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diff --git a/content/appendix.tex b/content/appendix.tex
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+% this file is called up by thesis.tex
+% content in this file will be fed into the main document
+
+%: ----------------------- name of chapter  -------------------------
+\chapter*{Appendix} % top level followed by section, subsection
+
+
+
+
+
+
+
+% ---------------------------------------------------------------------------
+%: ----------------------- end of thesis sub-document ------------------------
+% ---------------------------------------------------------------------------
+
diff --git a/content/background.tex b/content/background.tex
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+\chapter{Background}\label{s:background}
+
+
+\todo{
+This section provides the necessary context to help the reader understand the
+remainder of the thesis.
+}
+
+\lipsum[1-8]
+
diff --git a/content/conclusion.tex b/content/conclusion.tex
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+\chapter{Conclusion}\label{s:conclusion}
+
+
+\todo{
+Briefly summarize your contributions, and share a glimpse of the implications of
+this work for future research.
+}
+
+
+\lipsum[1-2]
+
diff --git a/content/design.tex b/content/design.tex
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+\chapter{Design}\label{s:design}
+
+
+\todo{
+In this section, you would provide a high-level description of the system or
+solution and explain your design choices.
+}
+
+
+\lipsum[1-10]
+
diff --git a/content/discussion.tex b/content/discussion.tex
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+\chapter{Discussion}\label{s:discussion}
+
+
+\todo{
+Here you put your results in context (possibly grouped by research question). Usually, this section focuses on analyzing the
+implications of the proposed work for current and future research and for practitioners.
+}
+
+
+\lipsum[1-8]
diff --git a/content/evaluation.tex b/content/evaluation.tex
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+\chapter{Evaluation}\label{s:evaluation}
+
+
+\todo{
+Discuss the design of your experiments, the results you obtained, and how they
+help in evaluating the claims you made in the introduction. You may also use the
+evaluation results in this section to justify your design choices or assess the
+contributions of different aspects  of your design towards the overall goals.
+}
+
+
+\lipsum[1-16]
+
diff --git a/content/implementation.tex b/content/implementation.tex
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+\chapter{Implementation}\label{s:implementation}
+
+
+This section presents important implementation details.
+
+
+\lipsum[1-6]
+
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: "../thesis"
+%%% End:
diff --git a/content/intro.tex b/content/intro.tex
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+++ b/content/intro.tex
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+\chapter{Introduction}\label{s:intro}
+
+\todo{
+This section includes some motivations behind the work, explicitly or implicitly
+highlights the research question, provides a high-level explanation of the
+solution, and describes the contributions.
+}
+
+
+\lipsum[1-2]
+
+
diff --git a/content/overview.tex b/content/overview.tex
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+\chapter{Overview}\label{s:overview}
+
+
+\todo{
+This section provides a high-level outline of the proposed system or solution.
+It typically illustrates the system architecture or the interactions between the
+different solution components (via a “boxes-and-arrows” diagram) from a user’s
+perspective.
+}
+
+
+\lipsum[1-6]
+
diff --git a/content/preamble/abstract.tex b/content/preamble/abstract.tex
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+
+% Thesis Abstract -----------------------------------------------------
+
+
+%\begin{abstractslong}    %uncommenting this line, gives a different abstract heading
+\begin{abstracts}        %this creates the heading for the abstract page
+
+\noindent \textit{Context}. 
+\todo{at the end}
+
+\noindent \textit{Goal}. 
+\todo{at the end}
+
+\noindent \textit{Method}. 
+\todo{at the end}
+
+\noindent \textit{Results}. 
+\todo{at the end}
+
+\noindent \textit{Conclusions}. 
+\todo{at the end}
+
+\end{abstracts}
+%\end{abstractlongs}
+
+
+% ---------------------------------------------------------------------- 
diff --git a/content/preamble/acknowledgement.tex b/content/preamble/acknowledgement.tex
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+% Thesis Acknowledgements ------------------------------------------------
+
+
+%\begin{acknowledgementslong} %uncommenting this line, gives a different acknowledgements heading
+%\begin{acknowledgements}      %this creates the heading for the acknowlegments
+
+
+%\end{acknowledgements}
+%\end{acknowledgmentslong}
+
+% ------------------------------------------------------------------------
+
+
diff --git a/content/preamble/dedication.tex b/content/preamble/dedication.tex
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+% Thesis Dedication ---------------------------------------------------
+
+%\begin{dedication} %this creates the heading for the dedication page
+
+%To ...
+
+%\end{dedication}
+
+% ----------------------------------------------------------------------
\ No newline at end of file
diff --git a/content/preamble/glossary.tex b/content/preamble/glossary.tex
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+% this file is called up by thesis.tex
+% content in this file will be fed into the main document
+
+% Glossary entries are defined with the command \nomenclature{1}{2}
+% 1 = Entry name, e.g. abbreviation; 2 = Explanation
+% You can place all explanations in this separate file or declare them in the middle of the text. Either way they will be collected in the glossary.
+
+% required to print nomenclature name to page header
+%\markboth{\MakeUppercase{\nomname}}{\MakeUppercase{\nomname}}
+
+
+% ----------------------- contents from here ------------------------
+
+
+%\nomenclature{LSY}{ehbfuefebbfbjkjkebfjbfbfw} 
+%\nomenclature{DEPC}{diethyl-pyro-carbonate; used to remove RNA-degrading enzymes (RNAases) from water and laboratory utensils}
+%\nomenclature{DMSO}{dimethyl sulfoxide; organic solvent, readily passes through skin, cryoprotectant in cell culture}
+%\nomenclature{EDTA}{Ethylene-diamine-tetraacetic acid; a chelating (two-pronged) molecule used to sequester most divalent (or trivalent) metal ions, such as calcium (Ca$^{2+}$) and magnesium (Mg$^{2+}$), copper (Cu$^{2+}$), or iron (Fe$^{2+}$ / Fe$^{3+}$)}
+
+
+
diff --git a/content/related.tex b/content/related.tex
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+\chapter{Related Work}\label{s:related}
+
+
+\todo{
+Describe here scientific papers similar to your experiment, both in terms of goal and methodology.  One paragraph for each paper (we expect about 5-8 papers to be discussed). Each paragraph contains: (i) a brief description of the related paper and (ii) a black-on-white description about how your work differs from the related paper. You may place this section immediately after the Background section, if necessary.
+}
+
+
+\lipsum[14-17][4-8]
+
diff --git a/content/threats.tex b/content/threats.tex
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+\chapter{Threats To Validity}\label{sec:threats}
+
+\todo{Report about each type of threat to the validity of the experiment, according to the classification framework proposed by Wohlin \etal \cite{wohlin12}.
+}
+
+\section{Internal Validity}
+\section{External Validity}
+\section{Construct Validity}
+\section{Conclusion Validity}
\ No newline at end of file