readme.txt

ENCODING AND RETRIEVAL IN A MODEL OF THE HIPPOCAMPAL CA1 MICROCIRCUIT
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This NEURON code implements a small network model (100 pyramidal cells
and 4 types of inhibitory interneuron) of storage and recall of patterns
in the CA1 region of the mammalian hippocampus. Patterns of PC activity
are stored either by a predefined weight matrix generated by Hebbian learning,
or by STDP at CA3 Schaffer collateral AMPA synapses.

Reference:
Cutsuridis, V., Cobb, S. and Graham, B.P. Encoding and Retrieval in
a model of the hippocampal CA1 microcircuit. Hippocampus, in press,
DOI 10.1002/hipo.20661, 2009.

Abstract:
It has been proposed that the hippocampal theta rhythm (4-7 Hz) can 
contribute to memory formation by separating encoding (storage) and 
retrieval of memories into different functional half-cycles 
(Hasselmo et al., 2002). We investigate, via computer simulations, 
the biophysical mechanisms by which storage and recall of spatio-temporal 
input patterns are achieved by the CA1 microcircuitry. A model of the CA1 
microcircuit is presented that uses biophysical representations of the 
major cell types, including pyramidal (P) cells and four types of inhibitory
interneurons: basket (B) cells, axo-axonic (AA) cells, bistratified (BS) cells 
and oriens lacunosum-molecurale (OLM) cells. Inputs to the network come from 
the entorhinal cortex (EC), the CA3 Schaffer collaterals and medial septum. 
The EC input provides the sensory information, whereas all other inputs provide 
context and timing information. Storage is accomplished via a local STDP mediated
hetero-association of the EC input pattern and the incoming CA3 input pattern on 
the pyramidal cell target synapses. The model simulates the timing of firing of
different hippocampal cell types relative to the theta rhythm in anaesthetized 
animals and proposes experimentally confirmed functional roles for the different 
classes of inhibitory interneurons in the storage and recall cycles 
(Klausberger et al., 2003, 2004). Measures of recall performance of new and 
previously stored input patterns in the presence or absence of various inhibitory
interneurons are employed to quantitatively test the performance of our model. 
Finally, the mean recall quality of the CA1 microcircuit is tested as the number 
of stored patterns is increased.

Main file: HAM_StoRec_par.hoc (parallel version)
           HAM_StoRec_ser.hoc (serial version - VERY SLOW!)

These files are configured to produce the results presented in figures 9 and 10
of the paper, showing recall of a stored pattern when the entorhinal cortex input
is disconnected from the CA1 pyramidal cells and so pattern recall is cued 
exclusively by CA3 Schaffer collateral input. Example results are in the Results
directory, in which there are also Matlab files for plotting them.
EC input can be restored by setting ECWGT to its non-zero value.
Other results were produced by setting particular connection weight variables to 0
to remove certain synaptic pathways.

*********WARNING******************
// Bug report, V. Cutsuridis and B. Graham, 21 Apr 2015
We have been informed of a bug in the IA mod file,
used for the OLM interneuron first introduced in ModelDB ac. 28316.
Simulations (those for Figs.9 and 10) were thus rerun with the bug fixed.
There are small quantitative differences from the published results, 
but the model still works as described.
To reproduce the published results, comment out the "rates(v)" line in the
DERIVATIVE block of IA.mod.
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