F-I plot: easthetic changes for thesis + inset.
Old changes for bifurcation analysis in F-I script.
Change the current units from nA to fA to allow finer tuning of input next to bifurcation point, plus some minor changes to plotting.
Add README.
Add NeuroML2 simulation for f-i comparison of the three morphologies.
Rotate morphology of original Golgi cell by Solinas.
Now all the morphologies in the project are oriented in the same way, making for nicer network visualisations.
Leftover changes made in preparation for data club on 05-09-2013.
Still working on coupling strength analysis.
Improve plots and add saving of sample network realisation, with edges weighted by the coupling coefficients, in graphml format for further exploration and plotting with Gephi.
Fix bug with coupling strength analysis for multiple net realisations.
The analysis/plot script was loading all data correctly, but using only the data from trial 0 to calculate the coupling coefficient of all trials.
Working on plot of coupling coefficient vs distance.
Working on better display of cc vd distance, using hexbin.
Add plot of cc distr for morph-connected cells, and degree distr.
Desync: shorten simulations. Add reduced-morphology only sims.
Add some exp data files.
Overhaul coupling strength analysis for 2010/2012 connectivity.
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Minor correction to GapJuncDiscrete allowed segment groups.
Added proper variability in number of gjs per connected pair.
Fixed: proper spatial distribution for gjs. Added background noise.
Now gjs are distributed on the dendritic tree according to the experimental data reported in Vervaeke2012. Also, added background Poisson noise as per network simulations in Vervaeke2010.
Fixed wrong synapse in apical stimulation.
Variable leak conductance over whole cell instead of just the soma.
Added actual heterogeneity for golgi somatic leak.
Anyway, it doensn't seem enough to desynchronise the network.
Fix: attempting to create gjs between nonexistent GoCs.
Now simulations run fine.
Implemented one nC group per golgi cell, needed for heterogen g_leak.
NEURON still crashes when trying to simulate, so it's not done yet.
Added plotting script for desynchronisation simulations. Also, enabled GJ connection strengths to be all different from each other.