search

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
149 stars 138 forks source link

[New feature] Extend declarative language to allow for specification of conn matrix #540

Open salvadord opened 4 years ago

salvadord commented 4 years ago

Although conn rules allow for more flexibility, simpler conn matrices are widely used -- these could be implemented as a special case to define connectivity, or there could be a method that converts these to conn rules.

salvadord commented 1 year ago

rquest from samneno: issue #110 "Convert tables/matrices to netpyne format (eg. pmat or wmat)" "Old-style simulations we've been using on neurosim include easy-to-read tables (wmat for weights, pmat for probability of connections, ...). These tables are typically indexed by cell type. Eg wmat[type1][type2] = 2 - means weight from type1 -> type2 is 2.0. NetPyne's syntax is more flexible/powerful but perhaps these tables are easier to read at a glance, with fast lookup of desired values via indexing. So - feature request is to have conversion to these types of tables (this is already possible given drawing of connection weights between types).

some commonly used tables: synloc - synaptic location (perhaps not general enough) delm (delays) wmatex - external weights wmat - weights pmat - probability of connections numc - number of cells of atype ix,ixe - starting/ending IDs of cells (indexed by cell type) allcells, icells, ecells - scalars representing # of cells in network and I and E cells

some tables could have added flexibility by combining with dictionaries..."

salvadord commented 1 year ago

An example of converting from pmat, wmat to netpyne conn rules is available in the M1 model