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Standardized README to Markdown format #1

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33 changes: 21 additions & 12 deletions readme.html → README.md
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<html><pre>
This is the readme for the code for the paper:

London M, Roth A, Beeren L, Hausser M, Latham PE (2010) Sensitivity to
perturbations in vivo implies high noise and suggests rate coding in
cortex. Nature 466:123-7
London M, Roth A, Beeren L, Hausser M, Latham PE (2010) Sensitivity to
perturbations in vivo implies high noise and suggests rate coding in
cortex. *Nature* 466:123-7

The network code was supplied by Peter Latham and updated by Tom Morse
for compiling in a modern linux (tested with g++ 4.4.3) by simply
typing "make". You can follow built-in help by running the executable
The network code was supplied by Peter Latham and updated by Tom Morse
for compiling in a modern linux (tested with g++ 4.4.3) by simply
typing "make". You can follow built-in help by running the executable
./theta1d without any arguments.

To run you can create a sample input file by typing:

```
./theta1d -s > sample_inputfile.txt
```

You can then edit sample_inputfile.txt as desired and then type

```
./theta1d sample_inputfile.txt
```

to run the model. The provided sample takes 10 seconds to run and
to run the model. The provided sample takes 10 seconds to run and
should produce graphs such as under matlab/octave commands:

For population averaged rate for excitatory (blue) and inhibitory
For population averaged rate for excitatory (blue) and inhibitory
cells (red):

```matlab
load arate;
figure
plot(arate(:,1),arate(:,2))
hold on
plot(arate(:,1),arate(:,3),'r')
```

<img src="screenshot.png" alt="screenshot">
![screenshot](screenshot.png)

For the last second of voltage activity of a selected neuron:

```matlab
load v;
figure
plot(v(9000:10000,1),v(9000:10000,2))
```

<img src="screenshot_v.png" alt="screenshot_v">
![screenshot_v](screenshot_v.png)

</pre></html>
---

2025-07-07: Converted README to Markdown.