Standardize readme

README.md

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+This simulation was used in the following article:
+
+Eguchi A, Neymotin SA, Stringer SM. (2014)  
+Color opponent receptive fields self-organize in a biophysical model 
+of visual cortex via spike-timing dependent plasticity. 
+*Front. Neural Circuits* 8:16. doi: 10.3389/fncir.2014.00016
+
+For questions email: akihiro dot eguchi at psy dot ox dot ac dot uk
+
+This simulation was tested/developed on LINUX systems, but may run on 
+Microsoft Windows or Mac OS.
+
+To run, you will need the NEURON simulator (available at 
+[http://www.neuron.yale.edu](http://www.neuron.yale.edu)) compiled with python enabled. To draw the 
+output you will need to have Matplotlib installed ([http://matplotlib.org/](http://matplotlib.org/)).
+
+### Instructions:
+
+- Unzip the contents of the zip file to a new directory.
+
+- Compile the mod files from the command line with:
+
+  ```
+  nrnivmodl *.mod
+  ```
+
+The `nrnivmodl` command will produce an architecture-dependent folder 
+with a script called `special`. On 64 bit systems the folder is 
+`x86_64`. To run the simulation from the command line use:
+
+```
+python runMe.py
+```
+
+Various parameters used in the simulation are set in the python codes. 
+State of the networks are exported and saved every n iterations as 
+`Network_` + `str(itr)` + `.obj` format so that various analysis can be 
+applied to the network with specific point during the training using 
+`runMe2.py` script.
+
+---
+
+2025-07-09: Converted README to Markdown.