Create NEURON AMI on top of Easy Deployment AMI

openworm / OpenWorm

Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues

http://openworm.org

MIT License

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Create NEURON AMI on top of Easy Deployment AMI #56

Closed slarson closed 11 years ago

slarson commented 11 years ago

On top of the Easy Deployment AMI, install the NEURON simulation engine.

Requirements:

Has NEURON installed and tested -- Installation instructions are available online
The tricky part: Making sure the NEURON GUI will work on the cloud instance.
Launches NEURON and everything else needed automatically upon bootup
Has documentation for how to startup the instance, log into the instance, load the OpenWorm spatial connectome in NEURON, and play around with running the model.
Is saved as a public AMI instance

vellamike commented 11 years ago

Why not just install NEURON without the GUI? I don't think it's used any more. I believe the switch when you config is "--without iv"

slarson commented 11 years ago

Because I think it is valuable to be able to visualize the output on the morphologies. Also valuable to see the graphs plotted in real time interactively. How would you propose visualizing the output without the GUI?

vellamike commented 11 years ago

If that is the functionality that you are thinking of then Neuronvisiohttp://michelemattioni.me/neuronvisio/by Michele Mattioni and Uri Cohen (copied) has many advantages over using the NEURON GUI. The main one is that it is much easier to install, use and I suspect also easier to forward over X. Michele also gives great support.

On 7 February 2013 16:35, Stephen Larson notifications@github.com wrote:

Because I think it is valuable to be able to visualize the output on the morphologies. Also valuable to see the graphs plotted in real time interactively. How would you propose visualizing the output without the GUI?

— Reply to this email directly or view it on GitHubhttps://github.com/openworm/OpenWorm/issues/56#issuecomment-13244344.

slarson commented 11 years ago

Good suggestion. I have tried this before. Do you know if it would be able to handle 300 multi-compartmental neurons at the same time? Last time I tried I think it was mainly set up for just one.

vellamike commented 11 years ago

I think that won't matter. Michele uses huge number of compartments afaik On Feb 7, 2013 6:03 PM, "Stephen Larson" notifications@github.com wrote:

Good suggestion. I have tried this before. Do you know if it would be able to handle 300 multi-compartmental neurons at the same time? Last time I tried I think it was mainly set up for just one.

— Reply to this email directly or view it on GitHubhttps://github.com/openworm/OpenWorm/issues/56#issuecomment-13250699.

slarson commented 11 years ago

New instructions on how to run the connectome obviates the need for this: https://github.com/openworm/OpenWorm/wiki/FAQ#how-do-i-run-the-neuroml-connectome