NetPyNE models
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Region / Feature modeledImplementersLinksNotes
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M1 (Izhikevich neurons)Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.comhttps://github.com/Neurosim-lab/netpyne/tree/development/examples/M1
http://www.opensourcebrain.org/projects/m1networkmodel
Mouse M1 model with 14 populations; size 300um x 300um x 1350um, has 10,734 Izhikevich cells, 5,029,610 synapses, and cortical depth-dependent connectivity based on published data.
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M1 (detailed HH neurons)Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
Samuel Neymotin, SUNY Downstate, samnemo@gmail.com
Donald Doherty, SUNY Downstate, donald.doherty@icloud.com
https://github.com/Neurosim-lab/netpyne/tree/development/examples/M1detailed
no.neurosim.downstate.edu://u/salvadord/Models/m1
https://www.biorxiv.org/content/early/2018/01/24/201707
Mouse M1 model with 14 populations; size 300um x 300um x 1350um, has 10,171 HH cells (from 2 to 700+ compartments), ~30M synapses, long-range inputs from 7 regions and cortical depth-dependent connectivity based on published data.
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NeuroML import of simple network examplePadraig Gleeson, UCL, p.gleeson@ucl.ac.uk
Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://github.com/Neurosim-lab/netpyne/tree/development/examples/NeuroMLImport3 Izhikevich cells
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M1 PT corticospinal cell (detailed)Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
Samuel Neymotin, SUNY Downstate, samnemo@gmail.com
https://github.com/Neurosim-lab/netpyne/tree/development/examples/PTcell
https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=195615
https://www.ncbi.nlm.nih.gov/pubmed/27760819
M1 pyramdial tract project (PT) corticospinal cell with 700+ compartments and multiple ionic channels, optimized to reproduce experimental data
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CSalvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
Cliff Kerr, University of Sydney, cliff@thekerrlab.com
David Kedziora, University of Sydney, davidkedz@hotmail.com
https://github.com/Neurosim-lab/netpyne/tree/development/examples/RL_arm
https://github.com/thekerrlab/compscaling/tree/master/sim
https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=183014 (related)
3 Izhikevich populations; 2-stick virtual arm
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Single cell (M1 PT) batch parameter exploration exampleSalvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://github.com/Neurosim-lab/netpyne/tree/development/examples/batchCell
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V1 network with detailed Allen Brain cells (example of saving and loading)Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://github.com/Neurosim-lab/netpyne/tree/development/examples/saveLoadV1
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Simple 2-population network tutorialsSalvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut2.py
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut3.py
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut4.py
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut6.py
tut2 - 1-comp HH
tut3 - 2-comp HH
tut4 - HH and Izhikevich
tut6 - different types of stimulation
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Simple 3-layer, 6-pop tutorial networkSalvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut5.pysimple cortical column, with distance-based conn probablity and delay
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Simple hopfield tutorial network (inhibition and synchrony)Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut7.py
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Simple network batch parameter exploration tutorialSalvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut8_init.py
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut8_cfg.py
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut8_netParams.py
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut8_batch.py
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut8_analysis.py
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Artificial cell network tutorial Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut_artif.py
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Importing exisiting cells tutorialSalvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut_import.py
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Simple network evolutionary parameter optimization tutorial (using Inspyred)Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
James Chen, SUNY Downstate, james.chen@downstate.edu
https://github.com/Neurosim-lab/netpyne/blob/development/doc/source/code/tut_optimization.py
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Simple HH, Izhi and Hybrid networks (parallelization paper)Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
Ali Seidenstein, SUNY Downstate, ahseidenstein@gmail.com
https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=188544
www.ncbi.nlm.nih.gov/pubmed/27557104
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Simple network driving robot car (VREP interface)Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
no.neurosim.downstate.edu://u/salvadord/Documents/ISB/Teaching/DMC_spring17/code/VREPNeed to upload to github /examples
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Claustrum networkJing Xuan, JHMI, jlim56@jhmi.edu
Erica Griffith, SUNY Downstate, erica.griffith@downstate.edu
Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
no.neurosim.downstate.edu://u/ericag/claus/
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Dendritic plateau generation in cortical simplified and detailed pyramidal neuron (EEE grant) Joe Graham, SUNY Downstate, joe.w.graham@gmail.com
Peng Gao, UConn, penggao.1987@gmail.com
Sergio Angluo, SUNY Downstate,
Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
no.neurosim.downstate.edu://u/graham/projects/eee
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Cortical ensembles based on dendritic plateau generation in PFC (EEE grant)Sergio Angulo, SUNY Downstate, sergio.angulo@gmail.com
Joe Graham, SUNY Downstate, joe.w.graham@gmail.com
Peng Gao, UConn, penggao.1987@gmail.com
Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
no.neurosim.downstate.edu://u/sergioangulo/projects/eee
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Ischemia effects on multiscale network with RxD
Ali Seidenstein, SUNY Downstate, ahseidenstein@gmail.com
Adam Newton, SUNY Downstate/Yale, adam.newton@yale.edu
no.neurosim.downstate.edu://u/ahs/Ischemia/
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CA3 network (Neymotin, Sheriff)Ben Tessler, SUNY Downstate, btessler92@gmail.com
Ernie Forzano, SUNY Downstate, eforzano@gmail.com
William Lytton, SUNY Downstate, billl@neurosim.downstate.edu
Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
no.neurosim.downstate.edu://u/billl/nrniv/ca3netpyne
no.neurosim.downstate.edu://u/btessler/ca3
no.neurosim.downstate.edu//u/eforzano/ca3ihdemo
https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=151282
https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=139421
think Ben Tessler's version reproduced original with very minor differences
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Traub thalamocortical networkPadraig Gleeson, UCL, p.gleeson@ucl.ac.uk
Vergil Haynes, vrhaynes@asu.edu
Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://github.com/OpenSourceBrain/Thalamocortical/tree/master/NeuroML2/pythonScripts/testNetpyne
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STDP in networks of biophysically detailed cells Anatoly Buchin, Allen Institute, anat.buchin@gmail.comthink no longer using
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Basal Ganglia with biophysically detailed cellsLucas Koelman, UCD Dublin, lucas.koelman@ucdconnect.ie
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LFP oscillations in networksChristian Fink, Ohio Wesleyan University, tcfink@owu.eduwaiting for LFP implementation
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Learning and dendritic computationsBirgit Kriener, University of Oslo (Einevoll lab), birgit.kriener@medisin.uio.no
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Epilepsy in thalamocortical network (Knox)Andrew Knox, University of Wisconsin, knox@neurology.wisc.edu
Ramazan Tekin, Batman University, Ramazan.Tekin@batman.edu.tr
Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=234233
https://github.com/rtekin/myKnoxRepo.git
no.neurosim.downstate.edu://u/salvadord/Models/knox
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Schizophrenia in cortical networkCristoph Metzner, Hertfordshire University, christoph.metzner@gmail.com port model from Genesis: https://www.frontiersin.org/articles/10.3389/fncom.2016.00089/full
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Spinal cord circuitsVittorio Caggiano, IBM Research, caggiano@gmail.comno.neurosim.downstate.edu://u/salvadord/Models/vitto
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Stimulation in thalamocortical networkBen Latimer, Missouri (Nair lab), LatimerB@missouri.edu
Brenyn Jungmann, Missouri (Nair lab), LatimerB@missouri.edu
no.neurosim.downstate.edu://u/salvadord/Models/brenyn
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Fear amygdala circuitsAliyah Taylor, Princeton/Missouri (Nair lab), Forum
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Macaque M1 TMS/tDCS stimulationAman Aberra, Duke University, aman.aberra@duke.eduInterested in using M1 model; had several meetings
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CA1 / CA3 network (Bezaire)Padraig Gleeson, UCL, p.gleeson@ucl.ac.uk
Andras Ecker, UCL, ecker.andris@gmail.com
Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://github.com/mbezaire/ca1/tree/development/NeuroML2/network
https://elifesciences.org/articles/18566
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Human Neocortical Solver, EEG/MEGSamuel Neymotin, SUNY Downstate, samnemo@gmail.com
Salvador Dura-Bernal, SUNY Downstate, salvadordura@gmail.com
https://salvi82@bitbucket.org/samnemo/hnn.git
http://hnn.brown.edu/doc/index.html
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CerebellumSergio Solinas, University of Pavia, smgsolinas@gmail.com
Stefano Masoli, University of Pavia, stefano.masoli@unipv.it
no.neurosim.downstate.edu://u/salvadord/Models/golgiSergio will send link to gitlab repo
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LFP in SUA vs MUAHarry Tran, Université de Lorraine CNRS, harrytran75005@gmail.comwaiting for LFP implementation
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CA1, memory retrieval, oscillationsAdam Sugi, LASCON18, adamhsugi@gmail.com
Angeles Tepper, LASCON18, angelestepper@gmail.com
Oussama Sabri, LASCON18, sabri@i3s.unice.fr
https://github.com/angietep/CA1-NetPyNE-model
https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=123815
http://sisne.org/lasconresources/mod/resource/view.php?id=1072
reproduced original results
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PFC decision-making networkEnver Oruro, LASCON18, envermiguel@gmail.com
Rodrigo Pena, LASCON18, rodrigo.pena@usp.br
http://sisne.org/lasconresources/mod/resource/view.php?id=1065
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Dentate gyrus network, dopamine modulationFacundo Rodriguez, LASCON18, frodriguez4600@gmail.com
Matías Mugnaini, LASCON18, matiasmugnaini@gmail.com
https://github.com/rodriguez-facundo/LASCON-project
https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=155568
http://sisne.org/lasconresources/mod/resource/view.php?id=1086
reproduced original model
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Potjans and Diesmann network neocortical networkCecília Romaro, LASCON18, cecilia.romaro@usp.br
Fernando A. Najman, LASCON18, fanajman@gmail.com
https://github.com/ceciliaromaro/PD_NetPyNE
http://sisne.org/lasconresources/mod/resource/view.php?id=1092
http://www.opensourcebrain.org/projects/potjansdiesmann2014
https://www.ncbi.nlm.nih.gov/pubmed/23203991
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4-layer M1 network with STDP and RL learns to drive simple virtual arm (IBM paper)Jaime A. Riascos, LASCON18, jarsalas@inf.ufrgs.br
Pablo A de Abreu Urbizagastegui, LASCON18, pabloabur@usp.br
Susana Paredes-Zúñiga, LASCON18, sparedesz@ug.uchile.cl
https://github.com/JARS29/LASCON_Project/tree/izhi/pyn
http://sisne.org/lasconresources/mod/resource/view.php?id=1078
https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=194897
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V1 network, ACh modulation
Vinicius Lima, LASCON18, vinicius.lima.cordeiro@usp.br
Sareh Rostami, LASCON18, rostami.sareh@sbmu.ac.ir
Parviz Ghaderi, LASCON18, parviz_gh2@yahoo.com
https://github.com/ViniciusLima94/pd_net_netpyne
http://sisne.org/lasconresources/mod/resource/view.php?id=1080
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Striatal microcircuits (detailed MSNs and FSIs)Hanbing Song, Franklin and Marshall College, hsong1@fandm.edu
Christina Weaver, Franklin and Marshall College, christina.weaver@fandm.edu
Ongoing
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Gentiletti et al. modelNoémie (NEURON Forum)https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=222321&file=/GentilettiEtAl2016/init.hoc#tabs-2
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Network with gap junctionsQuestion in forum - ask name and affiliation
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Owl brainBrian Fischer, UC Davis, bfischer.su@gmail.com
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Olfactory bulb and auditory cortexSharon Crook, ASU, Sharon.Crook@asu.edu
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Heart myocite network with gap junctionsSergio Solinas, University of Pavia, smgsolinas@gmail.com
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Rehabilitation in rat motor cortexMax Murphy, University of Kansas, m053m716@kumc.eduhttps://m053m716.github.io/fitting multi-unit recordings to network model
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Cerebellum model
Chaitanya Medini, University of Pavia, chaitanya.medini@unipv.it / mach512@gmail.com,
https://github.com/mach512/CerebellumModel
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Network with 100 neurons, astrocytes,calcium wave
Samuel Fernando, Universidade Federal do ABC Brazil, fernandofs051086@gmail.com
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Hypothalamic aggression circuits (?)Yuxin Tong, NYU Langone, Yuxin.Tong@nyulangone.org
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Apteronotus leptorhynchus spinal cord
Dan Hartman, Northeastern University, hartman.da@husky.neu.edu
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Multiscale model of seizures in cortex (with RxD)Wilson Truccolo, Brown University
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Ilknur Kayikcioglu
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TO DO
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M1 dystonia (with RxD)https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=189154
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Persistent activity in Neocortex (with RxD)https://senselab.med.yale.edu/modeldb/ShowModel.cshtml?model=185858
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