Standardized README to Markdown format

README.md

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+# Grid cell model
+
+This archive contains a spiking continuous attractor model of grid cells found in medial entorhinal cortex (MEC) of rodents. It was used for modeling the theta-nested gamma activity and grid firing fields in MEC and the results have been published in [PASTOLL2013]_. The code in this archive reproduces parts of the figures found in the published article.
+
+For installation and prerequisites necessary to run the model see the notes below or the INSTALL.rst file in this directory.
+
+[PASTOLL2013] Pastoll, H., Solanka, L., van Rossum, M. C. W., & Nolan, M. F. (2013). Feedback inhibition enables theta-nested gamma oscillations and grid firing fields. *Neuron*, 77(1), 141–154. doi:10.1016/j.neuron.2012.11.032
+
+When the model runs as described below it produces png images:
+
+![screenshot 1](./images/job0000_dump000_firing_rate_e.png)  
+![screenshot 2](./images/job0000_dump000_firing_snapshot_i.png)  
+![screenshot 3](./images/job0000_dump000_firing_snapshot_e.png)  
+
+a datafile and some traces in pdfs (not shown).
+
+20200323 Note from the ModelDB Administrator: Ian Hawes update steps below were simplified by a adding local copy of his Dockerfile to the archive so it no longer needs to be downloaded and also including an ubuntu 18.04 docker install notes file. Please follow the install notes in ubuntu18.04_docker_install_notes.txt to install docker on an ubuntu 18.04 system. You will also need to make sure the python files in this zip archive have excutable permission by executing the following in the GridCellModel folder:
+
+```bash
+chmod -R 755 *
+# If the above command fails you may need to run it with an "sudo " in front
+# Also create an output folder
+mkdir grid_cell_model/output
+```
+
+Then following Ian's below instructions below should work (except you no longer need to download the Dockerfile).
+
+20200306 Update from Ian Hawes:  
+I have uploaded a Dockerfile here: [https://gist.github.com/4iar/bd25c175614419e2a92c591d74a8dc29](https://gist.github.com/4iar/bd25c175614419e2a92c591d74a8dc29)
+
+Example steps to get a simulation running (I ran these commands on Ubuntu with Docker installed):
+
+1. Save the Dockerfile above into the GridCellModel folder  
+2. From the GridCellModel folder, build the Docker image:  
+   `docker build . -t pastoll2013`  
+3. From the GridCellModel folder, run a simulation:  
+   `docker run -it -v ${PWD}:/code -w /code/grid_cell_model pastoll2013 ./submit_basic_grids.py`
+
+If you prefer not to use Docker, you can try copying the commands from the Dockerfile into your terminal. I tested the environment on Ubuntu 14.04, but it should work with other versions as long as you can get those python packages installed.
+
+---
+
+2025-07-09: Converted README to Markdown.