Metadata-Version: 2.1
Name: blitzcurve
Version: 0.0.2
Summary: Time-resolved fluorescence anisotropy analysis.
Home-page: https://github.com/teese/blitzcurve
Author: Mark Teese and Philipp Heckmeier
Author-email: mark.teese@checkmytumhomepage.de
License: MIT
Download-URL: https://github.com/teese/blitzcurve/archive/0.0.2.tar.gz
Project-URL: LangoschLab, http://cbp.wzw.tum.de/index.php?id=9
Project-URL: TU_Munich, https://www.tum.de
Description: ==========
        blitzcurve
        ==========
        
        Data analysis of time-resolved fluorescence anisotropy measurements (TRAMs).
        
        TRAMs are state-of-the-art techniques that can be used to analyse protein function and interaction.
        
        Why use TRAM techniques?
        ~~~~~~~~~~~~~~~~~~~~~~~~
        
        To measure molecule rotation speeds (e.g. protein size, structure, ligand binding).
        
        To measure oligomerisation properties, via Foerster Resonance Energy Transfer (FRET) between two fluorescent molecules.
        
        What is blitzcurve for?
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        * fitting curves to experimental TRAM data
        * extracting useful fit parameters
        * comparing samples
        
        How does the experiment work?
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        * excitation of fluorescent molecules
        * measurement of the depolorisation of the emitted light (polarisation / anisotropy)
        * time-resolved methods: pulse excitation, and measurement of the change in anisotropy over time in nanoseconds
        
        Analysis methods
        ~~~~~~~~~~~~~~~~
        
        * appropriate fitting methods are still under development
        * current input: csv with anisotropy and time (ns) values
        * current fitting methods for anisotropy vs time
           - Savitzky Golay fit to all raw data
           - Exponential fit to initial decay data
           - Exponential fit to final decay data
        * key measured parameters:
           - r_inf (predicted anisotropy at an infinite range in time)
           - r_max (maximum anisotropy measured at any timepoint)
        
        Installation
        ~~~~~~~~~~~~
        ::
        
            pip install blitzcurve
        
        * Blitzcurve should be compatable with `Anaconda python`__ 3.x or any scientific python package
        
        .. _AnacondaLink: https://www.anaconda.com/download/
        
        __ AnacondaLink_
        
        Usage
        ~~~~~
        
        .. code:: python
        
            import blitzcurve
            # define data directory with csv files
            data_dir = r"D:\data\20180229_TRdata"
            # OPTIONAL: define which data files will be analysed
            file_list = ["10nM-FGC1-2min_aniso.txt", "10nM-FGC2-2min_aniso.txt"]
            # run blitzcurve function to fit curves to individual samples
            blitzcurve.run_fit(data_dir, figs_to_plot=file_list)
            # setup a dictionary to shorten long sample names
            name_dict = {"10nM-FGC1-2min_aniso.txt": "FGC1", "10nM-FGC2-2min_aniso.txt": "FGC2", "10nM-FGC3-2min_aniso.txt": "FGC3"}
            # run blitzcurve function to compare curves and parameters for multiple samples
            blitzcurve.run_compare(data_dir, name_dict=name_dict)
        
        Contribute
        ~~~~~~~~~~
        
        Collaborators and pull requests are welcome. Send us an email.
        
        License
        ~~~~~~~
        
        This python package is released under the permissive MIT license.
        
        Contact
        ~~~~~~~
        Contact details are available at the staff pages of `Mark Teese`__ or `Philipp Heckmeier`__ within the `Langosch lab`__
        of the Technical University of Munich.
        
        .. _MarkWebsite: http://cbp.wzw.tum.de/index.php?id=49&L=1
        .. _PhilippWebsite: http://cbp.wzw.tum.de/index.php?id=55
        .. _LangoschWebsite: http://cbp.wzw.tum.de/index.php?id=9
        
        __ MarkWebsite_
        __ PhilippWebsite_
        __ LangoschWebsite_
        
        
        .. image:: https://raw.githubusercontent.com/teese/eccpy/master/docs/images/signac_seine_bei_samois.png
           :height: 150px
           :width: 250px
        
        Examples
        ~~~~~~~~
        
        **fit to obtain r_max**
        
        .. image:: https://raw.githubusercontent.com/teese/blitzcurve/master/blitzcurve/images/aniso_savgol_fit.png
           :height: 500 px
           :width: 500 px
        
        **fit to obtain r_inf**
        
        .. image:: https://raw.githubusercontent.com/teese/blitzcurve/master/blitzcurve/images/aniso_seg2_fit.png
           :height: 500 px
           :width: 500 px
        
        **barchart comparing r_max**
        
        .. image:: https://raw.githubusercontent.com/teese/blitzcurve/master/blitzcurve/images/01_barchart_r_max.png
           :height: 200 px
           :width: 200 px
        
        **barchart comparing r_inf**
        
        .. image:: https://raw.githubusercontent.com/teese/blitzcurve/master/blitzcurve/images/02_barchart_r_inf.png
           :height: 200 px
           :width: 200 px
        
        **linechart comparing fit to full data for three samples**
        
        .. image:: https://raw.githubusercontent.com/teese/blitzcurve/master/blitzcurve/images/06_linechart_savgol.png
           :height: 500 px
           :width: 500 px
        
        **linechart comparing fit to r_inf for three samples**
        
        .. image:: https://raw.githubusercontent.com/teese/blitzcurve/master/blitzcurve/images/08_linechart_seg2.png
           :height: 500 px
           :width: 500 px
Keywords: fluorescence FRET rotation curve savitzky golay anisotropy time resolved TRAM single molecule protein bioinformatics biophysics microscopy
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3.6
Classifier: License :: OSI Approved :: MIT License
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Description-Content-Type: text/x-rst
