Antonino Ingargiola edited Introduction.tex  over 9 years ago

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\subsection{Installing FRETBursts}  FRETBursts is a standard python package that requires the "scipy stack", a set  of core scientific python packages. libraries.  The "scipy stack" is easily installed through by installing  a free scientific python distribution such as Continuum Anaconda, although some users may prefer another  distribution or a manual installation.  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 downloaded directly  from GitHub. For more information on different installation methods see the \href{http://fretbursts.readthedocs.org/en/latest/installation.html}{FRETBursts  documentation}. 

>>> from fretbursts import *  \end{verbatim}  that allows to skip the \verb|fb.| prefix and it  also imports some common numeric libraries (numpy (\textit{numpy}  and matplotlib.pyplot \textit{matplotlib.pyplot}  imported as \verb|np| and \verb|plt| respectively). Furthermore we We  encourage using FRETBursts through the IPython Notebook environment. IPython notebooks are web browser  documents that contains contain  both code and cells,  rich text and multimedia content. The In a notebook the code is   interspersed with prose in a structured document that can contain math   formulas, hyperlinks and figures (or anything else a web browser can display).  Furthermore, the  "notebook workflow"\cite{Shen_2014} has the advantage of automatically recording not only the all analysis commands and parameters but also the data file names, software versions and the full output (figures, tables, etc...) in a single document that can be interactively   modified and re-executed.  All the FRETBursts tutorials are   ipython notebooks and, in fact, the suggested way to start a new analysis is   by copying and modifying  a pre-existing FRETBursts notebook and modifying it. notebook.