Our lab has been dedicated to the dissemination of open-source software since 1992. Almost all of this software is for use with the NEURON simulation system. Most of the software is from specific models, both from our papers and from those of others posted on ModelDB. We also offer some analysis tools hosted on SimToolDB and simulation management tools on this website.
This page is divided into the following categories:
- Models from our papers
- Simulation and analysis tools
- Small NEURON scripts
- Models implemented from papers of others
Our latest tool is NetPyNE: a Python package to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON simulator.
- Composite spiking network/neural field model of Parkinsons (Kerr et al 2013) from Kerr CC, Van Albada SJ, Neymotin SA, Chadderdon GL, Robinson PA, Lytton WW. Cortical information flow in Parkinson's disease: a composite network/field model. Front Comput Neurosci 2013 7:39.
- Prosthetic electrostimulation for information flow repair in a neocortical simulation (Kerr et al. 2012) from Kerr CC, Neymotin SA, Chadderdon G, Fietkiewicz C, Francis JT, Lytton WW. Electrostimulation as a Prosthesis for Repair of Information Flow in a Computer Model of Neocortex. IEEE Trans Neural Syst Rehabil Eng 2012 20:153-160.
- Emergence of physiological oscillation frequencies in neocortex simulations (Neymotin et al. 2011) from Neymotin SA, Lee H, Park E, Fenton AA, Lytton WW (2011) Emergence of physiological oscillation frequencies in a computer model of neocortex. Front Comput Neurosci 5:19-75 [PubMed]
- Computational Surgery (Lytton et al. 2011) from Lytton WW, Neymotin SA, Wester JC, Contreras D (2011) Neocortical simulation for epilepsy surgery guidance: Localization and intervention Computational Surgery and Dual Training in press.
- Ketamine disrupts theta modulation of gamma in a computer model of hippocampus (Neymotin et al 2011) from Neymotin SA, Lazarewicz MT, Sherif M, Contreras D, Finkel LH, Lytton WW (2011) Ketamine disrupts theta modulation of gamma in a computer model of hippocampus Journal of Neuroscience, 31:11733-11743
- Synaptic information transfer in computer models of neocortical columns (Neymotin et al. 2010) from Neymotin SA, Jacobs KM, Fenton AA, Lytton WW (2010) Synaptic information transfer in computer models of neocortical columns. J Comput Neurosci [PubMed]
- Broadening of activity with flow across neural structures (Lytton et al. 2008) from Lytton WW, Orman R, Stewart M (2008) Broadening of activity with flow across neural structures. Perception 37:401-7 [PubMed]
- Tonic-clonic transitions in a seizure simulation (Lytton and Omurtag 2007) from Lytton WW, Omurtag A (2007) Tonic-clonic transitions in computer simulation. J Clin Neurophysiol 24:175-81 [PubMed] Neural Comput 20(11):2745-56 [PubMed]
- Signal integration in LGN cells (Briska et al 2003) from Briska AM, Uhlrich DJ, Lytton WW (2003) Computer model of passive signal integration based on whole-cell in vitro studies of rat lateral geniculate nucleus. Eur J Neurosci 17:1531-41[PubMed]
- Hippocampus temporo-septal engram shift model (Lytton 1999) from Lytton WW, Lipton P (1999) Can the hippocampus tell time? The temporo-septal engram shift model. Neuroreport 10:2301-6 [PubMed]
- Thalamic interneuron multicompartment model (Zhu et al. 1999) from Zhu JJ, Lytton WW, Xue JT, Uhlrich DJ (1999) An intrinsic oscillation in interneurons of the rat lateral geniculate nucleus. J Neurophysiol 81:702-11 [PubMed]
Zhu JJ, Uhlrich DJ, Lytton WW (1999) Burst firing in identified rat geniculate interneurons. Neuroscience 91:1445-60 [PubMed]
- Feedforward heteroassociative network with HH dynamics (Lytton 1998) from Lytton WW (1998) Adapting a feedforward heteroassociative network to Hodgkin-Huxley dynamics. J Comput Neurosci 5:353-64 [PubMed]
- Thalamic quiescence of spike and wave seizures (Lytton et al 1997) from Lytton WW, Contreras D, Destexhe A, Steriade M (1997) Dynamic interactions determine partial thalamic quiescence in a computer network model of spike-and-wave seizures. J Neurophysiol 77:1679-96 [PubMed]
- Computer model of clonazepam`s effect in thalamic slice (Lytton 1997) from Lytton WW (1997) Computer model of clonazepam's effect in thalamic slice. Neuroreport 8:3339-43 [PubMed]
The following are simulation or analysis tools. Analysis tools may be utilized for physiological or simulation data. Note that the posted versions of these tools are not always kept current; contact us for current versions if you want to use them.
- NetPyNE: a Python package to facilitate the development, parallel simulation and analysis of biological neuronal networks using the NEURON simulator.
- Measuring the quality of neuronal identification in ensemble recordings (2011) from Neymotin SA, Lytton WW, Olypher AO, Fenton AA (2011) Measuring the quality of neuronal identification in ensemble recordings. J Neurosci 31(45):16398-16409[PubMed]
- Spectral method and high-order finite differences for nonlinear cable (Omurtag and Lytton 2010) from Omurtag A, Lytton WW (2010) Spectral method and high-order finite differences for the nonlinear cable equation. Neural Comput 22:2113-36[PubMed]
- The virtual slice setup (Lytton et al. 2008) from Lytton WW, Neymotin SA, Hines ML (2008) The virtual slice setup. J Neurosci Methods 171:309-15 [PubMed]
- JitCon: Just in time connectivity for large spiking networks (Lytton et al. 2008) from Lytton WW, Omurtag A, Neymotin SA, Hines ML (2008) Just in time connectivity for large spiking networks (partially incorporated into NEURON simulator)
- NEURON interfaces to MySQL and the SPUD feature extraction algorithm (Neymotin et al. 2007) from Neymotin S, Uhlrich DJ, Manning KA, Lytton WW (2008) Data mining of time-domain features from neural extracellular field data Applic. of Comput. Intel. in Bioinf. and Biomed.: Current Trends and Open Problems 151:119-140
- Neural Query System NQS Data-Mining From Within the NEURON Simulator (Lytton 2006) from Lytton WW (2006) Neural Query System: Data-mining from within the NEURON simulator. Neuroinformatics 4:163-76 [PubMed]
- Parallel network simulations with NEURON (Migliore et al 2006) from Migliore M, Cannia C, Lytton WW, Markram H, Hines ML (2006) Parallel Network Simulations with NEURON. J Comp Neurosci 21:110-119 [PubMed] (incorporated into NEURON simulator)
- Local variable time step method (Lytton, Hines 2005) from Lytton WW, Hines ML (2005) Independent variable time-step integration of individual neurons for network simulations. Neural Comput 17:903-21 [PubMed] (incorporated into NEURON simulator)
- SIMCTRL: Simulation Control for the NEURON simulator in GNU Emacs (documentation only; packages available on request since not encapsulated)
- GRVEC:: Graphical user interface for vector manipulation in NEURON (documentation only; packages available on request since not encapsulated)
- Neural fingerprinting using NQS
- Genetic algorithm from NEURON NEURON interface to GAUL, a genetic algorithm library
- Hoc filter tool Low-pass filtering using NEURON's fft() routine (obsolete: use PYTHON)
- Embed hoc files Follow load_files() and xopen() commands in hoc to create a properly embedded single hoc file.
- Summed synapse mechanism A standard #INCLUDE postsynaptic mechanism for NMODL to utilize summed synapse mechanism based on Lytton WW. Optimizing synaptic conductance calculation for network simulations. Neural Comput. 1996;8:501-9.
- A timer
- Union template in hoc
- Sample Entropy
- Follow HOC_LIBRARY_PATH to find routines.
We depend on the kindness of strangers in developing our simulations and post models of others that we have successfully ported to NEURON (yes, there were a few that were not entirely successful -- i.e. couldn't quite replicate the figures)
- Thalamocortical augmenting response from Bazhenov M, Timofeev I, Steriade M, Sejnowski TJ (1998) Computational models of thalamocortical augmenting responses. J Neurosci 18:6444-65 [PUBMED]
- CA3 pyramidal cell: rhythmogenesis in a reduced Traub model from Pinsky PF, Rinzel J (1994) Intrinsic and network rhythmogenesis in a reduced Traub model for CA3 neurons. J Comput Neurosci 1:39-60 [PUBMED]
- Artificial neuron model from Izhikevich EM (2003) Simple model of spiking neurons. IEEE Trans Neural Netw 14:1569-72[PUBMED] ]
- Excitatory and inhibitory interactions in populations of model neurons from Wilson HR, Cowan JD (1972) Excitatory and inhibitory interactions in localized populations of model neurons. Biophys J 12:1-24 [PUBMED]
- Gamma oscillations in hippocampal interneuron networks from Wang XJ, Buzsaki G (1996) Gamma oscillation by synaptic inhibition in a hippocampal interneuronal network model. J Neurosci 16:6402-13 [PUBMED]
- Cortical network model of posttraumatic epileptogenesis(Bush et al 1999) from Bush PC, Prince DA, Miller KD (1999) Increased pyramidal excitability and NMDA conductance can explain posttraumatic epileptogenesis without disinhibition: a model. J Neurophysiol 82:1748-58 [PUBMED] (reprised for parallel simulation (parbush))