This directory contains information about modeled systems -- cells, their positions, and properties;
recurrent connections; and input connections from the LGN and from the background sources ("tw").

Unzip all the files.  The file cells_synapses_tw.zip contains information
about individual cell models, synapse properties, and the "tw" background inputs.
The remaining zip files are in the directory "build/" and should be unzipped
there.  They contain information about nodes in the model networks, recurrent
connections, and inputs from LGN.


The data presented corresponds to models LL1, LL2, LL3, LR1, LR2, LR3, RL1, RL2, RL3, RR1, RR2, RR3.
All these models consist of a biophysical core of 10,000 cells and LIF periphery of 35,000 cells.

Note that exactly the same files for cell representation and connectivity were used for our all-LIF
simulations.  In those simulations, the biophysical cells from the biophysical "core" were replaced
in software by appropriate LIF models.

The synaptic properties are described by the files
syn_data_278.json for LL1, LL2, and LL3 (for all-LIF simulations, syn_data_lif_z101_LL.json);
syn_data_287.json for LR1, LR2, and LR3 (for all-LIF simulations, syn_data_lif_z101_LR.json);
syn_data_285.json for RL1, RL2, and RL3 (for all-LIF simulations, syn_data_lif_z101_RL.json);
syn_data_282.json for RR1, RR2, and RR3 (for all-LIF simulations, syn_data_lif_z101_RR.json).

NOTE that for systems of LR and RR type, one should use the module connectcells0.py
in our simulation code, whereas for LL and RL one should use connectcells.py.


The models, recurrent connectivities, and input connectiviy from the LGN are
stored in the directory build/.

NOTE that all zip files should be unzipped if one needs to run simulations.

The information about cells and their properties is stored in files ll1.csv,
ll2.csv, etc.

NOTE that the only unique such files are ll1.csv, ll2.csv, and ll3.csv.  The
other files are simply copies of these three, created for convenience.
Specifically, the cells and their properties are identical for systems
LL1, LR1, RL1, and RR1;
LL2, LR2, RL2, and RR2;
LL3, LR3, RL3, and RR3.

NOTE that connectivities are identical between the systems LL1 and LR1; LL2
and LR2; LL3 and LR3; RL1 and RR1; RL2 and RR2; and RL3 and RR3.  These
connections are stored in zipped directories, such as ll2_connections.zip.
Again, copies of these directories, applying to the other models with identical
connectivities, are provided for convenience (e.g., ll2_connections.zip and
lr2_connections.zip).

Input connections from the LGN are stored in files
build/ll1_inputs_from_LGN.csv (for systems LL1, LR1, RL1, and RR1);
build/ll2_inputs_from_LGN.csv (for systems LL2, LR2, RL2, and RR2);
build/ll3_inputs_from_LGN.csv (for systems LL3, LR3, RL3, and RR3).


The input connections from background sources ("tw") are provided in the
zipped directory tw_data.zip.  The connections files are stored in the directories
ll1_tw_build/ (for systems LL1, LR1, RL1, and RR1);
ll2_tw_build/ (for systems LL2, LR2, RL2, and RR2);
ll3_tw_build/ (for systems LL3, LR3, RL3, and RR3).


Models of individual cells and their morphologies, as well as *.mod files
describing necessary mechanisms are stored in the zipped directory
cell_models.zip.