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--- downloads:frap_analysis [2010/03/03 16:33] – kota
+++ downloads:frap_analysis [2017/05/11 15:28] (current) – kota
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 ~~NOTOC~~
-[{{ http://cmci.embl.de/downloads/FRAPmanual_files/image069.jpg}}]
+[{{ http://cmci.embl.de/dls/FRAPmanual_files/image069.jpg}}]
 ====== FrapCalc ======
-Analyze FRAP curves and get parameter by curve fitting ([[downloads:frapDocumentation|documentation.]]).
+**Please jump to [[https://cmci-embl.gitlab.io/docs/analysis/frapcalc/|the new page!]]**
+/**
+Analyze FRAP curves and get parameter by curve fitting ([[http://cmci.embl.de/documents/frapmanu|documentation.]]). Lecture notes are also available ([[http://cmci.embl.de/documents/100420frapinternal | Lecture Notes (Apr. 2010)]])
 ===== Author =====
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 Tel: +49 6221 387 404
 ===== Questions & Comments =====
+ ?
 Please post in the commenting section below at the bottom of this page
@@ Line 26: / Line 31: @@
 ===== Installation =====
-Download [[http://cmci.embl.de/downloads/K_FRAPcalcV9j.ipf|K_FRAPcalcV9j.ipf]] to a place where you can access easily. Open the file in IgorPro and compile.
+Download [[http://cmci.embl.de/dls/K_FRAPcalcV9k.ipf|K_FRAPcalcV9k.ipf]] to a place where you can access easily (you might need to right click or ctrl-click and then save it to your local machine). Open the file in IgorPro and compile.
 ===== Description =====
 Analyze FRAP curves to derive recovery parameters.
-**More details are in the [[http://cmci.embl.de/downloads/FRAPmanual.htm|documentation.]]** ===== Features =====
+ ===== Features =====
   * 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.
@@ Line 40: / Line 46: @@
   * Graphing of the fitted curve and estimation curve without acquisition bleaching.
   * Batch Fitting
+===== Papers + Misc =====
+==== 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. [[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1500972&tool=pmcentrez&rendertype=abstract|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. [[http://www.ncbi.nlm.nih.gov/pubmed/17606616|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. [[http://www.ncbi.nlm.nih.gov/pubmed/17597070|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. [[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2814048&tool=pmcentrez&rendertype=abstract|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. [[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2654807&tool=pmcentrez&rendertype=abstract|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. [[http://www.ncbi.nlm.nih.gov/pubmed/21504832|Accessed January 30, 2012]].
+  * Caillier, B. et al., 2011. QRS widening and QT prolongation under bupropion: a unique cardiac electrophysiological profile. Fundamental & clinical pharmacology. [[http://www.ncbi.nlm.nih.gov/pubmed/21623902|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. [[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3099667&tool=pmcentrez&rendertype=abstract|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. [[ http://www.ncbi.nlm.nih.gov/pubmed/22467852|Accessed October 10, 2012]].
+... searches were done by google hits, so if YOURS is missing please tell me!
+==== Web Back Links ====
+  * [[http://www.leica-microsystems.com/science-lab/fluorescence-recovery-after-photobleaching-frap-its-offspring/|Leica Frap Page]]
+  * [[http://actinsim.uni.lu/eng/Downloads|Univ. of Luxemburg, ActSim download page]]
+    * MatLab-migrated version of FRAPCalc.
+  * [[http://adm.irbbarcelona.org/f-r-a-p|ADM, IRB Barcelona]]
+  * [[http://www.igorexchange.com/node/2330|IgorExchange Forum]]
+  * [[http://www.ncbi.nlm.nih.gov/pubmed?term=20063225%20| ... citing my lecture in a paper]]
+  * Dissertation using FRAPCalc
+    * [[http://hss.ulb.uni-bonn.de/2009/1863/1863.pdf|Luciana Renna, Univ. Bonn]]
 ===== History =====
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   * 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.
+    * 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 [[http://www.embl.org/cmci/weblog/2007/10/frap-analysis-macro-updates.html#links|blog]]
@@ Line 62: / Line 95: @@
   * 09-10-26 ver9h
     * Fitted parameters appear in plot legend even when mobile fraction >1.0. (C. Tischer's suggestion)
-    * Added documentation for gammaQ=1 cases. See -> 2.7. [[http://cmci.embl.de/downloads/FRAPmanual.htm#Evaluaiton2_7|Evaluation of the Curve Fitting: Goodness of Fit]] (N. Goldsmith's suggestion)
+    * Added documentation for gammaQ=1 cases. See -> 2.7. [[http://cmci.embl.de/dls/FRAPmanual.htm#Evaluaiton2_7|Evaluation of the Curve Fitting: Goodness of Fit]] (N. Goldsmith's suggestion)
   * 10-03-03 ver9j
     * Batch Processing funciton with averaging function (request from N. Goldsimth). See additional explanation in the [[documents:frapmanu |documentation page]]
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     * Fitting of averaged curve is done with actual standard deviation
     * BatchFitting() was added to the last line of BatchAverageAndFit()
+*/