c|c|}
-%        \hline \multicolumn{3}{|c|}{My Table}\\ \hline
-%        A1 & B2  & C3 \\ \hline
-%        A2 & ... & .. \\ \hline
-%        A3 & ..  & .  \\ \hline
-%      \end{tabular}
-%      }
-%  \subsection*{Table 2 - Sample table title}
-%    Large tables are attached as separate files but should
-%    still be described here.
-
-
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Additional Files              %%
-
-%\section*{Additional Files}
-%  \subsection*{Additional file 1 --- Sample additional file title}
-%    Additional file descriptions text (including details of how to
-%    view the file, if it is in a non-standard format or the file extension).  This might
-%    refer to a multi-page table or a figure.
-%
-%  \subsection*{Additional file 2 --- Sample additional file title}
-%    Additional file descriptions text.
-
-
-\end{bmcformat}
-\end{document}
-
-
-
-
-
-
-
+%% BioMed_Central_Tex_Template_v1.05
+%%                                      %
+%  bmc_article.tex            ver: 1.05 %
+%                                       %
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                                     %%
+%%  LaTeX template for BioMed Central  %%
+%%     journal article submissions     %%
+%%                                     %%
+%%         <27 January 2006>           %%
+%%                                     %%
+%%                                     %%
+%% Uses:                               %%
+%% cite.sty, url.sty, bmc_article.cls  %%
+%% ifthen.sty. multicol.sty		       %%
+%%									   %%
+%%                                     %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                                                                 %%	
+%% For instructions on how to fill out this Tex template           %%
+%% document please refer to Readme.pdf 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                                           %%
+%%                                                                 %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+\NeedsTeXFormat{LaTeX2e}[1995/12/01]
+\documentclass[10pt]{bmc_article}    
+
+
+
+% Load packages
+\usepackage{cite} % Make references as [1-4], not [1,2,3,4]
+\usepackage{url}  % Formatting web addresses  
+\usepackage{ifthen}  % Conditional 
+\usepackage{multicol}   %Columns
+\usepackage[utf8]{inputenc} %unicode support
+%\usepackage[applemac]{inputenc} %applemac support if unicode package fails
+%\usepackage[latin1]{inputenc} %UNIX support if unicode package fails
+\urlstyle{rm}
+ 
+ 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%	
+%%                                             %%
+%%  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{}
+
+
+
+\setlength{\topmargin}{0.0cm}
+\setlength{\textheight}{21.5cm}
+\setlength{\oddsidemargin}{0cm} 
+\setlength{\textwidth}{16.5cm}
+\setlength{\columnsep}{0.6cm}
+
+\newboolean{publ}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                                              %%
+%% You may change the following style settings  %%
+%% Should you wish to format your article       %%
+%% in a publication style for printing out and  %%
+%% sharing with colleagues, but ensure that     %%
+%% before submitting to BMC that the style is   %%
+%% returned to the Review style setting.        %%
+%%                                              %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ 
+
+%Review style settings
+\newenvironment{bmcformat}{\begin{raggedright}\baselineskip20pt\sloppy\setboolean{publ}{false}}{\end{raggedright}\baselineskip20pt\sloppy}
+
+%Publication style settings
+%\newenvironment{bmcformat}{\fussy\setboolean{publ}{true}}{\fussy}
+
+
+
+% Begin ...
+\begin{document}
+\begin{bmcformat}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                                          %%
+%% Enter the title of your article here     %%
+%%                                          %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\title{A sample article title}
+ 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                                          %%
+%% Enter the authors here                   %%
+%%                                          %%
+%% Ensure \and is entered between all but   %%
+%% the last two authors. This will be       %%
+%% replaced by a comma in the final article %%
+%%                                          %%
+%% Ensure there are no trailing spaces at   %% 
+%% the ends of the lines                    %%     	
+%%                                          %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+\author{Charles A Darwin\correspondingauthor$^{1,2}$%
+       \email{Charles A Darwin\correspondingauthor - charles@londonzoo.co.uk}%
+      \and
+         Jane E Doe\correspondingauthor$^2$%
+         \email{Jane E Doe\correspondingauthor - jane.e.doe@cambridge.co.uk}
+       and 
+         John RS Smith$^3$%
+         \email{John RS Smith - john.RS.Smith@cambridge.co.uk}%
+      }
+      
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                                          %%
+%% Enter the authors' addresses here        %%
+%%                                          %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\address{%
+    \iid(1)Life Sciences Department, Kings College London, Cornwall House,%
+        Waterloo Road, London, UK\\
+    \iid(2)Department of Zoology, Cambridge, Waterloo Road, London, UK\\
+    \iid(3)Marine Ecology Department, Institute of Marine Sciences Kiel, %
+        D\"{u}sternbrooker Weg 20, 24105 Kiel, Germany
+}%
+
+\maketitle
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                                          %%
+%% The Abstract begins here                 %%
+%%                                          %%
+%% The Section headings here are those for  %%
+%% a Research article submitted to a        %%
+%% BMC-Series journal.                      %%  
+%%                                          %%
+%% If your article is not of this type,     %%
+%% then refer to the Instructions for       %%
+%% authors on http://www.biomedcentral.com  %%
+%% and change the section headings          %%
+%% accordingly.                             %%   
+%%                                          %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+\begin{abstract}
+        % Do not use inserted blank lines (ie \\) until main body of text.
+        \paragraph*{Background:} Text for this section of the abstract. 
+      
+        \paragraph*{Results:} Text for this section of the abstract \ldots
+
+        \paragraph*{Conclusions:} Text for this section of the abstract \ldots
+\end{abstract}
+
+
+
+\ifthenelse{\boolean{publ}}{\begin{multicols}{2}}{}
+
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                                          %%
+%% The Main Body begins here                %%
+%%                                          %%
+%% The Section headings here are those for  %%
+%% a Research article submitted to a        %%
+%% BMC-Series journal.                      %%  
+%%                                          %%
+%% If your article is not of this type,     %%
+%% then refer to the instructions for       %%
+%% authors on:                              %%
+%% http://www.biomedcentral.com/info/authors%%
+%% and change the section headings          %%
+%% accordingly.                             %% 
+%%                                          %%
+%% 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}%%
+%%                                          %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+
+
+%%%%%%%%%%%%%%%%
+%% Background %%
+%%
+\section*{Background}
+ Text for this section.\cite{koon,oreg,khar,zvai,xjon,schn,pond,smith,marg,hunn,advi,koha,mouse}
+
+
+ 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Results and Discussion %%
+%%
+\section*{Results and Discussion}
+  \subsection*{Results sub-heading}
+    \subsubsection*{This is a sub-sub-heading}
+      Sub-sub-sub-headings are made with the \textsl{\\subsubsection} command. \pb
+      pb at end of lines ensures correct paragraph spacing.\pb
+	  Text for this sub-sub-section \ldots
+    \subsubsection*{Another sub-sub-sub-heading}
+      Text for this sub-sub-section \ldots
+
+  \subsection*{Another results sub-heading}
+    Text for this sub-section \ldots
+
+  \subsection*{Yet another results sub-heading}
+    Text for this sub-section.  More results \ldots
+
+
+    
+
+%%%%%%%%%%%%%%%%%%%%%%
+\section*{Conclusions}
+  Text for this section \ldots
+
+
+  
+%%%%%%%%%%%%%%%%%%
+\section*{Methods}
+  \subsection*{Methods sub-heading for this section}
+    Text for this sub-section \ldots
+
+  \subsection*{Another methods sub-heading for this section}
+    Text for this sub-section \ldots
+
+  \subsection*{Yet another sub-heading for this section}
+    Text for this sub-section \ldots
+
+
+    
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section*{Authors contributions}
+    Text for this section \ldots
+
+    
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section*{Acknowledgements}
+  \ifthenelse{\boolean{publ}}{\small}{}
+  Text for this section \ldots
+
+
+ 
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                  The Bibliography                       %%
+%%                                                         %%              
+%%  Bmc_article.bst  will be used to                       %%
+%%  create a .BBL file for submission, which includes      %%
+%%  XML structured for BMC.                                %%
+%%                                                         %%
+%%                                                         %%
+%%  Note that the displayed Bibliography will not          %% 
+%%  necessarily be rendered by Latex exactly as specified  %%
+%%  in the online Instructions for Authors.                %% 
+%%                                                         %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+{\ifthenelse{\boolean{publ}}{\footnotesize}{\small}
+ \bibliographystyle{bmc_article}  % Style BST file
+  \bibliography{bmc_article} }     % Bibliography file (usually '*.bib' ) 
+
+%%%%%%%%%%%
+
+\ifthenelse{\boolean{publ}}{\end{multicols}}{}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                               %%
+%% 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}
+  \subsection*{Figure 1 - Sample figure title}
+      A short description of the figure content
+      should go here.
+
+  \subsection*{Figure 2 - Sample figure title}
+      Figure legend text.
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                               %%
+%% Tables                        %%
+%%                               %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%% Use of \listoftables is discouraged.
+%%
+\section*{Tables}
+  \subsection*{Table 1 - Sample table title}
+    Here is an example of a \emph{small} table in \LaTeX\ using  
+    \verb|\tabular{...}|. This is where the description of the table 
+    should go. \par \mbox{}
+    \par
+    \mbox{
+      \begin{tabular}{|c|c|c|}
+        \hline \multicolumn{3}{|c|}{My Table}\\ \hline
+        A1 & B2  & C3 \\ \hline
+        A2 & ... & .. \\ \hline
+        A3 & ..  & .  \\ \hline
+      \end{tabular}
+      }
+  \subsection*{Table 2 - Sample table title}
+    Large tables are attached as separate files but should
+    still be described here.
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%                               %%
+%% Additional Files              %%
+%%                               %%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\section*{Additional Files}
+  \subsection*{Additional file 1 --- Sample additional file title}
+    Additional file descriptions text (including details of how to
+    view the file, if it is in a non-standard format or the file extension).  This might
+    refer to a multi-page table or a figure.
+
+  \subsection*{Additional file 2 --- Sample additional file title}
+    Additional file descriptions text.
+
+
+\end{bmcformat}
+\end{document}
+
+
+
+
+
+
+

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