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...
@inproceedings{Ingargiola_2013,
doi = {10.1117/12.2003704},
url = {http://dx.doi.org/10.1117/12.2003704},
year = {2013},
month = {feb},
publisher = {{SPIE}}, author =
{Antonino Ingargiola {Ingargiola, Antonino and
Panzeri, Francesco
Panzeri and
Sarkhosh, Niusha
Sarkhosh and
Gulinatti, Angelo
Gulinatti and
Rech, Ivan
Rech and
Ghioni, Massimo
Ghioni and
Weiss, Shimon
Weiss and Xavier Michalet},
editor = {Jörg Enderlein and Ingo Gregor and Zygmunt K. Gryczynski and
Rainer Erdmann and Felix Koberling}, Michalet, Xavier},
title =
{{8-spot {smFRET} {
8-spot smFRET analysis using two 8-pixel
{SPAD} arrays}}, SPAD arrays
},
publisher = {{SPIE}},
volume = {8590},
pages = {85900E-85900E-11},
year = {2013},
doi = {10.1117/12.2003704},
URL = { http://dx.doi.org/10.1117/12.2003704},
booktitle =
{Single {{Single Molecule Spectroscopy and Superresolution Imaging
{VI}}, VI}},
note = {doi:\href{http://dx.doi.org/10.1117/12.2003704}{10.1117/12.2003704}}
}
@article{M_ller_2005,
doi = {10.1529/biophysj.105.064766},
url = {http://dx.doi.org/10.1529/biophysj.105.064766},
...
url = {http://dx.doi.org/10.1007/978-1-4612-2544-7_5},
year = {1995},
publisher = {Springer Science $+$ Business Media},
volume = {103},
pages = {55--81},
author = {Jonathan B. Buckheit and David L. Donoho},
title = {{{WaveLab} and Reproducible Research}},
booktitle = {Wavelets and Statistics},
note = {\href{http://dx.doi.org/10.1007/978-1-4612-2544-7_5}{doi:10.1007/978-1-4612-2544-7\_5}},
}
...
@article{Murphy2014,
abstract = {Single molecule F\"{o}rster resonance energy transfer (smFRET) is a powerful experimental technique for studying the properties of individual biological molecules in solution. However, as adoption of smFRET techniques becomes more widespread, the lack of available software, whether open source or commercial, for data analysis, is becoming a significant issue. Here, we present pyFRET, an open source Python package for the analysis of data from single-molecule fluorescence experiments from freely diffusing biomolecules. The package provides methods for the complete analysis of a smFRET dataset, from burst selection and denoising, through data visualisation and model fitting. We provide support for both continuous excitation and alternating laser excitation (ALEX) data analysis. pyFRET is available as a package downloadable from the Python Package Index (PyPI) under the open source three-clause BSD licence, together with links to extensive documentation and tutorials, including example usage and test data. Additional documentation including tutorials is hosted independently on ReadTheDocs. The code is available from the free hosting site Bitbucket. Through distribution of this software, we hope to lower the barrier for the adoption of smFRET experiments by other research groups and we encourage others to contribute modules for specific analysis needs.},
archiveprefix = {arXiv},
arxivid = {1412.6402},
journal = {ArXiv},
...
title = {{pyFRET: A Python Library for Single Molecule Fluorescence Data Analysis}},
url = {http://arxiv.org/abs/1412.6402},
year = {2014},
note = {\href{http://arxiv.org/abs/1412.6402}{arXiv:1412.6402}},
}
...
journal = {Journal of Molecular Biology},
}
@misc{lmfit,
author =
{Newville, Matthew {Matt Newville and
Andrew Nelson and
Stensitzki,
Till
Stensitzki and
Antonino Ingargiola and
Dan Allan and
Michał and
Yoav Ram and
MerlinSmiles and
Li Li and
Glenn and
Christoph Deil and
Allen, Daniel B. Gustavo Pasquevich and
Ingargiola, Antonino}, Stuermer and
Tim Spillane and
stonebig and
Per A. Brodtkorb and
Nicholas Earl and
Anthony Almarza and
Ben Gamari and
Kostis Anagnostopoulos},
title =
{{LMFIT: Non-Linear Least-Square Minimization and Curve-Fitting for Python¶}}, {lmfit-py: release 0.9.3},
month =
{sep}, apr,
year =
{2014}, 2016,
doi =
{10.5281/zenodo.11813}, {10.5281/zenodo.49428},
url =
{http://dx.doi.org/10.5281/zenodo.11813}, {http://dx.doi.org/10.5281/zenodo.49428},
note = {\href{http://dx.doi.org/10.5281/zenodo.49428}{doi:10.5281/zenodo.49428}},
}
@misc{seaborn,
author = {Michael Waskom and
Olga Botvinnik and
drewokane and
Paul Hobson and
Yaroslav Halchenko and
Saulius Lukauskas and
Jordi Warmenhoven and
John B. Cole and
Yaroslav Halchenko Stephan Hoyer and
Jake Vanderplas and
Stephan Hoyer gkunter and
Santi Villalba and
Eric Quintero and
Marcel Martin and
Alistair Miles and
Kyle Meyer and
Tom Augspurger and
Tal Yarkoni and
Pete Bachant and
Constantine Evans and
Daniel Wehner Clark Fitzgerald and
Luc Rocher and Tobias Megies and Luis Pedro Coelho Tamas Nagy and
Erik Ziegler and
Travis Hoppe and Skipper Seabold and Sergio Pascual and Phillip Cloud and Miikka Koskinen Tobias Megies and
Chris Hausler Daniel Wehner and
kjemmett Samuel St-Jean and
Dmitrijs Milajevs Luis Pedro Coelho and
Adel Qalieh Gregory Hitz and
Dan Allan Antony Lee and
Kyle Meyer}, Luc Rocher},
title =
{{seaborn: v0.6.0 (June 2015)}}, {seaborn: v0.7.0},
month =
{jun}, jan,
year =
{2015}, 2016,
doi =
{10.5281/zenodo.19108}, {10.5281/zenodo.45133},
url =
{http://dx.doi.org/10.5281/zenodo.19108}, {http://dx.doi.org/10.5281/zenodo.45133},
note = {\href{http://dx.doi.org/10.5281/zenodo.45133}{doi:10.5281/zenodo.45133}},
}
...
year = {2016},
doi = {10.5281/zenodo.44579},
url = {http://dx.doi.org/10.5281/zenodo.44579},
note = {\href{http://dx.doi.org/10.5281/zenodo.44579}{doi:10.5281/zenodo.44579}},
}
...
author = {David A. W. Soergel},
title = {{Rampant software errors may undermine scientific results}},
journal = {F1000Research},
note = {\href{http://dx.doi.org/10.12688/f1000research.5930.2}{doi:10.12688/f1000research.5930.2}},
}
...
doi = {10.1117/12.2212085},
url = {http://dx.doi.org/10.1117/12.2212085},
year = {2016},
month = {mar}, publisher =
{{SPIE}-Intl Soc Optical Eng}, {{SPIE}},
volume = {971405},
author = {Antonino Ingargiola and Ted Laurence and Robert Boutelle and Shimon Weiss and Xavier Michalet},
editor = {Jörg Enderlein and Ingo Gregor and Zygmunt K. Gryczynski and Rainer Erdmann and Felix Koberling},
title = {{Photon-{HDF}5: open data format and computational tools for timestamp-based single-molecule experiments}},
booktitle = {Single Molecule Spectroscopy and Superresolution Imaging {IX}},
note = {\href{http://dx.doi.org/10.1117/12.2212085}{doi:10.1117/12.2212085}},
}
...
}
@techreport{Eglen_2016, @article{Eglen_2016,
doi = {10.1101/045104},
url = {http://dx.doi.org/10.1101/045104},
year = {2016},
month = {mar},
publisher = {Cold Spring Harbor Laboratory Press},
journal = {{bioRxiv}},
author = {Stephen Eglen and Ben Marwick and Yaroslav Halchenko and Michael Hanke and Shoaib Sufi and Padraig Gleeson and R. Angus Silver and Andrew Davison and Linda Lanyon and Mathew Abrams and Thomas Wachtler and David J Willshaw and Christophe Pouzat and Jean-Baptiste Poline},
title = {{Towards standard practices for sharing computer code and programs in neuroscience}},
note = {\href{http://dx.doi.org/10.1101/045104}{doi:10.1101/045104}},
}
