this is for holding javascript data
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.