GSoC 2021 Project Idea 23.1: Re-creating the Leech Heartbeat Network Model Tutorial using the Neuron Simulator in Python and NeuroML

The Calabrese Lab 8-cell Leech Tutorial that is described by Hill et al 2001 has been a staple for teaching computational neuroscience at Emory University for many years, and it has also been used in various summer courses. This tutorial is not only a fully constructed 8-cell circuit that can generate heart rhythms, but also a great teaching tool thanks to the visual interface where a student can turn on synaptic connections or change maximal ionic conductances. However, the original tutorial has been developed using the now obsolete Genesis simulator. Unfortunately, running the Genesis simulator nowadays requires complicated software set up that prevents many non-technical students from accessing the tutorial. We had previously started porting the tutorial to a more modern format that can be executed through a web browser (see 8-cell Leech Heartbeat Network Model Tutorial), increasing the accessibility of this classic tutorial for teaching and research purposes. At this summer’s GSoC, we would like to finish this port and make the tutorial available. We selected the Neuron simulator language for running the model using NeuroML and Python as the description languages.

Skills: Neuron simulator, Python, NeuroML
Lead Mentor: Cengiz Gunay @cengique (cgunay@ggc.edu)
Backup Mentor: Padraig Gleeson @pgleeson (p.gleeson@ucl.ac.uk)

Tags: computational neuroscience, NeuroML, Python, NEURON

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HI there, I read through the project definition and I am quite interested in it. I have experience in python and some experience with NeuroML, and I have to admit, I don’t have much knowledge about Nueron Simulator, but I have work on other simulation and rendering projects in the past in python/c++.
I would love to hear back from you, and maybe if you have any documentation for this project or any resources to help me out with Neuron Simulator. Hoping to hear back from you soon

Regards
Veer Shah

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Hi Veer,

Thank you for responding and showing interest! You seem to have an adequate background for the project. Can you share some of your previous work if they are public?

If you follow the Github link above and the Neuron simulator documentation, you can find some initial resources. Let me know if you have more questions.

Cengiz

hey @cengique .
Unfortunately, I don’t have any public projects related to the field, but is there any github issue or any mini coding problem I can try out.

Regards
Veer Shah

Unfortunately, we don’t have any clear issues laid out yet. We want to create a tutorial on Open Source Brain following the method describe in this paper (Fig 5). An example can be seen in the Pyramidal Cell Tutorial on OSB. (Also see the how-to for creating tutorials)

Hello Cengiz,

I am interested in this project because I enjoy the idea of helping make a useful tutorial accessible again and getting the opportunity to learn more about computational neuroscience. I have 2 years of experience in computational neuroscience research and understand the basics of neuroscience. Additionally, I have worked with NEURON via Python and made a tutorial to help students set the program up so they could access and interact with neuron models. I look forward to hearing back from you.

Thanks,

Charles Sugatapala

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hey @cengique
should I try creating the whole thing as described or should I just make a snippet ?

Regards
Veer Shah

Hello all!

I never got a chance to introduce myself, so my name is Elijah Noisin (A.K.A Psyogi Soma). I’ve recently graduated from Georgia Gwinnett College with a B.S. in Psychology-cognitive neuroscience! Here at GSoC I’m am working on updating an old Genesis tutorial for a leech heart to NeuroML. In the first week of GSoC I familiarmarized myself with NeuroML, Genesis, and the relevant information regarding the leech heart model. Last week, Dr. Gunay, my mentor, and I setup a virtual machine and RDP, so that I can access resources and work from home. We also ran both Genesis and NeuroML to find any discrepancies in the current NueroML model. This week, I analyzed the, neuron, channel graphs and pushed several files to: Leech-8Cell-Tutorial-NeuroML/README.md at master · RonCalabreseLab/Leech-8Cell-Tutorial-NeuroML · GitHub. I have gone through all the channels and haven’t found a discrepancy, yet.

Cheers,
Elijah Noisin

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