Actually commit scripts for synchrony in spatially random network.
Analyse desynchronisation in spatially random network.
Merge branch 'master' of github.com:epiasini/GJGolgi_ReducedMorph
Leftover plotting changes.
More aesthetical improvements on desynch video script.
Cosmetic improvements for static pictures of SW graph examples.
Small improvements to small world desynch animation script.
Plotting changes for small world simulations.
Don't save membrane potentials during small world simulations.
Add sim and analysis scripts for tunable small world-like network.
Var. spatial scale: fix wrong call to NEURON generation function.
Var. heterogen.: add reference to useful dataset.
Utils: add function for NEURON generate/compile/submit.
Use G(n,m) instead of G(n,p) as 'completely random' GJ network.
Var. spatial scale: add reference to useful dataset.
Var. heterogen: set gamma params to preserve mean syn strenght.
Changes to base nC project. Enable remote simulations.
Variable heterogeneity: add support for averaging over trials.
Running many repetitions of synch/spatial scale simulations.
Var. spatial scale: add support for averaging many trials.
Add synchrony analysis with varying spatial connectivity scale.
Separate graph->GJ net generation into its own function.
Desynch simulations: use same syn models as Vervaeke2010.
Variable heterog.: control mean and variance of syn strength distr.
README typo.
Variable heterogeneity: working towards a general code cleanup.
Variable heterogeneity: make simulation optional.
Also, properly regenerate cell positions at each trial (useul for spatial connectivity rules).
Synchrony analysis: add 2010-like and random clustered networks.
Messing with desynch in synthetic net, trying spatial connectivity.
Variable heterogeneity simulations: use E-R random graph.
Update fit/plot script for Fermi function with minor aesthetic stuff.
Old changes to IV plot for reduced morphology GoC model.
Add extra output to script for connection probability model fit.
Add script for fitting Fermi conn. prob model to exp data.
Retouch network-based rate IO analysis for inclusion in thesis.
Small plotting and doc fixes.
Small improvement to dend att plot. Add dependency on siunitx.
FI plot: add parameters for detailed inset.
Rate IO analysis: plot pf and mf stims on the same graph.
More plotting fixes for FI analysis.
Plotting: load default rc params from file in thesis folder.
FI plot: update matplotlib rc to use bera sans for numbers.
Add samples of CC-weighted graphs of network connectivity.
Rate IO analysis: use longer simulations and minor script cleanup.
F-I analysis: fix units, as nC uses ms to save sim data.
Git: update ignores.
Plotting fixes for dendritic attenuation comparison.
PLotting fixes for I-V curves of cells embedded in a GJ network.
Update FI plot for larger figure.
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.
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.
Manipulating heterogeneity of GJ connectivity as a graph-theoretical degree distribution.
Added plotting script for single cell current-voltage relationship.
Coupling strength simulation and plotting scripts.
Added current-voltage relation plotting script.
The current-voltage relation (and, consequently, the input resistance) doesn't seem to exhibit any significant heterogeneity induced by the gap junction distribution.
Added simulation script for input resistance heterogeneity analysis.
Analysis and plotting script is still to be implemented.
Added network (de)synchronisation analysis as in Vervaeke2010.
Two new simulation configurations, network_desynchronisation and network_desynchronisation_2010gap, try to reproduce the desynchronisation effect reported in Vervaeke2010. The expected behaviour seems to emerge only if the gap junction connectivity is...
Fixed missing GJ netconn and generally improved GJs for reduced model.
Now the first segment of the apical dendrites in the reduced model is considered as being still in the molecular layer. This is to better reproduce the choices made for the detailed model, and it plays an...
Rate-coded I/O analysis for parallel fibre input, with gap junctions.
Rate-coded I/O analysis for mossy input, with gap junctions.
The gap junctions, the network and the stimuli are implemented as in Vervaeke2012, except for heterogeneity. The detailed cell model replicates the results in the paper, and the simplified one seems to...
Renamed FI curve script. Added FI results plot to the repo.
Another attenuation estimate (same cells, new random probe placement).
The agreement between the models is good, and they are both quite close to the 52 micron experimental estimate in Vervaeke2012, figure 3C.
Updated attenuation result with latest version of the model.
Deleted old version of attenuation scripts and renamed the 'good' one.
The version that got deleted was confusing, as it wasn't immediately clear that it didn't have anything to do with the results in Vervaeke2012. Also, accordingly renamed the figure showing the...
Updated attenuation analysis to work with the latest model version.
Also, added some comments to make clearer which script is the one to be used to benchmark the model's behaviour against Koen's paper.
Reduced the basolateral dendrites' size.
This results in a better match for rate-coded I/O relationship for mossy fiber stimulation, but on the other hand the cell is now responding too much to apical stimulation. Also, the spike shape is less bad (the size of the little after-spike hump has decreased).
Enabled effective remote simulation for fi curve script.
Added: rate-coded I/O comparison (Vervaeke, Solinas and reduced).
Added various relevant scripts and nC project elements. Note that the existing nework connections in the nC project have been renamed, and this might have broken some of the old scripts.
At this point, the results of the rate-coded I/O relationship are:...
Updated segment groups.
Raised the simulation temperature to 30 degrees.
Rotated reduced model so that it points in the correct direction.
Minor simulation/plotting improvements.
Added plotting of detailed model's potential in spontaneous firing simulation, and aligned the stimulation points for the detailed cell in attenuation.py so that they match those that I'm forced to use in the simplified cell.
Fixed 'double spike' bug caused by on old KBK channel implementation.
This is a well-known problem with an old version of the mod file for the KBK channel, and had been squashed somewhere else (at least in the original model by Solinas - see relevant files on ModelDB and Open...
Formatting: preparing to modify KBK channel.
Modified axon and bl dendrites. Looking better.
Things that have improved: - resting potential (closer to Koen's model) - somatic response to single synaptic input on a dendrite (closer to Koen's model, but still a bit too weak) - spike shape (actually starting to look as "halfway between" Koen's...
Making larger changes in morphology beyond the apical dendrites.
I managed to get the dendritic attenuation length to match between the models, but the absolute response properties of the cell to synaptic input are still quite different (Koen's model is more reactive to...
Made the second apical dendrite identical to the first one.
Added two new scripts to better reproduce figure 3C in Vervaeke2012.
Koen clarified via email that the cell being tested was 210710_C1, that the attenuation was measured over an apical dendrite (one that he could have pathced during the experiments), and that it wasn't...