pyFRET

pyFRET: A Python Library for Analysis of Single Molecule Fluorescence Data
Talk given at EuroScipy 2014, Cambridge

Transcript

1. pyFRET: A Python Library for Analysis of Single Molecule Fluorescence Data Rebecca R. Murphy Department of Chemistry University of Cambridge @rebecca_roisin 30th August 2014
2. Förster Resonance Energy Transfer: FRET Images: Schuler, B. et al. Nature 419, 743-747 (2002) Roy R. et al. Nature Methods 5 507-516 (2008)
3. Single Molecule FRET: The Experiment
4. Single Molecule FRET: The Data
5. Software Issues in smFRET  Wide range of programming languages for data analysis  Python  C++  IgorPro  Matlab  Labview  No standard tools or file formats  Code on a USB drive ...
6. Introducing PyFRET  Open source library  Python library for smFRET data analysis  Supports:  Confocal measurements  Continuous excitation (FRET)  Alternating excitation (ALEX)
7. What can PyFRET do?
8. Data Analysis Using pyFRET  Short scripts  Reproducible analysis  Self-contained functions for data processing
9. Plotting Data with PyFRET
10. Plotting Data with PyFRET
11. PyFRET is Open Source  Download from PyPI: the Python Package Index  Documentation  Online tutorial  Unit tests
12. PyFRET is Online
13. Tutorial is Online
14. Conclusion  First free open-source software for smFRET data analysis  Simple  Easy to use  Useful to benchmark other tools  Needs a burst search algorithm ...
15. Acknowledgements • Funding: BBSRC  Supervision: – David Klenerman – Sophie Jackson  Everyone whose data I've borrowed: – Vladas – Laura – Marija – Magnus – Mathew •Libraries: – Numpy – Scipy – Matplotlib