Large-scale neural model of visual short-term memory (Ulloa, Horwitz 2016; Horwitz, et al. 2005,...)

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Accession:206337
Large-scale neural model of visual short term memory embedded into a 998-node connectome. The model simulates electrical activity across neuronal populations of a number of brain regions and converts that activity into fMRI and MEG time-series. The model uses a neural simulator developed at the Brain Imaging and Modeling Section of the National Institutes of Health.
References:
1 . Tagamets MA, Horwitz B (1998) Integrating electrophysiological and anatomical experimental data to create a large-scale model that simulates a delayed match-to-sample human brain imaging study. Cereb Cortex 8:310-20 [PubMed]
2 . Ulloa A, Horwitz B (2016) Embedding Task-Based Neural Models into a Connectome-Based Model of the Cerebral Cortex. Front Neuroinform 10:32 [PubMed]
3 . Horwitz B, Warner B, Fitzer J, Tagamets MA, Husain FT, Long TW (2005) Investigating the neural basis for functional and effective connectivity. Application to fMRI. Philos Trans R Soc Lond B Biol Sci 360:1093-108 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Prefrontal cortex (PFC);
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: Python;
Model Concept(s): Working memory;
Implementer(s): Ulloa, Antonio [antonio.ulloa at alum.bu.edu];
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lsnm_in_python-master
visual_model
subject_4
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weightslist.txt
                            
% Wed Aug 19 21:41:29 2015

% Input layer: (9, 9)
% Output layer: (9, 9)
% Fanout size: (5, 1)
% Fanout spacing: (1, 1)
% Specified fanout weights

Connect(ev4v, ev1v)  {
  From:  (1, 1)  {
    |              | 
    ([ 9, 1]  0.001572) 
    ([ 1, 1]  0.001491) 
    ([ 2, 1]  0.000081) 
    |              | 
  }
  From:  (1, 2)  {
    |              | 
    |              | 
    |              | 
    ([ 2, 2]  0.000205) 
    |              | 
  }
  From:  (1, 3)  {
    ([ 8, 3]  0.000980) 
    ([ 9, 3]  0.000692) 
    ([ 1, 3]  0.000044) 
    ([ 2, 3]  0.000966) 
    |              | 
  }
  From:  (1, 4)  {
    ([ 8, 4]  0.000682) 
    |              | 
    ([ 1, 4]  0.000618) 
    |              | 
    |              | 
  }
  From:  (1, 5)  {
    |              | 
    ([ 9, 5]  0.001621) 
    ([ 1, 5]  0.001993) 
    ([ 2, 5]  0.000541) 
    ([ 3, 5]  0.001341) 
  }
  From:  (1, 6)  {
    |              | 
    |              | 
    ([ 1, 6]  0.001374) 
    ([ 2, 6]  0.000465) 
    |              | 
  }
  From:  (1, 7)  {
    ([ 8, 7]  0.000690) 
    ([ 9, 7]  0.000138) 
    ([ 1, 7]  0.001164) 
    ([ 2, 7]  0.001364) 
    |              | 
  }
  From:  (1, 8)  {
    ([ 8, 8]  0.001101) 
    ([ 9, 8]  0.000651) 
    |              | 
    |              | 
    |              | 
  }
  From:  (1, 9)  {
    |              | 
    |              | 
    |              | 
    ([ 2, 9]  0.000930) 
    |              | 
  }
  From:  (2, 1)  {
    ([ 9, 1]  0.001146) 
    |              | 
    ([ 2, 1]  0.001590) 
    ([ 3, 1]  0.000555) 
    |              | 
  }
  From:  (2, 2)  {
    |              | 
    ([ 1, 2]  0.000034) 
    ([ 2, 2]  0.001774) 
    |              | 
    ([ 4, 2]  0.001719) 
  }
  From:  (2, 3)  {
    |              | 
    ([ 1, 3]  0.000195) 
    |              | 
    ([ 3, 3]  0.000233) 
    ([ 4, 3]  0.000144) 
  }
  From:  (2, 4)  {
    |              | 
    ([ 1, 4]  0.000088) 
    |              | 
    |              | 
    ([ 4, 4]  0.001083) 
  }
  From:  (2, 5)  {
    ([ 9, 5]  0.001899) 
    |              | 
    |              | 
    |              | 
    ([ 4, 5]  0.001781) 
  }
  From:  (2, 6)  {
    |              | 
    ([ 1, 6]  0.001856) 
    ([ 2, 6]  0.000557) 
    |              | 
    |              | 
  }
  From:  (2, 7)  {
    |              | 
    ([ 1, 7]  0.000155) 
    ([ 2, 7]  0.000526) 
    ([ 3, 7]  0.000407) 
    ([ 4, 7]  0.001356) 
  }
  From:  (2, 8)  {
    ([ 9, 8]  0.000866) 
    ([ 1, 8]  0.000504) 
    ([ 2, 8]  0.000769) 
    |              | 
    |              | 
  }
  From:  (2, 9)  {
    |              | 
    |              | 
    ([ 2, 9]  0.001149) 
    |              | 
    ([ 4, 9]  0.000644) 
  }
  From:  (3, 1)  {
    ([ 1, 1]  0.001955) 
    ([ 2, 1]  0.000176) 
    ([ 3, 1]  0.001177) 
    ([ 4, 1]  0.001297) 
    ([ 5, 1]  0.000770) 
  }
  From:  (3, 2)  {
    ([ 1, 2]  0.000741) 
    ([ 2, 2]  0.000746) 
    |              | 
    ([ 4, 2]  0.000321) 
    ([ 5, 2]  0.001466) 
  }
  From:  (3, 3)  {
    ([ 1, 3]  0.000315) 
    ([ 2, 3]  0.001949) 
    ([ 3, 3]  0.000697) 
    ([ 4, 3]  0.000194) 
    ([ 5, 3]  0.000268) 
  }
  From:  (3, 4)  {
    ([ 1, 4]  0.001569) 
    |              | 
    ([ 3, 4]  0.000246) 
    ([ 4, 4]  0.000729) 
    ([ 5, 4]  0.000523) 
  }
  From:  (3, 5)  {
    ([ 1, 5]  0.001373) 
    |              | 
    ([ 3, 5]  0.000318) 
    ([ 4, 5]  0.001763) 
    ([ 5, 5]  0.000541) 
  }
  From:  (3, 6)  {
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 5, 6]  0.001560) 
  }
  From:  (3, 7)  {
    |              | 
    ([ 2, 7]  0.001168) 
    |              | 
    ([ 4, 7]  0.000179) 
    |              | 
  }
  From:  (3, 8)  {
    |              | 
    |              | 
    |              | 
    ([ 4, 8]  0.001757) 
    ([ 5, 8]  0.001594) 
  }
  From:  (3, 9)  {
    ([ 1, 9]  0.001547) 
    |              | 
    ([ 3, 9]  0.001516) 
    ([ 4, 9]  0.000374) 
    ([ 5, 9]  0.001855) 
  }
  From:  (4, 1)  {
    ([ 2, 1]  0.001728) 
    ([ 3, 1]  0.001646) 
    |              | 
    |              | 
    |              | 
  }
  From:  (4, 2)  {
    ([ 2, 2]  0.001059) 
    ([ 3, 2]  0.000300) 
    |              | 
    ([ 5, 2]  0.000827) 
    |              | 
  }
  From:  (4, 3)  {
    ([ 2, 3]  0.001351) 
    |              | 
    |              | 
    ([ 5, 3]  0.001488) 
    |              | 
  }
  From:  (4, 4)  {
    ([ 2, 4]  0.001916) 
    ([ 3, 4]  0.001491) 
    |              | 
    |              | 
    |              | 
  }
  From:  (4, 5)  {
    |              | 
    ([ 3, 5]  0.000841) 
    ([ 4, 5]  0.000642) 
    |              | 
    ([ 6, 5]  0.001848) 
  }
  From:  (4, 6)  {
    |              | 
    ([ 3, 6]  0.000150) 
    |              | 
    |              | 
    |              | 
  }
  From:  (4, 7)  {
    |              | 
    |              | 
    ([ 4, 7]  0.001224) 
    ([ 5, 7]  0.000975) 
    ([ 6, 7]  0.000122) 
  }
  From:  (4, 8)  {
    ([ 2, 8]  0.001836) 
    |              | 
    ([ 4, 8]  0.000920) 
    ([ 5, 8]  0.001056) 
    ([ 6, 8]  0.001515) 
  }
  From:  (4, 9)  {
    |              | 
    |              | 
    |              | 
    ([ 5, 9]  0.000805) 
    |              | 
  }
  From:  (5, 1)  {
    ([ 3, 1]  0.000990) 
    |              | 
    |              | 
    ([ 6, 1]  0.000787) 
    |              | 
  }
  From:  (5, 2)  {
    |              | 
    ([ 4, 2]  0.000254) 
    ([ 5, 2]  0.001921) 
    ([ 6, 2]  0.000334) 
    |              | 
  }
  From:  (5, 3)  {
    ([ 3, 3]  0.001659) 
    ([ 4, 3]  0.000927) 
    |              | 
    |              | 
    |              | 
  }
  From:  (5, 4)  {
    ([ 3, 4]  0.001409) 
    |              | 
    ([ 5, 4]  0.001846) 
    |              | 
    |              | 
  }
  From:  (5, 5)  {
    ([ 3, 5]  0.001099) 
    |              | 
    ([ 5, 5]  0.001178) 
    ([ 6, 5]  0.000803) 
    ([ 7, 5]  0.000741) 
  }
  From:  (5, 6)  {
    ([ 3, 6]  0.001973) 
    ([ 4, 6]  0.000024) 
    |              | 
    ([ 6, 6]  0.001365) 
    ([ 7, 6]  0.000939) 
  }
  From:  (5, 7)  {
    ([ 3, 7]  0.000316) 
    ([ 4, 7]  0.001876) 
    ([ 5, 7]  0.000388) 
    |              | 
    |              | 
  }
  From:  (5, 8)  {
    |              | 
    ([ 4, 8]  0.001752) 
    ([ 5, 8]  0.000316) 
    |              | 
    ([ 7, 8]  0.001049) 
  }
  From:  (5, 9)  {
    ([ 3, 9]  0.000607) 
    ([ 4, 9]  0.001629) 
    |              | 
    ([ 6, 9]  0.001809) 
    ([ 7, 9]  0.001055) 
  }
  From:  (6, 1)  {
    ([ 4, 1]  0.000348) 
    ([ 5, 1]  0.001465) 
    ([ 6, 1]  0.000370) 
    |              | 
    ([ 8, 1]  0.001741) 
  }
  From:  (6, 2)  {
    ([ 4, 2]  0.000222) 
    |              | 
    |              | 
    ([ 7, 2]  0.000129) 
    |              | 
  }
  From:  (6, 3)  {
    ([ 4, 3]  0.001264) 
    ([ 5, 3]  0.001575) 
    |              | 
    ([ 7, 3]  0.000419) 
    |              | 
  }
  From:  (6, 4)  {
    ([ 4, 4]  0.001473) 
    ([ 5, 4]  0.001864) 
    ([ 6, 4]  0.000097) 
    ([ 7, 4]  0.000778) 
    |              | 
  }
  From:  (6, 5)  {
    ([ 4, 5]  0.000460) 
    |              | 
    ([ 6, 5]  0.000471) 
    |              | 
    |              | 
  }
  From:  (6, 6)  {
    ([ 4, 6]  0.000554) 
    ([ 5, 6]  0.000067) 
    ([ 6, 6]  0.001247) 
    |              | 
    ([ 8, 6]  0.001568) 
  }
  From:  (6, 7)  {
    ([ 4, 7]  0.000669) 
    |              | 
    |              | 
    ([ 7, 7]  0.001830) 
    |              | 
  }
  From:  (6, 8)  {
    ([ 4, 8]  0.000769) 
    |              | 
    ([ 6, 8]  0.000584) 
    |              | 
    |              | 
  }
  From:  (6, 9)  {
    |              | 
    ([ 5, 9]  0.001635) 
    ([ 6, 9]  0.000766) 
    ([ 7, 9]  0.001980) 
    ([ 8, 9]  0.001379) 
  }
  From:  (7, 1)  {
    |              | 
    ([ 6, 1]  0.001079) 
    |              | 
    |              | 
    ([ 9, 1]  0.001562) 
  }
  From:  (7, 2)  {
    ([ 5, 2]  0.000131) 
    |              | 
    ([ 7, 2]  0.000450) 
    |              | 
    ([ 9, 2]  0.000291) 
  }
  From:  (7, 3)  {
    |              | 
    |              | 
    |              | 
    |              | 
    |              | 
    ([ 1, 1]  0.001438)   }
  From:  (7, 4)  {
    ([ 5, 4]  0.000657) 
    ([ 6, 4]  0.000990) 
    |              | 
    ([ 8, 4]  0.001273) 
    |              | 
  }
  From:  (7, 5)  {
    |              | 
    ([ 6, 5]  0.000298) 
    ([ 7, 5]  0.000071) 
    ([ 8, 5]  0.000276) 
    |              | 
  }
  From:  (7, 6)  {
    ([ 5, 6]  0.001527) 
    |              | 
    |              | 
    ([ 8, 6]  0.001251) 
    ([ 9, 6]  0.000607) 
  }
  From:  (7, 7)  {
    ([ 5, 7]  0.001107) 
    ([ 6, 7]  0.000491) 
    |              | 
    ([ 8, 7]  0.001510) 
    |              | 
  }
  From:  (7, 8)  {
    ([ 5, 8]  0.001366) 
    ([ 6, 8]  0.001145) 
    ([ 7, 8]  0.001462) 
    ([ 8, 8]  0.000905) 
    ([ 9, 8]  0.001462) 
  }
  From:  (7, 9)  {
    |              | 
    ([ 6, 9]  0.001194) 
    |              | 
    ([ 8, 9]  0.000562) 
    ([ 9, 9]  0.001552) 
  }
  From:  (8, 1)  {
    |              | 
    |              | 
    ([ 8, 1]  0.001936) 
    |              | 
    ([ 1, 1]  0.001885) 
  }
  From:  (8, 2)  {
    ([ 6, 2]  0.000758) 
    ([ 7, 2]  0.000808) 
    ([ 8, 2]  0.001019) 
    |              | 
    ([ 1, 2]  0.000569) 
  }
  From:  (8, 3)  {
    |              | 
    |              | 
    |              | 
    ([ 9, 3]  0.000796) 
    ([ 1, 3]  0.001091) 
  }
  From:  (8, 4)  {
    |              | 
    ([ 7, 4]  0.000577) 
    ([ 8, 4]  0.001522) 
    ([ 9, 4]  0.000758) 
    |              | 
  }
  From:  (8, 5)  {
    ([ 6, 5]  0.000545) 
    |              | 
    ([ 8, 5]  0.000956) 
    |              | 
    ([ 1, 5]  0.000277) 
  }
  From:  (8, 6)  {
    |              | 
    ([ 7, 6]  0.000820) 
    ([ 8, 6]  0.000505) 
    ([ 9, 6]  0.000531) 
    |              | 
  }
  From:  (8, 7)  {
    |              | 
    ([ 7, 7]  0.001105) 
    ([ 8, 7]  0.001267) 
    ([ 9, 7]  0.001043) 
    ([ 1, 7]  0.000499) 
  }
  From:  (8, 8)  {
    ([ 6, 8]  0.001412) 
    ([ 7, 8]  0.001686) 
    |              | 
    |              | 
    ([ 1, 8]  0.000894) 
  }
  From:  (8, 9)  {
    |              | 
    ([ 7, 9]  0.001578) 
    |              | 
    ([ 9, 9]  0.001645) 
    ([ 1, 9]  0.000073) 
  }
  From:  (9, 1)  {
    |              | 
    |              | 
    ([ 9, 1]  0.001811) 
    ([ 1, 1]  0.001507) 
    ([ 2, 1]  0.000873) 
  }
  From:  (9, 2)  {
    |              | 
    ([ 8, 2]  0.001281) 
    |              | 
    ([ 1, 2]  0.001465) 
    ([ 2, 2]  0.000696) 
  }
  From:  (9, 3)  {
    ([ 7, 3]  0.000206) 
    ([ 8, 3]  0.000451) 
    |              | 
    |              | 
    ([ 2, 3]  0.000651) 
  }
  From:  (9, 4)  {
    |              | 
    ([ 8, 4]  0.001084) 
    ([ 9, 4]  0.000127) 
    |              | 
    |              | 
  }
  From:  (9, 5)  {
    ([ 7, 5]  0.001272) 
    ([ 8, 5]  0.001241) 
    |              | 
    |              | 
    |              | 
  }
  From:  (9, 6)  {
    |              | 
    |              | 
    ([ 9, 6]  0.000506) 
    ([ 1, 6]  0.001211) 
    |              | 
  }
  From:  (9, 7)  {
    ([ 7, 7]  0.001044) 
    ([ 8, 7]  0.001924) 
    ([ 9, 7]  0.000482) 
    ([ 1, 7]  0.000514) 
    |              | 
  }
  From:  (9, 8)  {
    |              | 
    ([ 8, 8]  0.000496) 
    ([ 9, 8]  0.000864) 
    ([ 1, 8]  0.000455) 
    ([ 2, 8]  0.001086) 
  }
  From:  (9, 9)  {
    |              | 
    |              | 
    |              | 
    ([ 1, 9]  0.001436) 
    ([ 2, 9]  0.000052) 
  }
}

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