This is an in-progress conversion of the Calabrese Lab 8-cell Leech Tutorial that is described in paper by Hill et al 2001 from the Genesis simulator language to a NeuroML model description language format. The original Genesis scripts can be found in the genesis-scripts folder. The current version of the NeuroML v2 leech tutorial files can be found under the NeuroML2 folder. The current NeuroML model can be exported to the Neuron simulator language and simulated.

The model can be run directly in jNeuroML simulator v0.8.3 using one of the LEMS model defitinion files at the base directory:

jnml run_4cells_Vm.xml

This will load the model files under NeuroML2 and produce the graphs defined in the LEMS .xml files. See other LEMS files for different run scenarios.

LEMS files that define the model and network can be converted to Neuron HOC/Python format using:

jnml run_4cells_Vm.xml -neuron -outputdir Exports/Neuron-8cell/

Then, you would need to navigate to the output folder Exports/Neuron-8cell/, and compile the MOD files for Neuron (only once after conversion):

cd Exports/Neuron-8cell/
nrnivmodl

You can make multiple exports with different LEMS files. Just make sure to use different export folders.

Navigate to the desired exports folder and run Neuron (requires Python version):

nrngui -python run_4cells_Vm_nrn.py

Some discrepancies between neuron models exist, which may require fine tuning ion channels:

• Verified that ionic current profiles match with original Genesis model
• Verify individual, isolated cell activity. In particular, Cell 3/4 are not behaving correctly.
• Verify network activity
• Slow synapses (SynS) that include membrane voltage modulation are not implemented because they require custom NeuroML components.

• Boima Reuben Massaquoi, <reubmann AT gmail.com> - Functional NeuroML version, synapses
• John Rose - Initial NeuroML code with ion channels
• Cengiz Gunay, cengique @ GitHub, <cengique AT users.sf.net>, <cgunay AT ggc.edu> - Project lead and technical support, some bugfixes, and documentation
• Ron Calabrese - Principal investigator and one of original Leech Tutorial authors
• Special thanks to Padraig Gleeson for help with NeuroML, recommendations, and fixing several bugs; and to Ankur Singha for help with documentation and NeuroFedora; and the International Neuroinformatics Coordinating Facility (INCF) organization for hosting our project.

• Participating in the 2021 Google Summer of Code (GSoC) with project Re-creating the Leech Heartbeat Network Model Tutorial using the Neuron Simulator in Python and NeuroML under the International Neuroinformatics Coordinating Facility (INCF) organization.
• Collaborate with OpenSourceBrain