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I am using this bioinformatics template. I am trying to compile it but can't seem to resolve these two errors.

About the undefined control sequence error, it seems it is caused by a wrong command. \maketitle is valid but it is still giving an error.

About the paragraph ended before \abstract was complete error, I read it could be because of imbalanced braces. That's not the case either.

Here's the code I am using.

\documentclass{bioinfo}
\copyrightyear{2005}
\pubyear{2005}

\usepackage{grffile}
\usepackage{epstopdf}
\usepackage{graphicx}

\begin{document}
\firstpage{1}

\title[short Title]{This is a title}
\author[Sample \textit{et~al}]{Corresponding Author\,$^{1,*}$, Co-Author\,$^{2}$ and Co-Author\,$^2$\footnote{to whom correspondence should be addressed}}
\address{$^{1}$Department of XXXXXXX, Address XXXX etc.\\
    $^{2}$Department of XXXXXXXX, Address XXXX etc.}

\history{Received on XXXXX; revised on XXXXX; accepted on XXXXX}

\editor{Associate Editor: XXXXXXX}

\maketitle

\begin{abstract}

    \section{Motivation:}
    Text Text Text  Text Text Text Text Text Text Text Text
    Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text.

    \section{Results:}
    Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text

    \section{Availability:}
    Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text

    \section{Contact:} \href{[email protected]}{[email protected]}
\end{abstract}

\section{Introduction}

Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure~\ref{fig:01} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citep{Bag01} wants to know about  text follows.

\begin{equation}
\sum x+ y =Z\label{eq:01}
\end{equation}


\section{Approach}

Equation~(\ref{eq:01}) Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text 


\begin{methods}
    \section{Methods}

    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text

    \begin{itemize}
        \item for bulleted list, use itemize
        \item for bulleted list, use itemize
        \item for bulleted list, use itemize
    \end{itemize}


    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text.


    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text



    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text


    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text



    \begin{table}[!t]
        \processtable{This is table caption\label{Tab:01}}
        {\begin{tabular}{llll}\toprule
                head1 & head2 & head3 & head4\\\midrule
                row1 & row1 & row1 & row1\\
                row2 & row2 & row2 & row2\\
                row3 & row3 & row3 & row3\\
                row4 & row4 & row4 & row4\\\botrule
            \end{tabular}}{This is a footnote}
        \end{table}

    \end{methods}

    \begin{figure}[!tpb]%figure1
        %\centerline{\includegraphics{fig01.eps}}
        \caption{Caption, caption.}\label{fig:01}
    \end{figure}

    \begin{figure}[!tpb]%figure2
        %\centerline{\includegraphics{fig02.eps}}
        \caption{Caption, caption.}\label{fig:02}
    \end{figure}

    \section{Discussion}

    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text.


    Table~\ref{Tab:01} shows that Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that
    the above method Text Text. Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that
    the above method Text Text. Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that
    the above method Text Text.


    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    %
    %     please remove the " % " symbol from \centerline{\includegraphics{fig01.eps}}
    %     as it may ignore the figures.
    %
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    \section{Conclusion}

    (Table~\ref{Tab:01}) Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.



    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text


    \begin{enumerate}
        \item this is item, use enumerate
        \item this is item, use enumerate
        \item this is item, use enumerate
    \end{enumerate}

    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text  Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text
    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text.


    Text Text Text Text Text Text  Text Text Text Text Text Text Text Text Text  Text Text Text Text Text Text. Figure \ref{fig:02} shows that the above method  Text Text Text Text


    \section*{Acknowledgement}
    Text Text Text Text Text Text  Text Text.  \citealp{Boffelli03} might want to know about  text text text text

    \paragraph{Funding\textcolon} Text Text Text Text Text Text  Text Text.

    %\bibliographystyle{natbib}
    %\bibliographystyle{achemnat}
    %\bibliographystyle{plainnat}
    %\bibliographystyle{abbrv}
    %\bibliographystyle{bioinformatics}
    %
    %\bibliographystyle{plain}
    %
    %\bibliography{Document}


    \begin{thebibliography}{}
        \bibitem[Bofelli {\it et~al}., 2000]{Boffelli03} Bofelli,F., Name2, Name3 (2003) Article title, {\it Journal Name}, {\bf 199}, 133-154.

        \bibitem[Bag {\it et~al}., 2001]{Bag01} Bag,M., Name2, Name3 (2001) Article title, {\it Journal Name}, {\bf 99}, 33-54.

        \bibitem[Yoo \textit{et~al}., 2003]{Yoo03}
        Yoo,M.S. \textit{et~al}. (2003) Oxidative stress regulated genes
        in nigral dopaminergic neurnol cell: correlation with the known
        pathology in Parkinson's disease. \textit{Brain Res. Mol. Brain
            Res.}, \textbf{110}(Suppl. 1), 76--84.

        \bibitem[Lehmann, 1986]{Leh86}
        Lehmann,E.L. (1986) Chapter title. \textit{Book Title}. Vol.~1, 2nd edn. Springer-Verlag, New York.

        \bibitem[Crenshaw and Jones, 2003]{Cre03}
        Crenshaw, B.,III, and Jones, W.B.,Jr (2003) The future of clinical
        cancer management: one tumor, one chip. \textit{Bioinformatics},
        doi:10.1093/bioinformatics/btn000.

        \bibitem[Auhtor \textit{et~al}. (2000)]{Aut00}
        Auhtor,A.B. \textit{et~al}. (2000) Chapter title. In Smith, A.C.
        (ed.), \textit{Book Title}, 2nd edn. Publisher, Location, Vol. 1, pp.
        ???--???.

        \bibitem[Bardet, 1920]{Bar20}
        Bardet, G. (1920) Sur un syndrome d'obesite infantile avec
        polydactylie et retinite pigmentaire (contribution a l'etude des
        formes cliniques de l'obesite hypophysaire). PhD Thesis, name of
        institution, Paris, France.

    \end{thebibliography}
\end{document

Here's a link to the bioinfo.cls file. https://www.dropbox.com/s/a65ubzzauuquxvf/bioinfo.cls?dl=0

6
  • 3
    Where can we find this bioinfo.cls?
    – user31729
    Feb 20, 2016 at 12:57
  • 1
    You cannot have an empty line in the abstract and you shoul not have a section in the abstract.
    – Johannes_B
    Feb 20, 2016 at 13:45
  • You might want to take a look at package blindtext or lipsum. All this text text text text is boring and bloating the quite extensive example even more.
    – Johannes_B
    Feb 20, 2016 at 13:47
  • That got resolved. But still getting the "Undefined control sequence. \maketitle" error.
    – Alchemist
    Feb 22, 2016 at 6:29
  • @ChristianHupfer I added the link to the bioinfo.cls in the question.
    – Alchemist
    Feb 22, 2016 at 6:33

1 Answer 1

1

In the bioinfo.cls there is a commented environment also named abstract.

%\newenvironment{abstract}{%
%  \begingroup
%  \let\section\absection
%  \fontfamily{\sfdefault}\fontsize{10}{12}\sffamily\selectfont
%  {\fontseries{b}\selectfont Abstract}\par}
%{\endgroup\bigskip\@afterheading\@afterindentfalse\vskip 12pt plus 3pt minus 1pt}

This can be an old version of the class and the template provided has not been updated. That is the reason why you have to define \abstract{my abstract here} and \corresp{corresponding author} before the beginning of the document (as mentioned by @Johannes_B)

Thus you have to have this structure:

\history{Received on XXXXX; revised on XXXXX; accepted on XXXXX}    
\editor{Associate Editor: XXXXXXX
\corresp{TEST}
\abstract{Short version of your abstract.}

\begin{document}
\firstpage{1}
\begin{abstract}
    The long version of your abstract.
\end{abstract}

\maketitle

\section{Introduction}
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