This repository contains the notebooks used for the analysis the paper:

Multi-spot single-molecule FRET: high-throughput analysis of freely diffusing molecules Ingargiola et al. PLOS ONE (2017) doi:10.1101/085027, or preprint bioRxiv (2016) doi:10.1101/085027

To explore the repository start here:

• index.ipynb

The previous link opens the main index notebook on nbviewer.

In order to execute these notebooks you need to install FRETBursts first. If you have already installed python through conda just type:

conda install fretbursts -c conda-forge

Otherwise see the instruction on the FRETBursts manual.

Download the ZIP archive from this link and extract the archive.

You also need to download two datasets from figshare. Put files from the single-spot dataset in the in the data/singlespot folder, and the files from the multi-spot dataset in the data/multispot folder.

The notebook index.ipynb contains links to all the other notebooks (with a brief explanation of what each notebook does). It also contains links the result data files (CSV format, stored in the results folder).

Running index notebook you will re-execute the full analysis and regenerate the output notebooks], the figures and all the numeric results.

You can re-run the analysis on the current (2016-2017) scientific python3 stack (numpy 1.11-1.12, scipy 1.18-1.19, pytables 3.x, lmfit 0.9.5, pandas 1.18-1.19). For reproducibility, use FRETBursts 0.5.9. New FRETBursts version give slight different results due to changes in bakground estimation (see details here).

In the future, new version some used library can introduce incompatibilities that break the code posted here. In this case, you can recreate the original conda environment used for running this analysis using the file environment_macos.yml.

All the text and documentation are released under the CC BY 4.0 license. All code is under the MIT license (see LICENSE.txt).

Copyright 2016 The Regents of the University of California, Antonino Ingargiola