Antonino Ingargiola edited Introduction.tex  almost 9 years ago

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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 noclear consensus on a  singleuniversal  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  isthat  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  Currently, in fact,  each research group have reimplemented its own unpublished or closed-source versions  of the analysis software, with very little collaboration or code sharing.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 smFRETsetup  can significantly vary (in number of polarization or spectral channels for example),   makes the problem only worst.  This situation, represents ahuge 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