# README for Extended Axon Modeling Project Author: Brandon Thio ModelDB entry originally from: 12/10/2020 Updated 2024-01-24 with fixes from Pelot: - mechanism name fix in cFiberBuilder - Ra changed from 35.5 to 35.4 ohm-cm - kiinf value # Overview This file contains a description of the file structure of the code. Note that the mod files containing the ion channel mechanisms must be compiled using mknrndll after migrating the files to a different machine or after making any edits. The resulting dll file must be stored in the directory in which the hoc files are stored. **Note the file structure is for organizational purposes**, and all the `.m`, `.hoc`, `.dll`, and `.csv` files need to be in the same directory to run properly. All mechanisms for the Sundt et al. 2015, Tigerholm et al. 2014, Rattay and Aberham 1993, and Schild et al 1994/97 are located in the `Mod` folder. # Simulations There are three HOC files which complete different simulation tasks. These are: - `CV.hoc` - runs conduction velocity test - `SD.hoc` - runs strength duration task - `PairPulseTrue.hoc` - runs recovery cycle task All simulation tasks call `cFiberBuilder.hoc` and if using the tigerholm fiber, `balanceTigerholm.hoc` will be called. ## cFiberBuilder.hoc `cFiberBuilder.hoc` creates a c-fiber model and takes in parameters associated with the fiber diameter, length, model type, temperature, segment density, and, if the fiber is a Schild fiber, a pair of flags for using Schild 94 or 97 parameters model type 1: Sundt 2015 2: Tigerholm 2014 3: Rattay and Aberham 1993 4: Schild 1997 5: Schild 1994 Instantiation of the fiber can be seen in any of the simulation task hoc files. # Matlab Scripts There is code to Batch the neuron code from matlab. Batch.m is the general format of the files. These files use `call_neuron_MATLAB.m` to interface with your machine's version of NEURON and run `.hoc` scripts. `Master.m` runs all the different simulation tasks serially.