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...