Neuronal simulations in MOOSEGUI¶
Neuronal models in various formats can be loaded and simulated in the MOOSE Graphical User Interface. The GUI displays the neurons in 3D, and allows visual selection and editing of neuronal properties. Plotting and visualization of activity proceed concurrently with the simulation. Support for creating and editing channels, morphology, and networks is planned for the future. MOOSEGUI uses SI units throughout.
Cerebellar granule cell
File -> Load -> ~/moose/moose-examples/neuroml/GranuleCell/GranuleCell.net.xml
This is a single compartment Cerebellar granule cell with a variety of channels Maex, R. and De Schutter, E., 1997 (exported from http://www.neuroconstruct.org/). Click on its soma, and See children for its list of channels. Vary the Gbar of these channels to obtain regular firing, adapting and bursty behaviour (may need to increase tau of the Ca pool).
Pyloric rhythm generator in the stomatogastric ganglion of lobster
File -> Load -> ~/moose/moose-examples/neuroml/pyloric/Generated.net.xml
File -> Load -> ~/moose/moose-examples/neuroml/PurkinjeCell/Purkinje.net.xml
This is a purely passive cell, but with extensive morphology [De Schutter, E. and Bower, J. M., 1994] (exported from http://www.neuroconstruct.org/). The channel specifications are in an obsolete ChannelML format which MOOSE does not support.
Olfactory bulb subnetwork
File -> Load -> ~/moose/moose-examples/neuroml/OlfactoryBulb/numgloms2_seed100.0_decimated.xml
This is a pruned and decimated version of a detailed network model of the Olfactory bulb [Gilra A. and Bhalla U., in preparation] without channels and synaptic connections. We hope to post the ChannelML specifications of the channels and synapses soon.
All channels cell
File -> Load -> ~/moose/moose-examples/neuroml/allChannelsCell/allChannelsCell.net.xml
This is the Cerebellar granule cell as above, but with loads of channels from various cell types (exported from http://www.neuroconstruct.org/). Play around with the channel properties to see what they do. You can also edit the ChannelML files in ~/moose/moose-examples/neuroml/allChannelsCell/cells_channels/ to experiment further.
NeuroML python scripts In directory ~/moose/moose-examples/neuroml/GranuleCell, you can run python FvsI_Granule98.py which plots firing rate vs injected current for the granule cell. Consult this python script to see how to read in a NeuroML model and to set up simulations. There are ample snippets in ~/moose/moose-examples/snippets too.