diff --git a/README b/README deleted file mode 100644 index 93fc683..0000000 --- a/README +++ /dev/null @@ -1,124 +0,0 @@ - - NEURON TUTORIAL FOR IMPLEMENTING SIMULATIONS OF NETWORKS - OF THALAMIC RETICULAR NEURONS - - Alain Destexhe - Laboratory for Computational Neuroscience - Unité de Neurosciences Intégratives et Computationnelles (UNIC) - Centre National de la Recherche Scientifique (CNRS) - 91198 Gif-sur-Yvette, France - - Formerly from (when this work was created): - Department of Physiology, Laval University, - Quebec G1K 7P4, Canada - - Destexhe@iaf.cnrs-gif.fr - http://cns.iaf.cnrs-gif.fr/Main.html - - -This package is running with the NEURON simulation program written by Michael -Hines and available on internet at: - http://www.neuron.yale.edu/neuron/ - http://neuron.duke.edu/ - -The package contains mechanisms (.mod files) and programs (.oc files) needed -to simulate networks of thalamic reticular (RE) neurons interacting with -inhibitory synapses. The approach followed here uses the object-oriented -facilities of NEURON to simulate networks, and can be applied to other types -of neurons and/or other types of synaptic interactions. - -This model studies the genesis of 10Hz oscillations by inhibitory networks of -RE neurons in the thalamus. Each neuron is described by a single-compartment -containing voltage- and calcium-dependent currents described by Hodgkin-Huxley -type of model. Synaptic interactions are handled by kinetic models of -postsynaptic receptors of the GABA_A and GABA_B types. - -The models given here are described in detail in the following paper: - - Destexhe, A., Contreras, D., Sejnowski, T.J. and Steriade, M. - A model of spindle rhythmicity in the isolated thalamic reticular nucleus. - Journal of Neurophysiology, 72: 803-818, 1994. - -A postscript version of this paper, including figures, is available on -internet at - http://cns.iaf.cnrs-gif.fr/Main.html - - PROGRAMS - ======== - -Each program reproduces one figure of the paper: - -Fig5A.hoc : 2 neurons connected with GABA_A synapses -Fig5B.hoc : 2 neurons connected with GABA_A synapses + self-connections -Fig6A.hoc : 5 neurons connected with GABA_A synapses (first-neighbor) -Fig6B.hoc : 5 neurons connected with GABA_A synapses (first-neighbor+self) -Fig6C.hoc : 5 neurons connected with GABA_A synapses (2nd-neighbor) -Fig6D.hoc : 5 neurons connected with GABA_A synapses (all-to-all) -Fig13A.hoc : 2 neurons connected with GABA_B synapses -Fig13B.hoc : 2 neurons connected with GABA_B synapses + self-connections - - - MECHANISMS - ========== - -HH2.mod : Hodgkin-Huxley kinetics for action potentials -IT2.mod : low-threshold calcium current of thalamic RE neurons -IAHP.mod : calcium-activated K+ current responsible for AHP -ICAN.mod : calcium-activated nonspecific cation current -capump.mod : calcium clearance mechanisms - -gaba.mod : two-state kinetic model for GABA_A receptors -gabab1.mod : two-state kinetic model for GABA_B receptors - - - HOW TO RUN - ========== - -Use autolaunch on modeldb or: - -unix platform: - - To compile the demo, NEURON and INTERVIEWS must be installed and working on - the machine you are using. Just type "nrnivmodl" to compile the mechanisms - given in the mod files. - - Then, execute the main demo program by typing: - - nrngui mosinit.hoc - -mswin platform: - - Compile the mechanism (mod) files by using mknrndll. Then start the simulation - by clicking on mosinit.hoc in windows explorer. - -back to any platform: - -Once the menu and graphics interface has appeared, click on a simulation from -the Simulations of thalamic reticular network window. Reposition the windows -to find the Run Control window. Then click on "Init and Run" button to start -the simulation on the RunControl window. - -For more information about how to get NEURON and how to install it, please -refer to the following sites: - http://www.neuron.yale.edu/neuron/ - http://neuron.duke.edu/ - -For further information, please contact: - -Alain Destexhe -Laboratory for Computational Neuroscience -Unité de Neurosciences Intégratives et Computationnelles (UNIC) -Centre National de la Recherche Scientifique (CNRS) -91198 Gif-sur-Yvette, France - -Destexhe@iaf.cnrs-gif.fr -http://cns.iaf.cnrs-gif.fr/Main.html - -7/11/2005 this model updated to close windows and reopen a run control -window between simulations. - -ModelDB-Note: This model updated for NEURON version 4.3.1 and higher. - -10-2007: AD, better synaptic mechanisms using counters -20120106 changed mod files for better solve methods (avoid euler) -as per web page http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592 diff --git a/README.md b/README.md new file mode 100644 index 0000000..18516a7 --- /dev/null +++ b/README.md @@ -0,0 +1,107 @@ +# NEURON Tutorial for Implementing Simulations of Networks of Thalamic Reticular Neurons + +Alain Destexhe +Laboratory for Computational Neuroscience +Unité de Neurosciences Intégratives et Computationnelles (UNIC) +Centre National de la Recherche Scientifique (CNRS) +91198 Gif-sur-Yvette, France + +Formerly from (when this work was created): +Department of Physiology, Laval University, +Quebec G1K 7P4, Canada + +Destexhe@iaf.cnrs-gif.fr +[http://cns.iaf.cnrs-gif.fr/Main.html](http://cns.iaf.cnrs-gif.fr/Main.html) + +--- + +This package is running with the NEURON simulation program written by Michael Hines and available on internet at: +- [http://www.neuron.yale.edu/neuron/](http://www.neuron.yale.edu/neuron/) +- [http://neuron.duke.edu/](http://neuron.duke.edu/) + +The package contains mechanisms (.mod files) and programs (.oc files) needed to simulate networks of thalamic reticular (RE) neurons interacting with inhibitory synapses. The approach followed here uses the object-oriented facilities of NEURON to simulate networks, and can be applied to other types of neurons and/or other types of synaptic interactions. + +This model studies the genesis of 10Hz oscillations by inhibitory networks of RE neurons in the thalamus. Each neuron is described by a single-compartment containing voltage- and calcium-dependent currents described by Hodgkin-Huxley type of model. Synaptic interactions are handled by kinetic models of postsynaptic receptors of the GABA_A and GABA_B types. + +The models given here are described in detail in the following paper: + +Destexhe, A., Contreras, D., Sejnowski, T.J. and Steriade, M. +A model of spindle rhythmicity in the isolated thalamic reticular nucleus. +*Journal of Neurophysiology*, 72: 803-818, 1994. + +A postscript version of this paper, including figures, is available on internet at +[http://cns.iaf.cnrs-gif.fr/Main.html](http://cns.iaf.cnrs-gif.fr/Main.html) + +## Programs + +Each program reproduces one figure of the paper: + +- **Fig5A.hoc** : 2 neurons connected with GABA_A synapses +- **Fig5B.hoc** : 2 neurons connected with GABA_A synapses + self-connections +- **Fig6A.hoc** : 5 neurons connected with GABA_A synapses (first-neighbor) +- **Fig6B.hoc** : 5 neurons connected with GABA_A synapses (first-neighbor+self) +- **Fig6C.hoc** : 5 neurons connected with GABA_A synapses (2nd-neighbor) +- **Fig6D.hoc** : 5 neurons connected with GABA_A synapses (all-to-all) +- **Fig13A.hoc** : 2 neurons connected with GABA_B synapses +- **Fig13B.hoc** : 2 neurons connected with GABA_B synapses + self-connections + +## Mechanisms + +- **HH2.mod** : Hodgkin-Huxley kinetics for action potentials +- **IT2.mod** : low-threshold calcium current of thalamic RE neurons +- **IAHP.mod** : calcium-activated K+ current responsible for AHP +- **ICAN.mod** : calcium-activated nonspecific cation current +- **capump.mod** : calcium clearance mechanisms + +- **gaba.mod** : two-state kinetic model for GABA_A receptors +- **gabab1.mod** : two-state kinetic model for GABA_B receptors + +## How to Run + +Use autolaunch on modeldb or: + +### Unix platform: + +To compile the demo, NEURON and INTERVIEWS must be installed and working on the machine you are using. Just type `nrnivmodl` to compile the mechanisms given in the mod files. + +Then, execute the main demo program by typing: + +``` +nrngui mosinit.hoc +``` + +### MS Windows platform: + +Compile the mechanism (mod) files by using mknrndll. Then start the simulation by clicking on `mosinit.hoc` in Windows Explorer. + +### Back to any platform: + +Once the menu and graphics interface has appeared, click on a simulation from the *Simulations of thalamic reticular network* window. Reposition the windows to find the Run Control window. Then click on **Init and Run** button to start the simulation on the RunControl window. + +For more information about how to get NEURON and how to install it, please refer to the following sites: +- [http://www.neuron.yale.edu/neuron/](http://www.neuron.yale.edu/neuron/) +- [http://neuron.duke.edu/](http://neuron.duke.edu/) + +For further information, please contact: + +Alain Destexhe +Laboratory for Computational Neuroscience +Unité de Neurosciences Intégratives et Computationnelles (UNIC) +Centre National de la Recherche Scientifique (CNRS) +91198 Gif-sur-Yvette, France + +Destexhe@iaf.cnrs-gif.fr +[http://cns.iaf.cnrs-gif.fr/Main.html](http://cns.iaf.cnrs-gif.fr/Main.html) + +--- +## Changelog +7/11/2005 this model updated to close windows and reopen a run control window between simulations. + +ModelDB-Note: This model updated for NEURON version 4.3.1 and higher. + +10/2007 AD, better synaptic mechanisms using counters + +1/6/2012 changed mod files for better solve methods (avoid euler) +as per web page [http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592](http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592) + +5/27/2025 Standardized to Markdown.