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I am using both TeXworks and Texmaker to write my thesis and have to somehow do my references. Moreover everything is supposed to be written using a 'book' environment.

I have found that JabRef is used for the IEEE referencing style that I want to use but I cannot use it in a book. It is obvious that I am doing something silly because I can use it in articles.

Is there any template that could be provided?

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Here is an example using IEEE bibliography style. Note that JabRef is just a GUI to maintain/add/remove adjust your bibliography entries. It doesn't have an effect on the document creation mechanism.

\documentclass{book}
% === Remove this up to the marked position to use your own bib file
\usepackage{filecontents} % For a dummy bibfile creation
\begin{filecontents*}{mybibfile.bib}
@ARTICLE{authora,
  author = {A. Aaaaa},
  title = {Some article},
  journal = {Journal of Dummy Article Names},
  year = {2012},
  volume = {99},
  pages = {1-5}
}

@ARTICLE{authorb,
  author = {B. Baaaa},
  title = {Another article},
  journal = {Journal of Dummy Article Names},
  year = {2012},
  volume = {99},
  pages = {6-10}
}

\end{filecontents*}
% =========== Up to here
\begin{document}
We cite papers \cite{authora,authorb}.
\bibliographystyle{ieeetran}
\bibliography{mybibfile} % Replace this with your original bib file
\end{document} 
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