by Konstantin Nikolic and Joaquim Loizu
Code developed in MATLAB using the Parallel Computing Toolbox, which allows computations on multicore computers and computer clusters. An appropriate graphic user interface was developed which gives very convenient and instructive presentation of the parameters used in the modelling.
Code covered by the BSD License (Matlab Central, File exchange), please see BSD_License.txt file or visit: http://www.mathworks.com/matlabcentral/fileexchange/view_license?file_info_id=22942
Please cite papers [1] and [2] if you use this code.
The main file is "Drosophila_Phototransduction.m" which when you run it opens the GUI. The GUI contains the preloaded values for parameters and should be mostly self-explanatory in combination with the paper [1]. It is possible to run stochastic and deterministic models for single and multiple runs. The output consists of a table for some average values and three graphs (for the average quantum bump, latency times distribution and peak current distribution). It is possible to produce some other plots currently commented out in gui_averageQBall.m and gui_singleQB_multi.m files.
In the stochastic mode QBs are filtered with (100Hz) low pass filter.
Averaging: QBs aligned by their half bump rise and fall times S. R. Henderson, H. Reuss
and R. C. Hardie, J. Physiol. 524, 2000, pp. 179-194, which was used as a source of
experimental values.
time: time period in ms you want to simulate (e.g. 120)
tstep: time step in ms for numerical solution (<=0.1)
flagM/G/P/D/T: to set deterministic mode (0) or stochastic mode (1) for each step
of the cascade
Any additional questions (but please note that the support for the software can NOT be guaranteed): k.nikolic@imperial.ac.uk
- Nikolic K, Loizu J, Degenaar P, Toumazou C: "A stochastic model of the single photon response in Drosophila photoreceptors", Integrative Biology, 2010, Vol:2, Pages:354-370. doi: 10.1039/C0IB00031K
- Nikolic K, Loizu J, Degenaar P: "Computational Modelling of the Drosophila Phototransduction Cascade", Biophysical Journal, Vol:98, Issue 3, Supplement 1, January 2010, Page 495a. doi: 10.1016/j.bpj.2009.12.2695