deletions | additions       diff --git a/Introduction.tex b/Introduction.tex  index 3dc6260..6976c49 100644  --- a/Introduction.tex  +++ b/Introduction.tex 
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To assure the correctness of the results, FRETBursts is developed using modern   software engineering techniques such as unit and regression tests.   The preferential way to execute FRETBursts is by running one of theFRETBursts  tutorials which are in the form of Jypyter notebooks. \href{http://ipython.org/notebook.html}{Jypyter notebooks}.  Jupyter (formerly IPython) notebooks are documents,   accessed through a web browser, that contain both code and   rich text (including formulas, hyperlinks, figures, etc...). 
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The list of FRETBursts notebooks can be found in the   \verb|FRETBurts_notebooks| repository on GitHub.  Although running the software is technically  simple, understanding the smFRET burst analysis requires several concepts and definitions.  This paper provides a broad overview of FRETBursts, introducing all the  the fundamental concepts and definitions needed to fully understand the  
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\subsection{Installing FRETBursts}  \label{sec:install}  Installing FRETBursts is analogous to installing any standard python  package. A The  python environment interpreter  needs to be installed, preferentially through a scientific python distribution which conveniently include   all the major scientific libraries. 
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section in the FRETBursts documentation.  FRETBursts depends on a standard set of scientific   python libraries, namely, numpy/scipy \href{http://www.numpy.org/}{numpy}/\href{http://www.scipy.org/}{scipy}  for numerical computations, matplotlib \href{http://matplotlib.org/}{matplotlib}  and seaborn \href{http://stanford.edu/~mwaskom/software/seaborn/}{seaborn}  for plotting. Optionally, a few core functions are optimized with cython \href{http://cython.org/}{cython}  and the software is preferentially run through a Jupyter \href{http://ipython.org/}{Jupyter  (IPython) Notebook Notebook}  (optional). For a A  complete list of dependencies can be found in the \href{http://fretbursts.readthedocs.org/en/latest/getting_started.html}{Getting Started}  section in the FRETBursts documentation.  \subsection{Running FRETBursts}  The preferential way to execute FRETBurts is by running one of the  FRETBursts tutorials which are in the form of Jypyther notebooks.  Jupyter (formerly IPython) notebooks are documents,   accessed through a web browser, that contain both code and   rich text (including formulas, hyperlinks, figures, etc...).  FRETBursts tutorials are notebook that can be re-executed,  modified or used to process new data files with minimal modifications.  The "notebook workflow"\cite{Shen_2014} not only eases   the analysis comprehension (by integrating the code in a rich document)  but also greatly enhance its reproducibility by storing an execution trail  that includes software versions, input files, parameters, commands and all  the analysis results (text, figures, tables, etc...).  Given the modality of execution, running FRETBurst does not require  any prior python knowledge. The user only needs familiarize with the  notebook graphical environment to be able to navigate and run the notebooks.  The list of FRETBursts notebooks can be found in the   \verb|FRETBurts_notebooks| repository on GitHub.