In my blog post from two days ago “Brain Modeling Using NEURON, Interneurons, and Resonant Circuits” the computational neuroscience paper under review “Computational modeling of distinct neocortical oscillations driven by cell-type selective optogenetic drive: separable resonant circuits controlled by low-threshold spiking and fast-spiking interneurons” (published November 22, 2010 in Frontiers in Human Neuroscience) referenced two NEURON models in the ModelDB online data repository. In this post we’ll look at one of the models “Pyramidal Neuron Deep, Superficial; Aspiny, Stellate (Mainen and Sejnowski 1996)” and the paper that describes it (“Influence of dendritic structure on firing pattern in model neocortical neurons” published July 25, 1996 in Nature).
Note: ModelDB is the computation neuroscience model repository within the larger SenseLab online data repository.
Figure 1. Example views of the “Pyramidal Neuron Deep, Superficial; Aspiny, Stellate (Mainen and Sejnowski 1996)” model downloaded from ModelDB and running in NEURON. (Left) A view of a reconstructed layer 5 pyramidal neuron. (Right) One second (1000 milliseconds) trace of the membrane potential voltage of a layer 3 pyramidal cell (blue) and a layer 5 pyramidal cell (red). The layer 5 pyramidal cell trace is from the neuron displayed left.
Neuron response properties are shaped by a combination of cell membrane conduction properties as defined by the types and distribution of ion channels and cell morphology as defined by the geometry of a neuron. The 1996 paper under review highlighted the importance of morphology by showing that neurons sharing common types and distributions of ion channels and differing only in the shapes of their dendrites could display many different firing patterns.
Note: Those with more than a passing interested in using NEURON may find the book or e-book by its creators useful “The NEURON Book.”
You can reproduce the paper’s figure 1 by running the “Pyramidal Neuron Deep, Superficial; Aspiny, Stellate (Mainen and Sejnowski 1996)” model downloaded from ModelDB in NEURON.
- FIrst download NEURON from the NEURON Download and install web page.
Note: NEURON runs under most computing environments. Details on setup and trouble shooting vary by platform but are well documented at the NEURON website.
- Next download the “Pyramidal Neuron Deep, Superficial; Aspiny, Stellate (Mainen and Sejnowski 1996)” model from ModelDB.
Note: Don’t forget to compile the files in the project folder. On the Macintosh computer you drag the project folder to NEURON’s mknrndll program icon.
- Load the model’s demofig1.hoc file.
The NEURON application should be running and displaying some windows. A window titled “Figure 1” should contain four buttons displaying the cerebral cortical layer and name of four different types of neuron. The letters a, b, c, and d correspond to the letters the paper’s Figure 1.
- Click on the “a. L3 Aspiny” button. A new window showing the same reconstructed cell as in the paper’s Figure 1a should open.
- Now go to the window titled “RunControl” and click on the “Init & Run” button. You should see the Aspiny neuron’s electrical activity actively being traced in a Graph window. When it’s finished, the 1 second (1000 millisecond) trace should be identical to the one in the paper’s Figure 1a.
This is how computational neuroscience papers should be published! Reconstruct the paper’s figures and play with the simulations while reading the paper itself.
Other related blog posts:
Brain Modeling Using NEURON, Interneurons, and Resonant Circuits
Mandatory Publication of Computational Brain Models Simultaneously with Paper!
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