deletions | additions       diff --git a/Introduction.tex b/Introduction.tex  index 7642701..eecae84 100644  --- a/Introduction.tex  +++ b/Introduction.tex 
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FRETBursts contributes to the ecosystem  of open tools for reproducible science in the single-molecule field.  \subsection{Paper Overview}  Since understanding smFRET burst analysis requires several concepts and definitions,  in this paper, we provide This paper is  an introduction to smFRET bursts burst  analysis andhow different steps are executed in FRETBursts.   We will no cover all  FRETBursts features and options but provide an usage.  Therefore, after a brief  overview detailed enough for starting  using of  FRETBursts and customizing the analysis. For additional information, features (section~\ref{sec:overview}),  we refer the reader to the FRETBursts Reference Documentation  (\href{http://fretbursts.readthedocs.org/}{link}) introduce core smFRET burst analysis concepts  and to terminology   (section~\ref{sec:concepts}). These concepts are used throughout  the FRETBursts µs-ALEX notebook  (\href{http://nbviewer.jupyter.org/github/tritemio/FRETBursts_notebooks/blob/master/notebooks/FRETBursts%20-%20us-ALEX%20smFRET%20burst%20analysis.ipynb}{link})  Finally, usage questions can be posted by opening an Issue  on GitHub (\href{https://github.com/tritemio/FRETBursts}{link}). paper  so reading section~\ref{sec:concepts} is highly recommended.  The paper is structured as follows.  In section~\ref{sec:overview} we give an overview of the software features,  the modality of execution and the development style.  In section~\ref{sec:concepts}, we  review basic concepts and terminology needed  to understand the smFRET burst analysis. In section~\ref{sec:analysis}, we detail the execution illustrate  the main practical  steps involved in smFRET burst analysis: data loading (section~\ref{sec:dataload}), defining  excitation alternation periods (section~\ref{sec:alternation}), background  correction (section~\ref{sec:bg_calc}), burst search (section~\ref{sec:burstsearch}),  burst selection (section~\ref{sec:burstsel}) and FRET fitting (section~\ref{sec:fretfit}).  The aim is to provide elucidating  the reader specificities and trade-off of various approaches  with enough information details  to understand the specificities of  the different algorithms and empowers reader new  to be able the field  to adapt customize  the analysis to new situations.  In section~\ref{sec:bva}, we show how to implement a new burst analysis in FRETBursts,  taking as an example their own needs.  For  the most advanced use-case, section~\ref{sec:bva} walks the reader thorough implementing  Burst Variance Analysis (BVA)~\cite{Torella_2011}.  In section~\ref{sec:dev} we describe the development process, the testing infrastructure (BVA)~\cite{Torella_2011} as an example of manipulating timestamps  and contributors guidelines. burst data.  Finally, in section~\ref{sec:conclusions}, we summarize what we believe to be  the strengths of FRETBursts software. 
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Finally, note that all commands here reported can be found in the   accompanying notebooks   (\href{https://github.com/tritemio/fretbursts_paper}{link}).  diff --git a/Overview.tex b/Overview.tex  index af2c987..2eddd7e 100644  --- a/Overview.tex  +++ b/Overview.tex 
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predefined and customizable plot functions which (thanks to the \textit{matplotlib}  graphic library) produce publication quality plots in a wide range of formats.  Information regarding \subsection{Software Availability}  FRETBursts is hosted and openly developed on GitHub. FRETBursts homepage   (\href{http://tritemio.github.io/FRETBursts}{link})  contains links the various resources. Installation instructions can be found in the  Reference Documentation (\href{http://fretbursts.readthedocs.org/en/latest/getting_started.html}{link}).   A description of  FRETBursts execution using Jupyter notebooks can be found is reported  in SI~\ref{sec:notebook}. Detailed information on developemnt style, tesing testing  strategies and contributions are reported in SI~\ref{sec:dev}. diff --git a/main.tex b/main.tex  index 67f1836..72c511c 100644  --- a/main.tex  +++ b/main.tex 
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\end{center}  \end{figure*}  \input{Coding-style}  \input{Conclusions}  \bibliography{bibliography/biblio}  \input{Supporting_Information}  \end{document}