Antonino Ingargiola edited Introduction.tex  over 9 years ago

Commit id: 99d0efbed34ea09cf4ff88241590270ac5b2200e

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after which all the FRETBursts functions will be availabe under the \verb|fb.|  prefix. In this article, for brevity, we assume that FRETBursts is imported   with the shortcut form: form instead:  \begin{verbatim}  >>> from fretbursts import *  \end{verbatim}  that allows to skip skiping  the \verb|fb.| prefix and it will  also imports import  some common numeric libraries (\textit{numpy} (i.e. \textit{numpy}  and \textit{matplotlib.pyplot} imported as \verb|np| and \verb|plt| respectively). We In order to enable the reproducibility of the analysis and to ease  the sharing of the complete workflow we  encourage using FRETBursts through the IPython Notebook environment. IPython notebooks areweb browser  documents that contain  both code cells, rich text and multimedia content. In a notebook, in which  the code is interspersed with prose in a structured document web-based format  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  

modified and re-executed.  All the FRETBursts tutorials are   ipython notebooks and, in fact, the suggested preferred  way to start a new analysis is copying and modifying a pre-existing FRETBursts notebook.