The virtual slice setup

J Neurosci Methods. 2008 Jun 30;171(2):309-15. doi: 10.1016/j.jneumeth.2008.03.005. Epub 2008 Mar 27.


In an effort to design a simulation environment that is more similar to that of neurophysiology, we introduce a virtual slice setup in the NEURON simulator. The virtual slice setup runs continuously and permits parameter changes, including changes to synaptic weights and time course and to intrinsic cell properties. The virtual slice setup permits shocks to be applied at chosen locations and activity to be sampled intra- or extracellularly from chosen locations. By default, a summed population display is shown during a run to indicate the level of activity and no states are saved. Simulations can run for hours of model time, therefore it is not practical to save all of the state variables. These, in any case, are primarily of interest at discrete times when experiments are being run: the simulation can be stopped momentarily at such times to save activity patterns. The virtual slice setup maintains an automated notebook showing shocks and parameter changes as well as user comments. We demonstrate how interaction with a continuously running simulation encourages experimental prototyping and can suggest additional dynamical features such as ligand wash-in and wash-out-alternatives to typical instantaneous parameter change. The virtual slice setup currently uses event-driven cells and runs at approximately 2 min/h on a laptop.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Action Potentials / physiology
  • Animals
  • Computer Simulation
  • Humans
  • Models, Neurological*
  • Nerve Net / cytology
  • Neurons / cytology
  • Neurons / physiology*
  • Synapses / physiology
  • User-Computer Interface*