Separation of sim and data

suny-downstate-medical-center / netpyne

A Python package to facilitate the development, parallel simulation, optimization and analysis of multiscale biological neuronal networks in NEURON.

http://www.netpyne.org

MIT License

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Separation of sim and data #109

Closed samnemo closed 8 years ago

samnemo commented 8 years ago

I sometimes separate simulation (sim.py) and simulation-data-reading code (simdat.py) - that way I don't have to load the whole sim to read sim data. However, to properly analyze simulation data, certain data structures are needed (number of cells, cell IDs, cell types, etc.). Is it easy for users to add the key data structures to NetPyne structures that get saved? Probably...

salvadord commented 8 years ago

Netpyne data is separated into:

netParams: network high-level specifications
simConfig: simulation configuration
net: network instance, including info on all pops, cells, conns, stims etc
simData: simulation output data, including spkt times, voltage traces, etc

It is already possible to save and load each of these separately. For most of the graphs you will need the net and simData structures.