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\subsection{What is FRETBursts}
In the last 20
years years, the field of single molecule spectroscopy has seen a remarkable
growth from a pioneristic technology to a widespread analysis performed by many labs
across the world. Among the techniques that probe freely-diffusing molecules,
single-molecule FRET (smFRET) is one of the most successful, able to provide
information on conformational changes or monitor binding-unbinding kinetics on
a single-molecule level.
The field of freely-diffusing smFRET data
analysis analysis, has seen a number of significant
contributions over the
years but still years. However, so far, beyond some fundamental steps such as the burst search,
there is no
clear consensus on a single
universal approach
for data analysis.
Even though a wide variety of algorithms have been proposed over the years, very few
of them have been widely embraced by that is universally accepted and broadly applied.
On one hand this situation stems from the
community at large. One of fact that
different approaches tend to answer different questions, even if there are overlaps.
On the
main issues other hand, this is
that the
analysis result of
smFRET data is complex the trade off in each research lab
between accuracy and
requires a significant
development effort. software complexity, in particular on the amount of effort
each group wants to invest in implementing new non-trivial methods reported in literature.
Currently,
in fact,
each research group have reimplemented its own unpublished or closed-source versions
of the analysis software, with very little collaboration or code sharing.
The fact that the
implementation of a setups for freely-diffusing smFRET
setup can significantly
vary (in number of polarization or spectral channels for example),
makes the problem only worst.
This situation, represents a
huge duplication of efforts and a real impediment to the scientific
progress. progress because:
(a) as new methods are proposed in literature, understandably, only few
groups are willing to invest the time necessary to reimplement it within
the internally used software. In
fact, the rare occasions when the new methods
is really groundbreaking (most of the science is incremental), the reimplementation requires
a huge duplication of efforts, and the correctness of the implementation
is difficult to validate.
(b) the differences in implementation details among the various software
are enough that a direct comparison of their results is very difficult.
This limits the ability to
validate cross-validate the correctness of
one software but also different
implementations of the same method or to compare the
performance accuracy
of different
algorithms
in estimating physical quantities. methods.
In order
to start addressing contrast these issues we developed FRETBursts,
an open source python software for burst analysis of freely-diffusing
single-molecule smFRET experiments.
With FRETRBursts we aim to provide a tool that is available to any scientist
to use, study and modify.
FRETBursts is hosted and openly developed~\cite{Prli__2012} on GitHub,
and we encourage users to send comments,
issues, contributions report issues or contribute code
through the GitHub website.
Understanding the smFRET burst analysis requires several concepts and definitions.
In this paper we aim to provide a brief introduction to smFRET analysis concepts