Standardized README to Markdown format

README.md

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+# Instructions
+
+1. Copy all the folders in your computer.
+
+2. Compile the mechanisms (in folder `../mechanism`) with command  
+   `nrnivmodl` (model is currently linux/unix only)
+
+3. This step is necessary only if some mechanism is changed by the user. In this version, the neurons are tuned with the current mechanisms. (Gómez et al, *Front Comput Neurosci* 2011)
+
+   For tuning the neuron:  
+   a) Select the cell that you want to tune in file  
+   `../experiment/tune-synapses/Simulation_gradient.hoc` in the variable `ID_cell=1,2...` (1=n123, 2=n125, 3=n128, 4=n129, 5=n130)  
+   b) Execute the tuning (`../experiment/tune-synapses/sh run_simulation_gradient`) and copy output file in  
+   `../junio/tuned-nXXX-trunk/`
+
+4. Run simulation:
+
+   a) Select the cell that you want to study in file  
+   `proximalCA1_1.hoc` in the variable `ID_cell=1,2...` (1=n123, 2=n125, 3=n128, 4=n129, 5=n130)  
+   b) Select the Parameters inside  
+   `../experiment/junio/ParameterFile.hoc`  
+   c) Design the protocols inside  
+   `../experiment/junio/ProtocolsFile.hoc`  
+   d) Execute `../experiment/junio/sh run_ProtocolsFile.hoc`
+
+---
+
+Gómez González JF, Mel BW, Poirazi P. Distinguishing Linear vs. Non-Linear Integration in CA1 Radial Oblique Dendrites: It's about Time. *Front Comput Neurosci*. 2011;5:44.  
+doi: 10.3389/fncom.2011.00044
+
+---
+
+2025-07-07: Converted README to Markdown.