Reformatted several parts; added reference to ModelDB

Readme.md

@@ -1,73 +1,107 @@
-This repository contains the code used for the following manuscript:
-
-
-Kumaraswamy, A., Maksutov, A., Kai, K., Ai, H., Ikeno, H., & Wachtler, T. (2017). Network simulations of interneuron circuits in the honeybee primary auditory center. *bioRxiv*. https://doi.org/10.1101/159533
-
-Authors:
-Ajayrama Kumaraswamy, ajkumaraswamy@tutamail.com
-Based on and contains parts of work by Aynur Maksutov during AMGEN program 2016 at Wachtlerlab, LMU.
-
-Installation:
-
-With anaconda (recommended):
-
-    1. conda create --name Ai2017Sim -c brian-team ipython>=6.1 numpy>=1.11.2 matplotlib>=1.5.3 seaborn>=0.7.1 brian2>=2.0.1 python>=3.5
-    2. source activate Ai2017Sim (unix) or activate Ai2017Sim (windows)
-    3. pip install <full path of this repository>
-
-without anaconda, normal python installation required (https://www.python.org/)
-
-    1. Install virtualenvwrapper (unix) or virtualenvwrapper-win (windows) be pre-installed with pip
-    2. (only on windows) Install microsoft Visual C++ 14.0. Get it with "Microsoft Visual C++ Build Tools": http://landinghub.visualstudio.com/visual-cpp-build-tools
-    3. mkvirtualenv Ai2017Sim
-    4. pip install <full path of this repository>
-
-Usage:
-    1. source activate Ai2017Sim (unix) or activate Ai2017Sim (windows)
-    2. Change the variable homeFolder in dirDefs.py to a folder. The results of the simulation will be stored here.
-    3. The scripts of this repo are described below. All of them have some parameters at their top. Change these and run the scripts as needed.
-
-
-Here is an overview of the contents:
-
-.  
-+-- Ai2017Sim.yml: A file that can be used to create a conda environment to run the scripts below. Essentially is a list of dependencies.
-+-- models
-|   +-- neuronModels.py: wrapper classes for brian2 neuron models
-|   +-- neurons.py: Model equations and static parameters for neurons  
-|   +-- synapses.py: Model equations for synapses  
-|  
-+-- paramLists  
-|   +-- AdExpPars.py: Parameter combinations for the AdExp model  
-|   +-- inputParsList.py: Stimulii definitions  
-|   +-- synapsePropsList.py: Parameter combinations for the difference of exponential synaptic conductance model  
-|  
-+-- brianUtils.py: utility function related to brian2  
-|  
-+-- dirDefs.py: directory definitions imported in other scripts  
-|  
-+-- DLInt1SynCurrent.py: Script to simulate DL-Int-1 recording membrane potential and synaptic currents in [NIX](https://github.com/G-Node/nixpy) files  
-|  
-+-- DLInt2try.py: Legacy code  
-|  
-+-- forAi2017.py: Script to generate a subplot of an upcoming manuscript.  
-|  
-+-- JODLInt1DLInt2: Class to run network simulations  
-|  
-+-- justDLInt1.py: Legacy code  
-|  
-+-- mplPars.py: matplotlib rc parameters  
-|  
-+-- neoNIXIO.py: adapted from GJEMS, utility functions to work jointly with [NIX](https://github.com/G-Node/nixpy) and [neo](https://github.com/NeuralEnsemble/python-neo).  
-|  
-+-- plotDLInt1DLInt2SynEffects.py: script to plot summary of DL-Int-1 and DL-Int-2 responses to pulse trains.  
-|  
-+-- plotShortStims.py: script to plot summary of DL-Int-1 and DL-Int-2 responses to short continuous pulses.  
-|  
-+-- plotSynCurrents.py: script to plot membrane potential and synaptic currents of DL-Int-1 and DL-Int-2 for one stimulus.  
-|  
-+-- runJODLInt1DLInt2Multiple.py: script to simulate the network for multiple stimulii. Out is saved as a [NIX](https://github.com/G-Node/nixpy) File.  
-|  
-+-- simSynCurrents.py: script to simulate DL-Int-1 and DL-Int-2 recording membrane potential and synaptics currents in a [NIX](https://github.com/G-Node/nixpy) file.  
+# Description
 
+This repository contains the code to simulate a neuronal network in the honeybee primary auditory center.
+
+Author:
+Ajayrama Kumaraswamy, ajayramak@bio.lmu.de
+
+Reference:
+>Kumaraswamy, A., Maksutov, A., Kai, K., Ai, H., Ikeno, H., & Wachtler, T. (2017). Network simulations of interneuron circuits in the honeybee primary auditory center. *bioRxiv*. https://doi.org/10.1101/159533
+
+This model has been added to ModelDB ([Accession number 239413](https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=239413#tabs-1))
+
+This repo contains parts of the code written by Aynur Maksutov during AMGEN program 2016 at Wachtlerlab, LMU, Munich.
+
+ 
+# Installation
+## With anaconda (recommended):
+
+Step 1: Download the repository
+ 
+
+Step 2: Create a new virtual environment and install some dependencies
+
+`conda create --name Ai2017Sim -c brian-team ipython>=6.1 numpy>=1.11.2 matplotlib>=1.5.3 seaborn>=0.7.1 brian2>=2.0.1 python>=3.5`
+
+Step 3: Activate the virtual environment
+
+`source activate Ai2017Sim` (unix) or `activate Ai2017Sim` (windows)
+
+
+Step 4: Install the package (the option '-e' is required)
+
+`pip install -e <full path of this repository>`
+
+
+## Without anaconda (normal python installation required, https://www.python.org/)
+
+Step 1: Download the repository 
+
+Step 2: Install virtualenvwrapper (unix) or virtualenvwrapper-win (windows) with pip
+
+Step 3: (only on windows) Install microsoft Visual C++ 14.0. Get it with "Microsoft Visual C++ Build Tools" [here](http://landinghub.visualstudio.com/visual-cpp-build-tools)
+
+Step 4: Create virtual environment
+
+`mkvirtualenv Ai2017Sim`
+
+
+Step 5: Install the package (the option '-e' is required)
+
+`pip install -e <full path of this repository>`
+
+# Usage:
+Step 1: Activate the virtual environment
+
+`source activate Ai2017Sim` (unix) or `activate Ai2017Sim` (windows)
+
+Step 2: Change the variable 'homeFolder' in the file 'dirDefs.py' to a folder of your choice. The results of the simulation will be stored here.
+
+Step 3: The scripts of this repository are described below. All of them have some parameters at their top. Change these and run the scripts as needed.
+
+
+# Overview of Contents
+
+* **HB-PAC_disinhibitory_network** 
+  * **Ai2017Sim.yml:** A file that can be used to create a conda environment to run the scripts below. Essentially is a list of dependencies.
+  
+  * **models**
+   
+     * **neuronModels.py:** wrapper classes for brian2 neuron models
+     * **neurons.py:** Model equations and static parameters for neurons  
+     * **synapses.py:** Model equations for synapses  
+  
+  * **paramLists**  
+    
+     * **AdExpPars.py:** Parameter combinations for the AdExp model  
+     * **inputParsList.py:** Stimulii definitions  
+     * **synapsePropsList.py:** Parameter combinations for the difference of exponential synaptic conductance model  
+     
+  * **brianUtils.py:** utility functions related to brian2  
+  
+  * **dirDefs.py:** directory definitions imported in other scripts  
+  
+  * **DLInt1SynCurrent.py:** Script to simulate DL-Int-1 recording membrane potential and synaptic currents in [NIX](https://github.com/G-Node/nixpy) files    
+  
+  * **DLInt2try.py:** Legacy code  
+  
+  * **forAi2017.py:** Script to generate a subplot of an upcoming manuscript.  
+  
+  * **JODLInt1DLInt2:** Class to run network simulations  
+  
+  * **justDLInt1.py:** Legacy code  
+  
+  * **mplPars.py:** matplotlib rc parameters  
+  
+  * **neoNIXIO.py:** adapted from [GJEphys](https://github.com/wachtlerlab/GJEphys), utility functions to work jointly with [NIX](https://github.com/G-Node/nixpy) and [neo](https://github.com/NeuralEnsemble/python-neo).  
+  
+  * **plotDLInt1DLInt2SynEffects.py:** script to plot summary of DL-Int-1 and DL-Int-2 responses to pulse trains.  
+  
+  * **plotShortStims.py:** script to plot summary of DL-Int-1 and DL-Int-2 responses to short continuous pulses.  
+  
+  * **plotSynCurrents.py:** script to plot membrane potential and synaptic currents of DL-Int-1 and DL-Int-2 for one stimulus.  
+  
+  * **runJODLInt1DLInt2Multiple.py:** script to simulate the network for multiple stimulii. Output is saved as a [NIX](https://github.com/G-Node/nixpy) File.  
+  
+  * **simSynCurrents.py:** script to simulate DL-Int-1 and DL-Int-2 recording membrane potential and synaptics currents in a [NIX](https://github.com/G-Node/nixpy) file.