A Taste of Neuroscience Papers in the Future

Kudos to the authors of the paper “Local Control of Postinhibitory Rebound Spiking in CA1 Pyramidal Neuron Dendrites” (published May 5, 2010 in the Journal of Neuroscience) described yesterday in my blog post “NEURON, SenseLab ModelDB, NeuroMorpho.org, and Signal Processing in Brain Microcircuitry.” Not only did they use the valuable resources provided by the NEURON simulator, SenseLab’s ModelDB repository, and the NeuroMorpho.org data repository but they also published their new Hippocampus Cornu Ammonis area 1 (CA1) pyramidal neuron model to ModelDB.

Note: Their hypothesis and conclusions were also very interesting and important but in this post I’m focusing on the future of neuroscience papers. For more about the reported findings please see yesterday’s blog post.

Model traces for neuron pc2b.
Figure 1. Model traces for neuron pc2b in NEURON using the “A1 pyramidal neuron: rebound spiking (Ascoli et al.2010)” model downloaded from ModelDB. Somatic (black) and dendritic (red) membrane potentials were recorded during and after a dendritic hyperpolarizing current injection while the neuron was bathed in 4-AP. The traces are the same (with a slight view modification) as in Figure 2d of the paper being reviewed. Please see text below for more details.

Note: A 3D graphic animation of neuron pc2b is displayed in Figure 1 of yesterday’s blog post. Neuron pc2b is from the NeuroMorpho.org data repository.

You can reproduce the paper’s figure 2b by running the “A1 pyramidal neuron: rebound spiking (Ascoli et al.2010)” model downloaded from ModelDB in NEURON.

Note: NEURON runs under most computing environments. Details on setup and trouble shooting vary by platform but are well documented at the NEURON website.

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 mosinit.hoc file.

The NEURON application should be running and displaying some windows. One window should contain five buttons labeled K_A, I_h, control, 4-AP, and 4-AP+ZD. The default K_A and I_h settings are the same as in the paper’s Figure 2d. Click on the control, 4-AP, or 4-AP+ZD button to run the model under each condition and get membrane potential traces from the soma (black) and dendrite (red). Figure 1 above shows the traces after clicking the “4-AP” button.

Note: Figure 2d in the paper places a trace from each of the three conditions (control, 4-AP, and 4-AP+ZD) together for the dendritic recording (top) and somatic recording (bottom). My Figure 1 above is of the somatic recording (black) and dendritic recording (red) under one condition (4-AP). However, all of the parameters and variables are the same.

This is a glimpse into how neuroscience will be published in the future. You won’t simply read a paper from a journal anymore. In fact, for the most part this already isn’t the case. It’s becoming rare to read an article that doesn’t include extensive online supplementary material. However, in the future research will be communicated in a seamless virtual environment that will enable you to play with models and drill into data while you read text.

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.”

Other related blog posts:

Brain Modeling Using NEURON: Superficial Pyramidal, Deep Pyramidal, Aspiny, and Stellate Neurons

Mandatory Publication of Computational Brain Models Simultaneously with Paper!

NEURON, SenseLab ModelDB, NeuroMorpho.org, and Signal Processing in Brain Microcircuitry