Clean up README

openworm · Aug 24, 2014 · 05d8611 · 05d8611
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diff --git a/README.md b/README.md
@@ -30,13 +30,13 @@ In addition to bionet, see the CElegans/Readme.txt for related projects
 that are specific to C. elegans.
 
 ##Required packages:
-
+```
 1. UNIX: the gcc compiler, make command, and the bash shell.
 2. Windows: Microsoft Visual C++ 2012 (or later) IDE.
 3. Pthreads.
-
+```
 ##Optional packages:
-
+```
 1. Fourier Transform undulation behavior evaluation:
    FFTW3 Fourier Transform package: www.fftw.org
 2. NEURON simulator evaluation:
@@ -64,15 +64,15 @@ that are specific to C. elegans.
 	  Stimuli:
 	  <neuron name>
 	  ...
-
+```
 ###To build:
-
+```
 UNIX: 
 1. 'make'
 2. For Fourier Transform undulation behavior evaluation: 'make fft_undulation_eval'
 
 Windows: use VC++ solution and project files.
-
+```
 ###Commands:
 
 **Create network:**

diff --git a/sim/Readme.txt → sim/neuron/Readme.txt b/sim/Readme.txt → sim/neuron/Readme.txt
diff --git a/sim/model/Acetylcholine.mod → sim/neuron/model/Acetylcholine.mod b/sim/model/Acetylcholine.mod → sim/neuron/model/Acetylcholine.mod
diff --git a/sim/model/CElegans.hoc → sim/neuron/model/CElegans.hoc b/sim/model/CElegans.hoc → sim/neuron/model/CElegans.hoc
diff --git a/sim/model/CellPositions.dat → sim/neuron/model/CellPositions.dat b/sim/model/CellPositions.dat → sim/neuron/model/CellPositions.dat
diff --git a/sim/model/CurrentClampVariable.mod → sim/neuron/model/CurrentClampVariable.mod b/sim/model/CurrentClampVariable.mod → sim/neuron/model/CurrentClampVariable.mod
diff --git a/sim/model/ElectricalInputs.dat → sim/neuron/model/ElectricalInputs.dat b/sim/model/ElectricalInputs.dat → sim/neuron/model/ElectricalInputs.dat
diff --git a/sim/model/Generic_GJ.mod → sim/neuron/model/Generic_GJ.mod b/sim/model/Generic_GJ.mod → sim/neuron/model/Generic_GJ.mod
diff --git a/sim/model/Glutamate.mod → sim/neuron/model/Glutamate.mod b/sim/model/Glutamate.mod → sim/neuron/model/Glutamate.mod
diff --git a/sim/model/I1L.hoc → sim/neuron/model/I1L.hoc b/sim/model/I1L.hoc → sim/neuron/model/I1L.hoc
diff --git a/sim/model/I1R.hoc → sim/neuron/model/I1R.hoc b/sim/model/I1R.hoc → sim/neuron/model/I1R.hoc
diff --git a/sim/model/I2L.hoc → sim/neuron/model/I2L.hoc b/sim/model/I2L.hoc → sim/neuron/model/I2L.hoc
diff --git a/sim/model/I2R.hoc → sim/neuron/model/I2R.hoc b/sim/model/I2R.hoc → sim/neuron/model/I2R.hoc
diff --git a/sim/model/I3.hoc → sim/neuron/model/I3.hoc b/sim/model/I3.hoc → sim/neuron/model/I3.hoc
diff --git a/sim/model/I4.hoc → sim/neuron/model/I4.hoc b/sim/model/I4.hoc → sim/neuron/model/I4.hoc
diff --git a/sim/model/I5.hoc → sim/neuron/model/I5.hoc b/sim/model/I5.hoc → sim/neuron/model/I5.hoc
diff --git a/sim/model/I6.hoc → sim/neuron/model/I6.hoc b/sim/model/I6.hoc → sim/neuron/model/I6.hoc
diff --git a/sim/model/LeakConductance.mod → sim/neuron/model/LeakConductance.mod b/sim/model/LeakConductance.mod → sim/neuron/model/LeakConductance.mod
diff --git a/sim/model/M1.hoc → sim/neuron/model/M1.hoc b/sim/model/M1.hoc → sim/neuron/model/M1.hoc
diff --git a/sim/model/M2L.hoc → sim/neuron/model/M2L.hoc b/sim/model/M2L.hoc → sim/neuron/model/M2L.hoc
diff --git a/sim/model/M2R.hoc → sim/neuron/model/M2R.hoc b/sim/model/M2R.hoc → sim/neuron/model/M2R.hoc
diff --git a/sim/model/M3L.hoc → sim/neuron/model/M3L.hoc b/sim/model/M3L.hoc → sim/neuron/model/M3L.hoc
diff --git a/sim/model/M3R.hoc → sim/neuron/model/M3R.hoc b/sim/model/M3R.hoc → sim/neuron/model/M3R.hoc
diff --git a/sim/model/M4.hoc → sim/neuron/model/M4.hoc b/sim/model/M4.hoc → sim/neuron/model/M4.hoc
diff --git a/sim/model/M5.hoc → sim/neuron/model/M5.hoc b/sim/model/M5.hoc → sim/neuron/model/M5.hoc
diff --git a/sim/model/MCL.hoc → sim/neuron/model/MCL.hoc b/sim/model/MCL.hoc → sim/neuron/model/MCL.hoc
diff --git a/sim/model/MCR.hoc → sim/neuron/model/MCR.hoc b/sim/model/MCR.hoc → sim/neuron/model/MCR.hoc
diff --git a/sim/model/MI.hoc → sim/neuron/model/MI.hoc b/sim/model/MI.hoc → sim/neuron/model/MI.hoc
diff --git a/sim/model/NSML.hoc → sim/neuron/model/NSML.hoc b/sim/model/NSML.hoc → sim/neuron/model/NSML.hoc
diff --git a/sim/model/NSMR.hoc → sim/neuron/model/NSMR.hoc b/sim/model/NSMR.hoc → sim/neuron/model/NSMR.hoc
diff --git a/sim/model/NetworkConnections.dat → sim/neuron/model/NetworkConnections.dat b/sim/model/NetworkConnections.dat → sim/neuron/model/NetworkConnections.dat
diff --git a/sim/model/Serotonin_Glutamate.mod → sim/neuron/model/Serotonin_Glutamate.mod b/sim/model/Serotonin_Glutamate.mod → sim/neuron/model/Serotonin_Glutamate.mod
diff --git a/sim/model/cellCheck.hoc → sim/neuron/model/cellCheck.hoc b/sim/model/cellCheck.hoc → sim/neuron/model/cellCheck.hoc
diff --git a/sim/model/nCtools.hoc → sim/neuron/model/nCtools.hoc b/sim/model/nCtools.hoc → sim/neuron/model/nCtools.hoc
diff --git a/sim/model/nrnmech.dll → sim/neuron/model/nrnmech.dll b/sim/model/nrnmech.dll → sim/neuron/model/nrnmech.dll
diff --git a/sim/model/simulation.props → sim/neuron/model/simulation.props b/sim/model/simulation.props → sim/neuron/model/simulation.props
diff --git a/sim/model/simulator.props → sim/neuron/model/simulator.props b/sim/model/simulator.props → sim/neuron/model/simulator.props