FrapCalc

Analyzes FRAP curves with various models

frap curve fitting IgorPro

Description

FrapCalc analyzes FRAP curves to quantitatively estimate parameters of protein dynamics.

  • Import FRAP measurement tab-delimited text files of Zeiss data format (6 different data structures)
  • Leica data format (7 different data structures) - Three different ways of normalizing FRAP curve - Curve fitting by single and double exponential formula and 2 diffusion formula. Correction for the acquisition bleaching.
  • Output of half-max, diffusion coefficient, mobile/immobile fractions.
  • Weighting for the fitting.
  • Evaluation of goodness of fit by chi-square and gamma function.
  • Graphing of the fitted curve and estimation curve without acquisition bleaching.
  • Batch Fitting

Dependency

IgorPro Ver.5 - 6. Not throughly tested for Ver.7

Installation

Download the FRAPCalc package from the following site:

Unpacakge the ZIP archive and place the file K_FRAPcalcV9k.ipf to somewhere you can access easily. Open the file in IgorPro and compile it. A new menu item “FrapCalc” then appears.

Usages

Usage details are written in its documentation contained in the downloaded package or a bit older version accessible here. A lecture note (Apr. 2010) is also available for the theory about FRAP.

Code Repository

https://github.com/miura/FrapCalc

License

Released under the GNU General Public License.

Papers Using This script

  • Runz, H. et al., 2006. Sterols regulate ER-export dynamics of secretory cargo protein ts-O45-G. The EMBO journal, 25(13), p.2953-65. Accessed February 7, 2012.
  • Atlason, P.T. et al., 2007. N-Methyl-D-aspartate (NMDA) receptor subunit NR1 forms the substrate for oligomeric assembly of the NMDA receptor. The Journal of biological chemistry, 282(35), p.25299-307. Accessed February 7, 2012.
  • Pooler, A.M. & McIlhinney, R.A.J., 2007. Lateral diffusion of the GABAB receptor is regulated by the GABAB2 C terminus. The Journal of biological chemistry, 282(35), p.25349-56. Accessed February 7, 2012.
  • Hoppa, M.B. et al., 2009. Chronic palmitate exposure inhibits insulin secretion by dissociation of Ca(2+) channels from secretory granules. Cell metabolism, 10(6), p.455-65. Accessed February 7, 2012.
  • Treeck, M. et al., 2009. Functional analysis of the leading malaria vaccine candidate AMA-1 reveals an essential role for the cytoplasmic domain in the invasion process. PLoS pathogens, 5(3), p.e1000322. Accessed February 7, 2012.
  • Bancaud, A., Huet, S., Rabut, G., Ellenberg, J., 2010. Fluorescence perturbation techniques to study mobility and molecular dynamics of proteins in live cells: FRAP, photoactivation, photoconversion, and FLIP. Cold Spring Harb. Protoc. 2010, pdb.top90.
  • Bosch-Presegué, L. et al., 2011. Stabilization of Suv39H1 by SirT1 is part of oxidative stress response and ensures genome protection. Molecular cell, 42(2), p.210-23. Accessed January 30, 2012.
  • Caillier, B. et al., 2011. QRS widening and QT prolongation under bupropion: a unique cardiac electrophysiological profile. Fundamental & clinical pharmacology. Accessed February 7, 2012.
  • Díaz, A. et al., 2011. Processivity and subcellular localization of glycogen synthase depend on a non-catalytic high affinity glycogen-binding site. The Journal of biological chemistry, 286(21), p.18505-14. Accessed February 7, 2012.
  • Coutinho-Budd J, Ghukasyan V, Zylka MJ, Polleux F. The F-BAR domains from srGAP1, srGAP2 and srGAP3 regulate membrane deformation differently. Journal of cell science. 2012;125(Pt 14):3390–401. Accessed October 10, 2012.

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History (2005 - 2010).

For history after 2010, please check the header of the file and also git log.

  • 05-9-9
    • 1st version
  • 07-3-28
    • 9th version
  • 07-8-27 ver 9a
    • Added Leica new file format importing (csv format)
    • Made K_SoumpasisHalfLife2(fitwave,amplitude) for calculateing Half max. Previous one had problem when point 1 is larger than 0.5 ? Changes for the texts in the graph (Half max value added to diffusion fittings) see more details in the code.
  • 07-10-30 ver9b
    • For details, read the blog
  • 08-03-25 ver 9c
  • 08-07-24 ver 9e
    • Added two data set types for importing. Olympus .cvs file is now possible.
  • 08-10-07 ver9f
    • Added Excel file importing funciton (Four column, with Time-Frap-All Cell- Base, with the first line containg column name) and tab-delimited text file.
  • 08/12/11 ver9g
    • Replaced fitting function for double-exponential fitting, follwoing the recommendation of wavemetrics.
    • Half-time estimation for double exponential fitting had a bug, when data range is below the half-max intensity. This is now done by extrapolation.
  • 09-10-26 ver9h
  • 10-03-03 ver9j
    • Batch Processing funciton with averaging function (request from N. Goldsimth). See additional explanation in the documentation page
    • K_FrapCalcCore() was modified so that averaged curve could be fitted as well. Since averaged curve does not have original normalizaton process is not required but then several parameters which are calculated during normalization will be missing. For this, flag “G_doAveraged” was added
    • getAverageGApRatio(Gfilelist): Gap Ratio is calculated by averaging individual
    • Fitting of averaged curve is done with actual standard deviation
    • BatchFitting() was added to the last line of BatchAverageAndFit()