Associations between in vitro, in vivo and in silico cell classes in mouse primary visual cortex (Wei et al, 2021)

Instructions

• 1. Create a virtual environment

     $ conda create -n bmtk-ateam python=2.7 
     $ conda activate bmtk-ateam
     $ conda install pandas numpy matplotlib scikit-learn
     

• 2. Install bmtk

      $ git clone https://github.com/yinawei/bmtk.git
      $ pip install -e /Users/yinawei/Documents/Allen/bmtk-ateam
     

• 3. Install NEURON

     $ pip install neuron
     

• 4. Install ateam-tools

     $pip install -e ateam-tools
     

• 5. Compile the modifiles

     After installing bmtk, run

     $ cd examples/biophys_components/mechanisms 
     $ nrnivmodl modfiles/ # this should create a directory x86_64
     

  If you have trouble in this step, make sure you have deleted "x86_84" before compling the modfiles.

• 6. Run simulations

     In the example folder "395830185", run the simulations using the following commands:

     $ python build_network.py
     $ python run_bionet.py
     

Dependencies

• Python 2.7
• pandas
• Matplotlib
• scikit-learn
• numpy