Modeling data resources

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neuromau
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Joined: Mon Apr 20, 2009 7:02 pm

Modeling data resources

Post by neuromau » Thu Jun 20, 2013 8:11 pm

Here are some resources that have data useful for detailed modeling:

The NeuroElectro website displays cellular electrophysiology data from multiple articles, very nicely. For a variety of properties (resting membrane potential, membrane time constant, input resistance, rheobase, etc), it graphs the values found in the literature. If you mouse over a datapoint on the graph, it shows you the reference it came from, and if you click a datapoint, it takes you to a page for that reference, showing you all the values for ephys properties found in that reference. Pretty cool!

It's still in beta, and there is some work to be done (ex, you can't easily get to an article's summary page from the article index when you have an article in mind, can only get there by clicking a datapoint on the graphs), but it is already quite useful. It even tracks the methods of the article, so you know the preparations used to obtain that particular datapoint.

Also, Ivan and I are publishing an anatomical quantitative assessment of the rat CA1 in Hippocampus. It takes advantage of decade(s) of anatomical data that have been published about neurons in the CA1. It uses marker distribution data to calculate the number of each interneuron type in the CA1. Then, it combines the neuron number estimates with published data about bouton counts from various interneuron types to calculate the total divergence (output connections) of each interneuron type, pyramidal cells, and major CA1 afferents. Then, it compares the total available excitatory and inhibitory boutons with the input synapses on pyramidal cells (and more generally, interneurons as a whole) in calculating the convergence of each cell type onto pyramidal cells and interneurons as a whole. We did find gaps in the experimental data where more experiments need to be done (for ex, the total number of GABAergic boutons available for synapsing on CA1 pyramidal cells only accounts for about 60% of the available inhibitory input synapses on CA1 pyramidal cells). However, the data should be a good starting point for people wishing to design anatomically detailed models of the CA1.

The most useful tables for modelers are:
  • Table 4 (number of each interneuron type)
  • Table 5 (divergence of each interneuron type)
  • Tables 22 (excitatory convergence onto pyramidal cells)
  • Tables 23 & 24 (inhibitory convergence onto pyramidal cells)
  • Tables 26 (excitatory convergence onto interneurons)
  • Tables 27 (inhibitory convergence onto interneurons)
The article itself is pretty long, so we're creating a clickable graphic on our website to direct people to info of interest (once the html version of the paper goes online) at http://www.ivansolteszlab.org/quantitat ... sment.html

~ Marianne

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