Mapping Pacemaker Neurons

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cameron...@gmail.com

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Oct 27, 2018, 8:10:39 AM10/27/18
to VFB support
Hey!

First off, thank you so much for the extensive database. It is incredibly impressive and very useful to many researchers.

I am a mathematician looking at modelling the pacemaker neurons (s-LNv, l-LNv, DN1-3, LNd, and LNp) and would love to use your database for constructing the model. However, I assume due to my biological ignorance, I am having a hard time navigating the site properly. My goal is to see the various connections (peptidergic, glutamatergic, synaptic, etc.) between the seven groups and create a "circuit" diagram between them.

I started off trying to do this via the VirtualFlyBrain tool by, for example, searching for CRY- LNd neuron (FBbt_00047187) and s-LNv neuron (FBbt_00007428), which should be connected via PDF. However, when I search for CRY- LNd I see that it has four connections to regions in the fly brain under the Relationship category, but the Query category says no neuron has pre, post, or synaptic terminals in CRY- LNd. Are the Relationship and Query categories connected in any way? Is it better to use one or another for my specific task?

I then attempted to use the NBLAST tool to create an image similar to the ones shown in the tutorial, but the ID given for CRY- LNd from VirtualFlyBrain just returns an error. I assume that either the ID given is not the ID needed to use NBLAST or I am attempting to use the tool improperly.

If there is a way to create a circuit diagram using any part of your database, I would greatly appreciate any advice you would be willing to give. I do apologise for my lack of biological knowledge, which I assume is the problem I am having in navigating your database.

All the best,
Cameron

David Osumi-Sutherland

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Oct 29, 2018, 10:02:17 AM10/29/18
to cameron...@gmail.com, VFB support, Clare Pilgrim
Dear Cameron,

Many thanks for contacting us. You can find a list of all adult pacemaker neurons here: http://www.virtualflybrain.org/do/ont_bean_list.html?action=subclass&id=FBbt:00100163 (Subclasses query after searching for 'adult pacemaker neuron’).  We don’t currently have curated connectivity for these neurons, but this may be due to a lag in curation.  We also don’t yet have any curated 3D images of these neurons (needed for NBLAST). I’ve CC’d Clare, our anatomy ontology curator.  She should be able to let you know if any curation of papers on pacemaker connectivity is in progress.   I’ve appended a list of all curated papers we have.  Any suggestions for missing papers/data would be most welcome.

Note - We curate connectivity in two ways:  neuron to region using ‘has (pre/post)synaptic terminal in’ (probably not useful to you?) & neuron to neuron via 'synapsed by/to’.   We do not (yet) curate non synaptic connections (e.g. due to diffusion of PDF outside of a synaptic context). 

We are working on a tool to display circuits on VFB using the synapse_by/to relations.  We plan for this to be available early in the New Year.  Would you be interested in testing beta versions of this tool & providing feedback?

 Here’s an example of what we have planned.

PastedGraphic-1.pdf
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