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Antonino Ingargiola Shorten abstract
about 8 years ago
Commit id: 478ad690f7b0269db2f0deac9befc2cba2e4d331
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In this paper, we introduce FRETBursts, an open source software
for analysis of freely-diffusing smFRET data.
Fundamental steps in the analysis involve identifying photon bursts
from single molecules in a continuous stream of photons, estimating
background and other correction factors, filtering bursts and extracting
the corrected FRET efficiencies for each sub-population. FRETBursts allows executing all
these the fundamental steps
of smFRET bursts
analysis using
both state-of-the-art
algorithms and improved techniques.
FRETBursts provides as well as novel techniques,
while providing an open, robust and well-documented
implementation for commonly employed algorithms and implementation.
Therefore FRETBursts represents an ideal platform for comparison
and development of new methods in burst analysis.
We employ modern software engineering principles in order to
minimize
the chance of bugs and facilitate long-term maintainability.
Furthermore, we place a strong focus on reproducibility by relying on
Jupyter notebooks for
the execution of FRETBursts
workflows. execution.
Notebooks are executable documents capturing all the steps of the
analysis (including data files, input parameters, and results) and can
be easily shared to replicate complete smFRET analyses.
This execution model allows Notebooks allow beginners to execute complex workflows
and advanced users to customize the analysis for their own needs.
By
unifying bundling in a single document analysis description, code
and
results in a single document, results, FRETBursts allows
to seamless
sharing of workflows, share analysis workflows
and results, encourages reproducibility and facilitates collaboration
among researchers in the single-molecule
community and beyond. community.