deletions | additions       diff --git a/Introduction.tex b/Introduction.tex  index af8b71e..c551bb8 100644  --- a/Introduction.tex  +++ b/Introduction.tex 
...
%(\href{https://www.mozillascience.org/effective-code-review-for-journals}{Mills 2015})  %(\href{http://ivory.idyll.org/blog/2015-we-live-in-a-bubble.html}{Brown 2015} and \href{http://ivory.idyll.org/blog/on-code-review-of-scientific-code.html}{2013}).  Other disciplines have started tackling this issue   (cite http://biorxiv.org/content/early/2016/03/24/045104 once doi activated), issue~\cite{Eglen_2016},  and even in the single-molecule field a few recent publications have included or presented provided  software for analysis of surface-immobilized experiments~\cite{McKinney_2006,Bronson_2009,Greenfeld_2012,van_de_Meent_2014}.  For freely-diffusing smFRET experiments, although it is common to find mention of   "code available from the authors upon request" in publications, there is a dearth   of such open source code, with, to our knowledge, the notable exception of a single   example~\cite{Murphy2014}.  To address this issue, we have developed FRETBursts,  an open source Python software for analysis of freely diffusing freely-diffusing  single-molecule FRET measurement. measurements.  FRETBursts can be used, inspected and modified by anyone interested in using   state-of-the art smFRET analysis methods or implementing modifications or completely new techniques.   FRETBursts therefore represents an ideal platform 
...
in a document which is easy to share and execute.  To minimize the possibility of bugs being introduced inadvertently~\cite{Soergel_2015}   we employ modern software engineering techniques  such as unit testing and continuous integration~\cite{Wilson_2014}  (cite http://biorxiv.org/content/early/2016/03/24/045104 once doi activated). integration~\cite{Wilson_2014,Eglen_2016}.  FRETBursts is hosted on GitHub~\cite{Blischak_2016,Prli__2012},  where users can write comments, report issues or contribute code.  In a related effort, we recently introduced Photon-HDF5~\cite{Ingargiola2016},  a an  open file format for timestamp-based single-molecule fluorescence experiments. An other related open source tool is PyBroMo~\cite{Ingargiola_2016},  a freely-diffusing smFRET simulator which produces Photon-HDF5 files that are  directly analyzable with FRETBursts. 
...
correction (section~\ref{sec:bg_calc}), (iv) burst search (section~\ref{sec:burstsearch}),  (v) burst selection (section~\ref{sec:burstsel}) and (vi) FRET histogram fitting (section~\ref{sec:fretfit}).  The aim of this section is to illustrate the specificities and trade-off involved in various approaches  with sufficient details to enable readersnew to the field (or Jupyter Notebooks)  to customize the analysis for their own needs.  Section~\ref{sec:bva} walks the reader thorough implementing  Burst Variance Analysis (BVA)~\cite{Torella_2011}, as an example of implementation  
...
we have concentrated Python-specific details in subsections entitled  \textit{Python details}. These subsections provide deeper insights for readers  already familiar with Python and can be initially skipped by readers who are not.  Finally, note that all commands here reported and figures in this paper  can be found in regenerated   using  the accompanying notebooks (\href{https://github.com/tritemio/fretbursts_paper}{link}).