nt.prediction local SQLite synapse data

[Emil Kind]

Hi nat-users,

I find the synapse connectivity implementation in fafbseg package really help. I was hoping I could also use the neurotransmitter prediction but as far is I can tell from here and here I would need to have a local version of the SQLite synapse data. Would it be possible to some how get a copy of the SQLite synapse data? Thank you very much!

All the best,

Emil

[Greg Jefferis]

Dear Emil,

I'm glad to hear that the live synaptic connectivity information has been useful. When you run a query in fafbseg, it fetches the data from a microservice run by Eric Perlman on behalf of the BRAIN initiative grant awarded to Davi Bock and myself. We haven't really advertised it too heavily, because stimulated by our implementation (and with some input from us) the flywire team have been working on their own implementation which should be more efficient and integrated. I don't know when to expect that because they are working on a number of other related enhancements, but it should be soon. 

The neurotransmitter prediction is still very experimental – Nils Eckstein in Jan Funke's lab only ran the whole brain predictions a month ago – but Jan and I agreed that the results should be made available to the flywire community as soon as possible and so we have given the information to Sven Dorkenwald and colleagues to integrate with the flywire synapse service that I mention above.

Should it take more than a week or so for this synapse information to appear via flywire, we can arrange a workaround using the same database microsevice that powers the synapse queries you are running from fafbseg.

All the best,

Greg.

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