From 880b5d10f4ee29a15a7ee02d62dd4b11452e24ce Mon Sep 17 00:00:00 2001 From: EnfxcFCb6 Date: Mon, 2 Jun 2025 17:40:04 -0400 Subject: [PATCH 1/2] Standardized README to Markdown format --- README.md | 30 +++++++++++++++++++++++++ readme.txt | 66 ------------------------------------------------------ 2 files changed, 30 insertions(+), 66 deletions(-) create mode 100644 README.md delete mode 100644 readme.txt diff --git a/README.md b/README.md new file mode 100644 index 0000000..c32e73e --- /dev/null +++ b/README.md @@ -0,0 +1,30 @@ +# ENCODING AND RETRIEVAL IN A MODEL OF THE HIPPOCAMPAL CA1 MICROCIRCUIT + +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. +********************************** + +Changelog +--------- +2022-05: Updated MOD files to contain valid C++ and be compatible with the upcoming versions 8.2 and 9.0 of NEURON. + +--- + +2025-06-02: Converted README to Markdown. \ No newline at end of file diff --git a/readme.txt b/readme.txt deleted file mode 100644 index 0e30a07..0000000 --- a/readme.txt +++ /dev/null @@ -1,66 +0,0 @@ -ENCODING AND RETRIEVAL IN A MODEL OF THE HIPPOCAMPAL CA1 MICROCIRCUIT ---------------------------------------------------------------------- - -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. -********************************** - -Changelog ---------- -2022-05: Updated MOD files to contain valid C++ and be compatible with - the upcoming versions 8.2 and 9.0 of NEURON. From ab7deb2699f9b7499b0b0325d55e9d0e89462242 Mon Sep 17 00:00:00 2001 From: rsakai Date: Mon, 2 Jun 2025 17:55:34 -0400 Subject: [PATCH 2/2] Update README.md --- README.md | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index c32e73e..80bfc4a 100644 --- a/README.md +++ b/README.md @@ -16,15 +16,12 @@ These files are configured to produce the results presented in figures 9 and 10 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****************** +## 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. -********************************** Changelog --------- 2022-05: Updated MOD files to contain valid C++ and be compatible with the upcoming versions 8.2 and 9.0 of NEURON. ---- - -2025-06-02: Converted README to Markdown. \ No newline at end of file +2025-06-02: Converted README to Markdown.