Antonino Ingargiola edited Introduction.tex  over 9 years ago

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FRETBursts is a python package for burst analysis of confocal single-molecule FRET   (smFRET) data.  \subsection{Installation}  FRETBursts \textit{Expand abstract to introduce smFRET and what  is a standard python package that requires the "scipy stack", a set of core   scientific python packages.  The "scipy stack" is easily installed through a free scientific python distribution such as Continuum Anaconda, although some users may prefer another distribution or a manual installation. burst analisys}.  FRETBursts can be installed through the standard python package manager (PIP) with   the command \texttt{pip install fretbursts}. Alternatively the latest development version can be installed from GitHub.  For more information on different installation methods see the \href{http://fretbursts.readthedocs.org/en/latest/installation.html}{FRETBursts documentation}.  \subsection{Executing FRETBursts}  For interactive work, we strongly encourage to use FRETBursts through the IPython Notebook environment. All the FRETBursts tutorials are ipython notebook documents and, indeed, a quick way to start a new analysis is copying a pre-existing FRETBursts notebook and modifying it.  The "notebook workflow"\cite{Shen_2014} has the advantage of automatically recording all the analysis steps including  data file names, software versions, analysis details and the full output (figures, tables, etc...).