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Antonino Ingargiola edited Introduction.tex
over 9 years ago
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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 are
web 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.