From 880c7a274685662b423ba5bfca32efc1c0b72d04 Mon Sep 17 00:00:00 2001 From: EnfxcFCb6 Date: Fri, 30 May 2025 16:40:33 -0400 Subject: [PATCH 1/2] Standardized README to Markdown format --- README.md | 34 ++++++++++++++++++++++++++++++++++ readme.txt | 48 ------------------------------------------------ 2 files changed, 34 insertions(+), 48 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..0b4bec8 --- /dev/null +++ b/README.md @@ -0,0 +1,34 @@ +# This is the model associated with the paper + +Anderson WS, Kudela P, Cho J, Bergey GK, Franaszczuk PJ (2007) Studies of stimulus parameters for seizure disruption using neural network simulations. *Biol Cybern* 97:173-94 + +To use first type make in the HopkinsModel directory. + +Currently I'm (Stan Anderson) running it on a 32-bit 16-node cluster, also running an older Redhat version. I've been compiling it on a 64-bit machine, but in 32-bit mode, the 64-bit machine is running a newer Suse version. + +## As far as the individual c-codes: + +- **mknode.c** is the code that sets up the intracolumnar connections and produces a synapse table that is passed to each node. + +- **mklink.c** is the code that sets up the extracolumnar connections, which produces an unsorted link table that undergoes further manipulations. This code also calculates which neurons in the simulation will undergo action potentials during a stimulation pulse. + +- **sublink.c** assigns the previously computed extracolumnar links to specific neurons, and strips away intranodal links, turning that information into synaptic structures as created in mknode.c. Extranodal links (i.e. computer to computer) are maintained as link structures. + +- **link_sort.c** sorts the link structures into an order more easily read by the simulation code. + +- **crl.c** actually writes the link information into a file of link structures that is passed to each node. + +- **netclustwacnmdadiff.c** is the main simulation code running on each node with the integration loop, and accounting of synaptic currents. + +- **clust_cn.c** handles communication via nodes via packet protocols (very slow in this setting) + +- The **lnet.h** and **clust_cn.h** files are the most important header files, and most variables can be found here. + +- **mkpar.c** enables the user to fill the parameter tables for each cell class in terms of individual channel kinetic properties. + +Version: 20111007 +This version contains changes in the sublink.c file. + +--- + +2025-05-30: Standardized to Markdown \ No newline at end of file diff --git a/readme.txt b/readme.txt deleted file mode 100644 index e0e7189..0000000 --- a/readme.txt +++ /dev/null @@ -1,48 +0,0 @@ -This is the model associated with the paper - -Anderson WS, Kudela P, Cho J, Bergey GK, Franaszczuk PJ (2007) Studies -of stimulus parameters for seizure disruption using neural network -simulations. Biol Cybern 97:173-94 - -To use first type make in the HopkinsModel directory. - -Currently I'm (Stan Anderson) running it on a 32-bit 16-node cluster, -also running an older Redhat version. I've been compiling it on a -64-bit machine, but in 32-bit mode, the 64-bit machine is running a -newer Suse version. - -As far as the individual c-codes: - -mknode.c is the code that sets up the intracolumnar connections and -produces a synapse table that is passed to each node. - -mklink.c is the code that sets up the extracolumnar connections, which -produces an unsorted link table that undergoes further -manipulations. This code also calculates which neurons in the -simulation will undergo action potentials during a stimulation pulse. - -sublink.c assigns the previously computed extracolumnar links to -specific neurons, and strips away intranodal links, turning that -information into synaptic structures as created in -mknode.c. Extranodal links (i.e. computer to computer) or maintained -as link structures. - -link_sort.c sorts the link structures into an order more easily read -by the simulation code. - -crl.c actually writes the link information into a file of link -structures that is passed to each node. - -netclustwacnmdadiff.c is the main simulation code running on each node -with the integration loop, and accounting of synaptic currents. - -clust_cn.c - handles communication via nodes via packet protocols -(very slow in this setting) - -the lnet.h and clust_cn.h files are the most important header files, -and most variables can be found here. - -mkpar.c enables the user to fill the parameter tables for each cell -class in terms of individual channel kinetic properties. - -Version: 20111007 This version contains changes in the sublink.c file. From 63210897af4f9fd6da7b649c532c9cdeeb1d3831 Mon Sep 17 00:00:00 2001 From: rsakai Date: Fri, 30 May 2025 17:13:39 -0400 Subject: [PATCH 2/2] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 0b4bec8..961e00f 100644 --- a/README.md +++ b/README.md @@ -26,9 +26,9 @@ Currently I'm (Stan Anderson) running it on a 32-bit 16-node cluster, also runni - **mkpar.c** enables the user to fill the parameter tables for each cell class in terms of individual channel kinetic properties. +--- Version: 20111007 This version contains changes in the sublink.c file. ---- - -2025-05-30: Standardized to Markdown \ No newline at end of file +20250530 +Standardized to Markdown.