NeuroVM

Discussions about SimAgent, a tool for submitting jobs directly to NSG from your local computer

Moderator: tyler

Post Reply
tyler
Posts: 5
Joined: Mon May 06, 2019 8:55 pm

NeuroVM

Post by tyler » Wed Jul 31, 2019 2:05 pm

All,

I'd like to introduce NeuroVM - a pre-built Ubuntu-based virtual appliance with all the tools you need to conduct large scale computational neuroscience simulations (with Neuron primarily in mind). Developed by the Neural Engineering Lab at the University of Missouri, NeuroVM has saved hours of troubleshooting Neuron/Python installation issues on student machines. Simply download the VM and run it in VirtualBox. Drag and drop your model onto the virtual desktop and you're ready to go!

Download and instructions here: https://cyneuro.github.io/research/tools/neurovm/

Software provided:
Neuron 7.5 (with IV and MPI) - ​https://www.neuron.yale.edu/neuron/
Anaconda 3 - ​https://www.anaconda.com/distribution/
Jupyter Notebooks - https://jupyter.org/
Nest - ​http://www.nest-simulator.org/
BMTK - ​https://github.com/Alleninstitute/bmtk
SimAgent - ​https://tylerbanks.net/SimAgentMPI/
BMTools - ​https://github.com/tjbanks/bmtools
VSCode - ​https://code.visualstudio.com/

If you have suggestions on ways to improve NeuroVM let me know!

Tyler

camilhamdane
Posts: 8
Joined: Mon Aug 05, 2019 7:37 am

Re: NeuroVM

Post by camilhamdane » Wed Aug 07, 2019 5:19 am

Just wanted to say thank you, sincerely, as you saved me extra hours of struggling to install both Neuron and Nest on the same machine.

RobinDS
Posts: 19
Joined: Mon Nov 04, 2019 12:17 pm

Re: NeuroVM

Post by RobinDS » Fri Nov 22, 2019 2:44 pm

Will there be anyone maintaining this with new versions?

tyler
Posts: 5
Joined: Mon May 06, 2019 8:55 pm

Re: NeuroVM

Post by tyler » Fri Nov 22, 2019 2:48 pm

RobinDS wrote:
Fri Nov 22, 2019 2:44 pm
Will there be anyone maintaining this with new versions?
Definitely! Since the original post we've created a new NeuroVM with Neuron 7.7.

https://tylerbanks.net/assets/CompNeuro ... ctions.pdf

If you have suggestions or would like to see additional software in the VM we'll definitely look at getting it put in as well.

RobinDS
Posts: 19
Joined: Mon Nov 04, 2019 12:17 pm

Re: NeuroVM

Post by RobinDS » Sat Nov 23, 2019 3:43 am

Looks good! Thanks for this

Post Reply