deletions | additions       diff --git a/Introduction.tex b/Introduction.tex  index 692e45d..5b78d69 100644  --- a/Introduction.tex  +++ b/Introduction.tex 
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%(\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}).  Recently, Other disciplines have started tackling this issue   (cite http://biorxiv.org/content/early/2016/03/24/045104 once doi activated),  and even in the single-molecule field  a few recent  publications have included or presented   open source  software implementation for analysis  ofmethods used to analyze  surface immobilizedsingle-molecule  experiments~\cite{Bronson_2009,Greenfeld_2012, K_nig_2013}. In the field of For  freely-diffusing smFRET, 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 forthe  analysis of freely diffusing single-molecule FRET bursts. measurement.  FRETBursts can be used, inspected and modified by anyone interested in using state-of-the art smFRET analysis method methods  or implementing modifications or completely new techniques. FRETBursts therefore represents an ideal platform for quantitative comparison of different methods for smFRET burst analysis.  Technically, a strong emphasis has been given to the reproducibility of complete analysis  workflows. FRETBursts uses Jupyter Notebooks~\cite{Shen_2014}, 
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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}. integration~\cite{Wilson_2014}  (cite http://biorxiv.org/content/early/2016/03/24/045104 once doi activated).  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},