rbm_web

This software wraps Neuron software (https://neuron.yale.edu/neuron/) and provides easy to use GUI.

features

• visualize, edit, import and export swc files in 2D.
• full simulation: from user paramets (e.g mechanism, process etc) to plots.
• brute force - search for a set of parameters by specifying the ouput plot result.
• heatmap animation.
• session management: export and import session files to manage your simulations.
• continue to work on python: looking for complex simulations and other neuron features, you can load exported seassion / plots to our python app. we also added a complexParams.py under server folder with an example of a more complex parameter settings, its for you to change!

examples

• find a section by using the tree and navigation

• edit a single section or multiple sections parameters

• simulate and view the results in a plot

• simulate and view the results in a heatmap animation

• brute force:

1. specify the output plot - using draw or import a 2d vector

2. specify the parameters, e.g: diam of axon[0] will range from 0 to 90 (can change as much you like)

3. explore the results

install

• client: install node/npm: https://nodejs.org/en/download/
• server: install python 3.7+ pip install -r requirements

Run

• client:
  • first time and on every git pull run on cmd: 'npm install' in app/ dir
  • run on cmd: 'npm start' in app/ dir
• server:
  • edit server/config.py with path to swc file and neuron folder
  • run 'python app.py' in server/ dir or use an IDE and start app.py

note: in the beta version we run locally both the client and backend so we suggest closing other application running on localhost (port 8080).